- B. Li, L. R. Valverde, F. Zhang, Y. Zhou, S. Li, Y. Diao, W. L. Wilson, C. M. Schroeder, “Macroscopic Alignment and Assembly of pi-conjugated Oligopeptides using Colloidal Microchannels”, ACS Applied Materials & Interfaces, 10.1021/acsami.7b13978 (2017).
One-dimensional (1-D) supramolecular self-assembly offers a powerful strategy to achieve long-range unidirectional ordering of organic semiconducting materials via non-covalent interactions. Using hierarchical assembly, electronic and optoelectronic materials can be constructed for applications including organic conducting nanowires, organic field-effect transistors (OFETs), and organic light-emitting devices (OLEDs). Despite recent progress, it remains challenging to precisely align and assemble 1-D structures over large areas in a rapid and straightforward manner. In this work, we demonstrate a facile strategy to macroscopically align supramolecular fibers using a templating method based on sacrificial colloidal microchannels. Using this approach, colloidal microchannels are generated on a solid surface using a simple fabrication method, followed by the spontaneous self-assembly of π-conjugated oligopeptides inside large arrays of microchannels triggered by solvent evaporation. Following oligopeptide assembly and removal of sacrificial microchannels, the structural properties of oligopeptide fibers were characterized using atomic force microscopy (AFM), atomic force microscope infrared-spectroscopy (AFM-IR), photo-induced force microscopy (PiFM), fluorescence polarization microscopy, and electron microscopy. These results reveal macroscopic alignment of oligopeptide fibers into ordered structures over millimeter length scales, facilitated by colloidal microchannel templating. In addition, the charge transport properties (I-V curves) of π-conjugated oligopeptides assembled using this method were determined under a wide range of applied voltages using interdigitated array electrodes and conductive AFM. Overall, this work illustrates a simple yet robust strategy to pattern 1-D supramolecular fibers over large areas, thereby offering new routes for assembling materials for organic electronics.
- S. Kumar, J. S. Katz, C. M. Schroeder, “Heterogeneous Drying and Non-monotonic Contact Angle Dynamics in Concentrated, Film-forming Latex Drops”, Physical Review Fluids, 2, 114304 (2017).
The dynamic drying process is studied in spatially heterogeneous film-forming latex suspensions across a wide range of dispersion concentrations using optical imaging techniques. Systematic changes in latex suspension concentration are found to affect lateral drying heterogeneity and surface topology. A nonmonotonic decay in contact angle is observed at the edges of drying droplets by continuously monitoring evaporation dynamics, which is quantitatively characterized by the peak strain and peak formation time. An analytical model is developed to explain the nonmonotonic contact-angle decay by considering a transient dilational stress imposed on a viscoelastic solid model for the particle network. Importantly, the latex concentration dependence of this phenomenon provides evidence for a smooth transition from fluid-line pinning to fluid-line recession behavior during drying, leading to ringlike to volcanolike deposition patterns, respectively. Using experimental data for drying heterogeneity, we quantitatively explore the influence of Marangoni flow and capillary pressure on drying behavior. Moreover, our results show that latex concentration and particle packing can also be strategically used to reduce contact-line friction, thereby affecting fluid-line recession. Taken together, these results show that studying latex suspensions in seemingly simple droplet geometries provides insight into the emergent spatially heterogeneous viscoelastic properties during film formation.
- J. P. Berezney, A. B. Marciel, C. M. Schroeder, O. A. Saleh, “Scale-dependent Stiffness and Internal Tension of a Model Brush Polymer”, Physical Review Letters, 116, 127801 (2017).
Bottle-brush polymers exhibit closely grafted side chains that interact by steric repulsion, thereby causing stiffening of the main polymer chain. In this letter, we use single-molecule elasticity measurements of model brush polymers to quantify this effect. We find that stiffening is only significant on long length scales, with the main chain retaining flexibility on short scales. From the elasticity data, we extract an estimate of the internal tension generated by side-chain repulsion; this estimate is consistent with the predictions of blob-based scaling theories.
- K. W. Hsiao, J. Dinic, Y. Ren, V. Sharma, C. M. Schroeder, “Passive Non-linear Microrheology for
Determining Extensional Viscosity”, Physics of Fluids, 29, 121603 (2017).
Extensional viscosity is a key property of complex fluids that greatly influences the non-equilibrium behavior and processing of polymer solutions, melts, and colloidal suspensions. In this work, we use microfluidics to determine steady extensional viscosity for polymer solutions by directly observing particle migration in planar extensional flow. Tracer particles are suspended in semi-dilute solutions of DNA and polyethylene oxide (PEO), and a Stokes trap is used to confine single particles in extensional flows of polymer solutions in a cross-slot device. Particles are observed to migrate in the direction transverse to flow due to normal stresses, and particle migration is tracked and quantified using a piezo-nano positioning stage during the microfluidic flow experiment. Particle migration trajectories are then analyzed using a second-order fluid model that accurately predicts that migration arises due to normal stress differences. Using this analytical framework, extensional viscosities can be determined from particle migration experiments, and the results are in reasonable agreement with bulk rheological measurements of extensional viscosity based on a dripping-onto-substrate (DoS) method. Overall, this work demonstrates that non-equilibrium properties of complex fluids can be determined by passive yet non-linear microrheology.
- Y. Zhou, B. Li, S. Li, H. A. M. Ardoena, W. L. Wilson, J. D. Tovar, C. M. Schroeder, “Concentration-Driven Assembly and Sol-Gel Transition pi-Conjugated Oligopeptides”, ACS Central Science, DOI: 10.1021/acscentsci.7b00260 (2017).
Advances in supramolecular assembly have enabled the design and synthesis of functional materials with well-defined structures across multiple length scales. Biopolymer-synthetic hybrid materials can assemble into supramolecular structures with a broad range of structural and functional diversity through precisely controlled noncovalent interactions between subunits. Despite recent progress, there is a need to understand the mechanisms underlying the assembly of biohybrid/synthetic molecular building blocks, which ultimately control the emergent properties of hierarchical assemblies. In this work, we study the concentration-driven self-assembly and gelation of pi-conjugated synthetic oligopeptides containing different pi-conjugated cores (quaterthiophene and perylene diimide) using a combination of particle tracking microrheology (PTM), confocal fluorescence microscopy, optical spectroscopy, and electron microscopy. Our results show that pi-conjugated oligopeptides self-assemble into beta-sheet rich fiber-like structures at neutral pH, even in the absence of electrostatic screening of charged residues. A critical fiber formation concentration cfiber and a critical gel concentration cgel are determined for fiber-forming pi-conjugated oligopeptides, and the linear viscoelastic moduli (storage modulus G‘ and loss modulus G”) are determined across a wide range of peptide concentrations. These results suggest that the underlying chemical structure of the synthetic pi-conjugated cores greatly influences the self-assembly process, such that oligopeptides appended to pi-conjugated cores with greater torsional flexibility tend to form more robust fibers upon increasing peptide concentration compared to oligopeptides with sterically constrained cores. Overall, our work focuses on the molecular assembly of pi-conjugated oligopeptides driven by concentration, which is controlled by a combination of enthalpic and entropic interactions between oligopeptide subunits.
- L. W. Cuculis and C. M. Schroeder, “Molecular Mechanisms for Genome Editing Proteins: Single Molecule Studies of TALEs and CRISPR/Cas9”, Annual Review of Chemical and Biomolecular Engineering, 8, 577-597 (2017).
Exciting new advances in genome engineering have unlocked the potential to radically alter the treatment of human disease. In recent years, three major biotechnologies have emerged as efficient tools for the precise editing of DNA for therapeutic applications: zinc finger nucleases, transcription activator-like effector nucleases, and the clustered regularly interspaced short palindromic repeats/CRISPR-associated system. These technologies have facilitated a striking number of gene editing applications in a variety of organisms; however, we are only beginning to understand the molecular mechanisms governing the DNA editing properties of these systems. In this review, we discuss the DNA search and recognition process for TALEs and Cas9 that have been revealed by recent single-molecule experiments.
- B. Li, S. Li, Y. Zhou, H. A. M. Ardona, L. R. Valverde, W. L. Wilson, J. D. Tovar, C. M. Schroeder, “Non-equilibrium Self-assembly of pi-conjugated Oligopeptides in Solution”, ACS Applied Materials & Interfaces, 9, 3977-3984 (2017).
Supramolecular assembly is a powerful method that can be used to generate materials with well-defined structures across multiple length scales. Supramolecular assemblies consisting of biopolymer-synthetic polymer subunits are specifically known to exhibit exceptional structural and functional diversity, as well as programmable control of non-covalent interactions through hydrogen bonding in biopolymer subunits. Despite recent progress, there is a need to control and quantitatively understand assembly under non-equilibrium conditions. In this work, we study the non-equilibrium self-assembly of π-conjugated synthetic oligopeptides using a combination of experiments and analytical modeling. By isolating an aqueous peptide solution droplet within an immiscible organic layer, the rate of peptide assembly in the aqueous solution can be controlled by tuning the transport rate of acid that is used to trigger assembly. Using this approach, peptides are guided to assemble under reaction-dominated and diffusion-dominated conditions, with results showing a transition from a diffusion-limited reaction front to spatially homogeneous assembly as the transport rate of acid decreases. Interestingly, our results show that the morphology of self-assembled peptide fibers is controlled by the assembly kinetics, such that increasingly homogeneous structures of self-assembled synthetic oligopeptides were generally obtained using slower rates of assembly. We further developed an analytical reaction-diffusion model to describe oligopeptide assembly, and experimental results are compared to the reaction-diffusion model across a range of parameters. Overall, this work highlights the importance of molecular self-assembly under non-equilibrium conditions, specifically showing that oligopeptide assembly is governed by a delicate balance between reaction kinetics and transport processes.
- C. Sasmal, K. Hsiao, C. M. Schroeder, J. R. Prakash, “Parameter-free Prediction of DNA Dynamics in Planar Extensional Flow of Semi-dilute Solutions”, Journal of Rheology, 61, 169-186 (2017).
The dynamics of individual DNA molecules in semidilute solutions undergoing planar extensional flow is simulated using a multiparticle Brownian dynamics algorithm, which incorporates hydrodynamic and excluded volume interactions in the context of a coarse-grained bead-spring chain model for DNA. The successive fine-graining protocol [P. Sunthar and J. R. Prakash, Macromolecules (2005); R. Prabhakar et al., J. Rheol. (2004)], in which simulation data acquired for bead-spring chains with increasing values of the number of beads Nb, is extrapolated to the number of Kuhn steps NK in DNA (while keeping key physical parameters invariant), is used to obtain parameter-free predictions for a range of Weissenberg numbers and Hencky strain units. A systematic comparison of simulation predictions is carried out with the experimental observations of Hsiao et al. [J. Rheol. (2017)], who have recently used single molecule techniques to investigate the dynamics of dilute and semidilute solutions of λ-phage DNA in planar extensional flow. In particular, they examine the response of individual chains to step-strain deformation followed by cessation of flow, thereby capturing both chain stretch and relaxation in a single experiment. The successive fine-graining technique is shown to lead to quantitatively accurate predictions of the experimental observations in the stretching and relaxation phases. Additionally, the transient chain stretch following a step strain deformation is shown to be much smaller in semidilute solutions than in dilute solutions, in agreement with experimental observations.
- K. Hsiao, C. Sasmal, J. R. Prakash, C. M. Schroeder, “Direct Observation of DNA Dynamics in Semi-dilute Solutions in Extensional Flow”, Journal of Rheology, 61, 151-167 (2017).
The dynamic behavior of semidilute polymer solutions is governed by an interplay between solvent quality, concentration, molecular weight, and flow type. Semidilute solutions are characterized by large fluctuations in polymer concentration, wherein polymer coils interpenetrate but may not be topologically entangled at equilibrium. In nonequilibrium flows, it is generally thought that polymer chains can “self-entangle” in semidilute solutions, thereby leading to entanglements in solutions that are nominally unentangled at equilibrium. Despite recent progress in the field, we still lack a complete molecular-level understanding of the dynamics of polymer chains in semidilute solutions. In this work, we use single molecule techniques to investigate the dynamics of dilute and semidilute solutions of λ-phage deoxyribonucleic acid in planar extensional flow, including polymer relaxation from high stretch, transient stretching dynamics in step-strain experiments, and steady-state stretching in flow. Our results are consistent with a power-law scaling of the longest polymer relaxation time in semi-dilute solutions. Based on these results, an effective excluded volume exponent ν ≈ 0.56 was found, which is in good agreement with recent bulk rheological experiments. We further studied the nonequilibrium stretching dynamics of semidilute polymer solutions, including transient (1 c*) and steady-state (0.2 c* and 1 c*) stretching dynamics in planar extensional flow using an automated microfluidic trap. Our results show that polymer stretching dynamics in semidilute solutions is a strong function of concentration. In particular, a decrease in transient polymer stretch in semidilute solutions at moderate Weissenberg number (Wi) compared to dilute solutions is observed. Moreover, our experiments reveal a milder coil-to-stretch transition for semidilute polymer solutions at 0.2 c* and 1 c* compared to dilute solutions. Interestingly, a unique set of molecular conformations during the transient stretching process for single polymers in semidilute solutions is observed, which suggests transient stretching pathways for polymer chains in semidilute solutions are qualitatively different compared to dilute solutions due to intermolecular interactions. Taken together, this work provides a molecular framework for understanding the nonequilibrium stretching dynamics of semidilute solutions in strong flows.
- Y. Zhou and C. M. Schroeder, “Transient and Average Unsteady Dynamics of Single Polymers in Large-amplitude Oscillatory Extension”, Macromolecules, 49, 8018-8030 (2016).
Oscillatory rheometry has been widely used in bulk rheological measurements of complex fluids such as polymer solutions and melts. Despite recent progress on bulk oscillatory rheology, however, the vast majority of single polymer studies has focused on chain dynamics in simple on/off step strain-rate experiments. In order to fully understand dynamic polymer microstructure and to establish connections with bulk rheology, there is a clear need to study the dynamics of single polymers in more realistic, non-idealized model flows with transient forcing functions. In this work, we study the dynamics of single polymers in large amplitude oscillatory extensional (LAOE) flow using experiments and Brownian dynamics (BD) simulations, and we characterize transient polymer stretch, orientation angle, and average unsteady stretch as functions of the flow strength (Weissenberg number, Wi) and probing frequency (Deborah number, De). Small and large amplitude sinusoidal oscillatory extensional flow is generated in a cross-slot microfluidic geometry, which is facilitated by using an automated flow device called the Stokes trap. This approach allows the conformational dynamics of single DNA molecules to be observed in oscillatory extensional flow for long times. In this way, we observe a characteristic periodic motion of polymers in LAOE including compression, rotation, and stretching between the time-dependent principle axes of extension and compression. Interestingly, distinct polymer conformations are observed in LAOE that appear to be analogous to buckling instabilities for rigid or semi-flexible filaments under compression. Average unsteady polymer extension is further characterized for single polymers in oscillatory extension across a wide range of Wi and De. In the limit of low Wi, average polymer stretch is interpreted using analytical results based on a Hookean dumbbell model, which can be used to define a critical Wi at the linear to non-linear transition in oscillatory extension. These results reveal the existence of a master curve for average polymer stretch when plotted as a function of an effective Weissenberg number Wieff. Experimental results are compared to BD simulations, and we observe good agreement between simulations and experiments for transient and average unsteady dynamics. Finally, average transient dynamics in oscillatory extensional flow are further interpreted in the context of Pipkin space, defined by the two-dimensional space described by Wi and De.
- D. J. Mai and C. M. Schroeder, “Single Polymer Dynamics of Topologically Complex DNA”, Current Opinion in Colloid and Interface Science, 26, 28-40 (2016).
Single molecule studies allow for the direct observation of polymer dynamics in dilute and concentrated solutions, thereby revealing polymer chain conformations and molecular sub-populations that may be obscured in ensemble-level measurements. Over the past two decades, researchers have used DNA as a model system to study polymer dynamics at the molecular level. The vast majority of studies has focused on linear DNA molecules; however, researchers have recently begun to study polymers with complex topologies and architectures at the single molecule level. Here, we explore recent work in single polymer dynamics focused on topologically complex DNA, including knots, ring polymers, and branched polymers. Experimental, computational, and theoretical advances have enabled in-depth studies of topologically complex DNA, with recent efforts focused on complex molecular conformations, intermolecular interactions, and topology-dependent dynamics. In this article, we highlight recent work aimed at understanding the interplay between molecular-scale behavior and the emergent properties of polymeric materials.
- Y. Zhou and C. M. Schroeder, “Single Polymer Dynamics in Large Amplitude Oscillatory Extension”, Physical Review Fluids, 1, 053301 (2016).
Understanding the conformational dynamics of polymers in time-dependent flows is of key importance for controlling materials properties during processing. Despite this importance, however, it has been challenging to study polymer dynamics in controlled time-dependent or oscillatory extensional flows. In this work, we study the dynamics of single polymers in large amplitude oscillatory extension (LAOE) using a combination of experiments and Brownian dynamics (BD) simulations. Two-dimensional LAOE flow is generated using a feedback-controlled stagnation point device known as the Stokes trap, thereby generating an oscillatory planar extensional flow with alternating principal axes of extension and compression. Our results show that polymers experience periodic cycles of compression, re-orientation, and extension in LAOE, and dynamics are generally governed by a dimensionless flow strength (Weissenberg number Wi) and dimensionless frequency (Deborah number De). Single molecule experiments are compared to BD simulations with and without intramolecular hydrodynamic interactions (HI) and excluded volume (EV) interactions, and good agreement is obtained across a range of parameters. Moreover, transient bulk stress in LAOE is determined from simulations using the Kramers relation, which reveals interesting and unique rheological signatures for this time-dependent flow. We further construct a series of single polymer stretch-flow rate curves (defined as single molecule Lissajous curves) as a function of Wi and De, and we observe qualitatively different dynamic signatures (butterfly, bow tie, arch, and line shapes) across the two-dimensional Pipkin space defined by Wi and De. Finally, polymer dynamics spanning from the linear to nonlinear response regimes are interpreted in the context of accumulated fluid strain in LAOE.
- L. W. Cuculis, Z. Abil, H. Zhao, C. M. Schroeder, “TALE Proteins Search DNA Using a Rotationally Decoupled Mechanism”, Nature Chemical Biology, 12, 831-837 (2016).
See also: News and Views, Nature Chemical Biology
Transcription activator-like effector (TALE) proteins are a class of programmable DNA binding proteins used extensively for gene editing. Despite recent progress, however, little is known regarding their sequence search mechanism. Here, we use single molecule experiments to study TALE search along DNA. Our results show that TALEs utilize a rotationally decoupled mechanism for non-specific search, despite remaining associated with DNA templates during the search process. Our results suggest that the protein helical structure enables TALEs to adopt a loose wrapped conformation around DNA templates during non-specific search, facilitating rapid one-dimensional (1-D) diffusion under a range of solution conditions. Furthermore, this model is consistent with a previously reported two-state mechanism for TALE search that allows these proteins to overcome the search speed-stability paradox. Taken together, our results suggest that TALE search appears to be unique amongst the broad class of sequence-specific DNA binding proteins and supports efficient 1-D search along DNA.
- C. M. Schroeder, S. Köster, Y. Huang, “Emerging Investigators 2016: Discovery Science Meets Technology”, Lab on a Chip, 16, 2974-2976 (2016).
Guest editors Charles M. Schroeder, Sarah Köster and Yanyi Huang introduce the 2016 Emerging Investigators themed issue of Lab on a Chip.
- A. Shenoy, C. V. Rao, C. M. Schroeder, “Stokes Trap for Multiplexed Particle Manipulation and Assembly Using Fluidics”, Proceedings of the National Academy of Sciences, 113, 3976-3981 (2016).
See also: Research Highlights, Nature Physics
The ability to confine and manipulate single particles and molecules has revolutionized several fields of science. Hydrodynamic trapping offers an attractive method for particle manipulation in free solution without the need for optical, electric, acoustic, or magnetic fields. Here, we develop and demonstrate the Stokes trap, which is a new method for trapping multiple particles using only fluid flow. We demonstrate simultaneous manipulation of two particles in a simple microfluidic device using model predictive control. We further show that this approach can be used for fluidic-directed assembly of multiple particles in solution. Overall, this technique opens new vistas for fundamental studies of particle–particle interactions and provides a new method for the directed assembly of colloidal particles.
- K. Hsiao, C. M. Schroeder, C. E. Sing, “Ring Polymer Dynamics are Governed by a Coupling Between Architecture and Hydrodynamic Interactions”, Macromolecules, 49(5), 1961-1971, (2016).
The behavior of linear polymer chains in dilute solution flows has an established history. Polymers often possess more complex architectures, however, such as branched, dendritic, or ring structures. A major challenge lies in understanding how these nonlinear chain topologies affect the dynamic properties in nonequilibrium conditions, in both dilute and entangled solutions. In this work, we interrogate the single-chain dynamics of ring polymers using a combination of simulation, theory, and experiment. Inspired by recent experimental results by Li et al., we demonstrate that the presence of architectural constraints has surprising and pronounced effects on the dynamic properties of polymers as they are driven out of equilibrium. Ring constraints lead to two behaviors that contrast from linear chains. First, the coil–stretch transition occurs at larger values of the dimensionless flow strength (Weissenberg number) compared to linear chains, which is driven by coupling between intramolecular hydrodynamic interactions (HI) and chain architecture. Second, a large loop conformation is observed for ring polymers in extensional flow at intermediate to large Weissenberg numbers, and we show that this open loop conformation is driven by intramolecular HI. Our results reveal the emergence of new paradigms in chain architecture–hydrodynamic coupling that may be relevant for solution-based processing of polymeric materials and could provide new opportunities for precise flow-based polymer conformation control to guide material properties.
2015 Back to Top
- D. T. Reilly, S. H. Kim, J. A. Katzenellenbogen, C. M. Schroeder, “Fluorescent Nanoconjugate Derivatives with Enhanced Photostability for Single Molecule Imaging”, Analytical Chemistry, 87(21), 11048-11057, (2015).
Fluorescence-based imaging techniques critically rely on bright and photostable probes for precise detection of biological molecules. Recently, a new class of multichromophoric probes based on fluorescent dendrimer nanoconjugates (FDNs) was developed for single molecule fluorescence microscopy (SMFM). FDNs are generated by covalent conjugation of multiple fluorescent dyes onto macromolecular polymeric scaffolds and show marked increases in brightness and long-term photostability relative to their single organic dye constituents. Multichromophoric probes, however, are generally known to suffer from transient fluorescence emission intensities and long excursions into dark states. To overcome these issues, photostabilizers can be added to bulk solution, though some small molecule additives may exhibit poor aqueous solubility or biological toxicity. In this work, we develop enhanced FDN derivatives by covalently linking a redox-active photostabilizer (Trolox) directly onto FDN molecular scaffolds. In one approach, multiple organic dyes (Cy5) and Trolox molecules are randomly distributed on dendritic scaffolds in tunable stoichiometric amounts, and in a second approach, Cy5 dyes are covalently linked to Trolox in a precise 1:1 stoichiometry followed by covalent attachment of Cy5-Trolox conjugates onto dendrimers. In all cases, FDN-Trolox conjugates show increases in photostability, brightness, and reduced fluctuations in transient fluorescent intensity relative to FDN probes. Bulk and single molecule photophysical data for FDN probes are compared to single self-healing dye systems such as Cy5-Trolox, and as a proof-of-principle demonstration, we use FDN-Trolox derivatives for bulk immunofluorescence imaging. Overall, our work suggests that self-healed multichromophoric systems such as FDN-Trolox probes present a useful strategy for increasing fluorescent probe photostability.
- Y. Li, K. Hsiao, C. A. Brockman, D.Y. Yates, R. M. Robertson-Anderson, J. A. Kornfield, M. J. San Francisco, C. M. Schroeder, G. B. McKenna, “When Ends Meet: Circular DNA Stretches Differently in Elongational Flows”, Macromolecules, 48(16), 5997–6001, (2015).
Chain topology has a profound impact on the flow behavior of single macromolecules. For circular polymers, the absence of free ends results in a unique chain architecture compared to linear or branched chains, thereby generating distinct molecular dynamics. Here, we report the direct observation of circular DNA dynamics in transient and steady flows for molecular sizes spanning the range of 25.0–114.8 kilobase pairs (kbp). Our results show that the longest relaxation times of the rings follow a power-law scaling relation with molecular weight that differs from that of linear chains. Also, relative to their linear counterparts, circular DNA molecules show a shifted coil-to-stretch transition and less diverse “molecular individualism” behavior as evidenced by their conformational stretching pathways. These results show the impact of chain topology on dynamics and reveal commonalities in the steady state behavior of circular and linear DNA that extends beyond chain architecture.
- X. Li, C. M. Schroeder, K. D. Dorfman, “Modeling the Stretching of Wormlike Chains in the Presence of Excluded Volume”, Soft Matter, 11, 5947-5954 (2015).
We propose an interpolation formula (the EV-WLC relation) for the force-extension behavior of wormlike chains in the presence of hard-core excluded volume interactions, analogous to the classic interpolation formula from Marko and Siggia for ideal wormlike chains. Using pruned-enriched Rosenbluth method (PERM) simulations of asymptotically long, discrete wormlike chains in an external force, we show that the error in the EV-WLC interpolation formula to describe discrete wormlike chains is systematically smaller than the error in the Marko-Siggia interpolation formula, except for the saturation region in which both formulas have the same limiting behavior. We anticipate that the EV-WLC interpolation formula will prove useful in the coarse-graining of wormlike chain models for dynamic simulations. Related results for the excess free energy due to excluded volume provide strong support for the physical basis of the Pincus regime.
- L. W. Cuculis, Z. Abil, H. Zhao, C. M. Schroeder, “Direct Observation of TALE Protein Dynamics Reveals a Two-state Search Mechanism”, Nature Communications, 6, 7277 (2015).
Transcription activator-like effector (TALE) proteins are a class of programmable DNA-binding proteins for which the fundamental mechanisms governing the search process are not fully understood. Here we use single-molecule techniques to directly observe TALE search dynamics along DNA templates. We find that TALE proteins are capable of rapid diffusion along DNA using a combination of sliding and hopping behaviour, which suggests that the TALE search process is governed in part by facilitated diffusion. We also observe that TALE proteins exhibit two distinct modes of action during the search process—a search state and a recognition state—facilitated by different subdomains in monomeric TALE proteins. Using TALE truncation mutants, we further demonstrate that the N-terminal region of TALEs is required for the initial non-specific binding and subsequent rapid search along DNA, whereas the central repeat domain is required for transitioning into the site-specific recognition state
- R. Mohan, C. Sanpitakseree, A. V. Desai, S. E. Sevgen, C. M. Schroeder, P. J. A. Kenis, “A Microfluidic Approach to Study the Effect of Bacterial Interactions on Antimicrobial Susceptibility in Polymicrobial Cultures”, RSC Advances, 5, 35211-35223 (2015).
Polymicrobial infections are caused by more than one pathogen. They require antimicrobial dosing regimens that are different from those prescribed for monomicrobial infections because these interactions are predicted to influence the antimicrobial susceptibility of the individual pathogens. Here we report on a microfluidic approach to study the effect of bacterial interactions in polymicrobial cultures on the antimicrobial susceptibility. The use of microfluidics enables real-time quantification of bacterial growth dynamics in the presence and absence of antimicrobials, which is challenging to achieve using current methods. We studied microbial interactions between Pseudomonas aeruginosa, and Escherichia coli and Klebsiella pneumoniae. A key observation was that in co-cultures with relatively high initial cell numbers of P. aeruginosa, the co-cultured partner bacteria exhibited initial growth followed by lyses or growth stasis. In addition, we observed a significantly higher antimicrobial tolerance of P. aeruginosa in polymicrobial cultures, as evident by up to 8-fold increases in the minimum inhibitory concentration of the antimicrobials, compared to those observed in monomicrobial cultures. This work demonstrates the potential of microfluidics to study bacterial interactions and their effect on antimicrobial susceptibility, which in turn will aid in determining appropriate antimicrobial treatment for polymicrobial infections.
- D. J. Mai, A. B. Marciel, C.E. Sing, C. M. Schroeder, “Topology-Controlled Relaxation Dynamics of Single Comb Polymers”, ACS Macro Letters, 4, 446-452 (2015).
In this work, we report the synthesis and direct observation of branched DNA polymers using single molecule techniques. Polymer topology plays a major role in determining the properties of advanced materials, yet understanding the dynamics of these complex macromolecules has been challenging. Here, we study the conformational relaxation dynamics of single surface-tethered comb polymers from high stretch in a microfluidic device. Our results show that the molecular topology of individual branched polymers plays a direct role on the relaxation dynamics of polymers with complex architectures. Macromolecular DNA combs are first synthesized using a hybrid enzymatic-synthetic approach, wherein chemically modified DNA branches and DNA backbones are generated in separate polymerase chain reactions, followed by a “graft-onto” reaction via strain-promoted [3 + 2] azide–alkyne cycloaddition. This method allows for the synthesis of branched polymers with nearly monodisperse backbone and branch molecular weights. Single molecule fluorescence microscopy is then used to directly visualize branched polymers, such that the backbone and side branches can be tracked independently using single- or dual-color fluorescence labeling. Using this approach, we characterize the molecular properties of branched polymers, including apparent contour length and branch grafting distributions. Finally, we study the relaxation dynamics of single comb polymers from high stretch following the cessation of fluid flow, and we find that polymer relaxation depends on branch grafting density and position of branch point along the main chain backbone. Overall, this work effectively extends single polymer dynamics to branched polymers, which allows for dynamic, molecular-scale observation of polymers with complex topologies.
- A. B. Marciel, D. J. Mai, C. M. Schroeder, “Template-Directed Synthesis of Structurally Defined Branched Polymer Architectures”, Macromolecules, 48(5), 1296-1303 (2015).
A grand challenge in materials chemistry is the synthesis of macromolecules and polymers with precise shapes and architectures. In this work, we describe a hybrid synthetic strategy to produce structurally defined branched polymer architectures based on chemically modified DNA. Overall, this approach enables precise control over branch placement, grafting density, and chemical identity of side branches. We utilize a two-step scheme based on polymerase chain reaction (PCR) for site-specific incorporation of non-natural nucleotides along the main polymer backbone, followed by copper-free “click” chemistry for grafting side branches at specific locations. In this way, linear DNA backbones are first synthesized via PCR by utilizing the promiscuity of a high yield thermophilic DNA polymerase to incorporate nucleotides containing bioorthogonal dibenzocyclooctyne (DBCO) functional groups at precise locations along one strand of the DNA backbone. Following PCR, copper-free “click” chemistry is used to attach synthetic polymer branches or oligonucleotide branches to the DNA backbone, thereby allowing for the synthesis of a variety of precise polymer architectures, including three-arm stars, H-polymers, and graft block copolymers. Branched polymer architectures are characterized using polyacrylamide gel electrophoresis, denaturing high performance liquid chromatography (HPLC), and matrix-assisted laser desorption/ionization (MALDI) mass spectrometry. In a proof-of-principle demonstration, we synthesize miktoarm stars with AB2 structures via attachment of mPEG-azide branches (1 and 10 kDa) at precise locations along a DNA backbone, thereby expanding the chemical functionality of structurally defined DNA topologies.
- A. Mukherjee and C. M. Schroeder, “Flavin-based Fluorescent Proteins: Emerging Paradigms in Biological Imaging”, Current Opinion in Biotechnology, 31, 16-23 (2015).
Flavin-based fluorescent proteins (FbFPs) are an emerging class of fluorescent reporters characterized by oxygen-independent fluorescence and a small size — key advantages compared to the green fluorescent protein (GFP). FbFPs are at a nascent stage of development. However, they have already been used as versatile reporters for studying anaerobic biosystems and viral assemblies. Recently, FbFPs with improved brightness and photostability have been engineered. In addition, several FbFPs show high degrees of thermal and pH stability. For these reasons, FbFPs hold strong promise to extend bioimaging to clinically and industrially significant systems that have been challenging to study using GFPs. In this review, we highlight recent developments in the FbFP toolbox and explore further improvements necessary to maximize the potential of FbFPs.
2014 Back to Top
- F. Latinwo, K. Hsiao, C. M. Schroeder, “Nonequilibrium Thermodynamics of Dilute Polymer Solutions in Flow”, The Journal of Chemical Physics, 141, 174903 (2014).
Modern materials processing applications and technologies often occur far from equilibrium. To this end, the processing of complex materials such as polymer melts and nanocomposites generally occurs under strong deformations and flows, conditions under which equilibrium thermodynamics does not apply. As a result, the ability to determine the nonequilibrium thermodynamic properties of polymeric materials from measurable quantities such as heat and work is a major challenge in the field. Here, we use work relations to show that nonequilibrium thermodynamic quantities such as free energy and entropy can be determined for dilute polymer solutions in flow. In this way, we determine the thermodynamic properties of DNA molecules in strong flows using a combination of simulations, kinetic theory, and single molecule experiments. We show that it is possible to calculate polymer relaxation timescales purely from polymer stretching dynamics in flow. We further observe a thermodynamic equivalence between nonequilibrium and equilibrium steady-states for polymeric systems. In this way, our results provide an improved understanding of the energetics of flowing polymer solutions.
- A. Shenoy, M. Tanyeri, C. M. Schroeder, “Characterizing the Performance of the Hydrodynamic Trap Using a Control-based Approach”, Microfluidics and Nanofluidics, (2014).
Hydrodynamic trapping allows for the confinement and manipulation of small objects in free solution, away from solid boundaries and without the need for optical or magnetic fields. In order to achieve robust trapping over long time scales, it is imperative to evaluate trap performance using different control schemes and to understand the effect of system parameters on trap stability. In this work, we investigate the performance of a hydrodynamic trap actuated by varying combinations of proportion-integral-derivative controllers. We further develop a control-based model of the trap, and we characterize trap performance for a wide range of particle Peclet numbers and response times. Overall, an increased understanding of trap performance will facilitate the design of improved controllers to enable robust trapping under variable system parameters.
- A. Mukherjee, K. B. Weyant, J. Walker, U. Agrawal, I. Cann, C. M. Schroeder, “Engineering and Characterization of New LOV-based Fluorescent Proteins from Chlamydomonas reinhardtii andVaucheria frigida“, ACS Synthetic Biology, DOI: 10.1021/sb500237x (2014).
Flavin-based fluorescent proteins (FbFPs) are a new class of fluorescent reporters that exhibit oxygen-independent fluorescence, which is a key advantage over the green fluorescent protein. Broad application of FbFPs, however, has been generally hindered by low brightness. To maximize the utility of FbFPs, there is a pressing need to expand and diversify the limited FbFP library through the inclusion of bright and robust variants. In this work, we use genome mining to identify and engineer two new FbFPs (CreiLOV and VafLOV) from Chlamydomonas reinhardtii and Vaucheria frigida. We show that CreiLOV is a thermostable, photostable, and fast-maturing monomeric reporter that outperforms existing FbFPs in brightness and operational pH range. Furthermore, we show that CreiLOV can be used to monitor dynamic gene expression in Escherichia coli. Overall, our work introduces CreiLOV as a robust addition to the FbFP repertoire and highlights genome mining as a powerful approach to engineer improved FbFPs.
- E. M. Johnson-Chavarria, U. Agrawal, M. Tanyeri, T. E. Kuhlman, C. M. Schroeder, “Automated Single Cell Microbioreactor for Monitoring Intracellular Dynamics and Cell Growth in Free Solution”, Lab on a Chip, 14, 2688-2697 (2014).
We report an automated microfluidic-based platform for single cell analysis that allows for cell culture in free solution with the ability to control the cell growth environment. Using this approach, cells are confined by the sole action of gentle fluid flow, thereby enabling non-perturbative analysis of cell growth away from solid boundaries. In addition, the single cell microbioreactor allows for precise and time-dependent control over cell culture media, with the combined ability to observe the dynamics of non-adherent cells over long time scales. As a proof-of-principle demonstration, we used the platform to observe dynamic cell growth, gene expression, and intracellular diffusion of repressor proteins while precisely tuning the cell growth environment. Overall, this microfluidic approach enables the direct observation of cellular dynamics with exquisite control over environmental conditions, which will be useful for quantifying the behaviour of single cells in well-defined media.
- K. S. Lee, A. B. Marciel, A. G. Kozlov, C. M. Schroeder, T. M. Lohman, T. Ha, “Ultrafast Re-distribution ofE. coli SSB Along Long Single-Stranded DNA via Intersegment Transfer”, Journal of Molecular Biology,426, 2413-2421 (2014).
Single-stranded DNA binding proteins (SSBs) selectively bind single-stranded DNA (ssDNA) and facilitate recruitment of additional proteins and enzymes to their sites of action on DNA. SSB can also locally diffuse on ssDNA, which allows it to quickly reposition itself while remaining bound to ssDNA. In this work, we used a hybrid instrument that combines single-molecule fluorescence and force spectroscopy to directly visualize the movement of Escherichia coli SSB on long polymeric ssDNA. Long ssDNA was synthesized without secondary structure that can hinder quantitative analysis of SSB movement. The apparent diffusion coefficient of E. coli SSB thus determined ranged from 70,000 to 170,000 nt2/s, which is at least 600 times higher than that determined from SSB diffusion on short ssDNA oligomers, and is within the range of values reported for protein diffusion on double-stranded DNA. Our work suggests that SSB can also migrate via a long-range intersegment transfer on long ssDNA. The force dependence of SSB movement on ssDNA further supports this interpretation.
- F. Latinwo and C. M. Schroeder, “Determining Elasticity from Single Polymer Dynamics”, Soft Matter,10, 2178-2187 (2014).
The ability to determine polymer elasticity and force–extension relations from polymer dynamics in flow has been challenging, mainly due to difficulties in relating equilibrium properties such as free energy to far-from-equilibrium processes. In this work, we determine polymer elasticity from the dynamic properties of polymer chains in fluid flow using recent advances in statistical mechanics. In this way, we obtain the force–extension relation for DNA from single molecule measurements of polymer dynamics in flow without the need for optical tweezers or bead tethers. We further employ simulations to demonstrate the practicality and applicability of this approach to the dynamics of complex fluids. We investigate the effects of flow type on this analysis method, and we develop scaling laws to relate the work relation to bulk polymer viscometric functions. Taken together, our results show that nonequilibrium work relations can play a key role in the analysis of soft material dynamics.
2013 Back to Top
- A. B. Marciel, M. Tanyeri, B. D. Wall, J. D. Tovar, C. M. Schroeder*, W. L. Wilson*, “Fluidic-directed Assembly of Aligned Oligopeptides with π -conjugated Cores”, Advanced Materials, 25, 6398-6404 (2013).
A microfluidic-based directed assembly strategy is employed to form highly aligned supramolecular structures. Formation of aligned synthetic oligopeptide nanostructures is accomplished using planar extensional flow, which induces alignment of underlying material suprastructures. Fluidic-directed assembly of supramolecular structures allows for unprecedented manipulation at the nano- and mesoscales, which has the potential to provide rapid and efficient control of functional material properties.
- F. Latinwo and C. M. Schroeder, “Nonequilibrium Work Relations for Polymer Dynamics in Dilute Solutions”, Macromolecules, 46, 8345-8355 (2013).
Equilibrium and nonequilibrium free energies of complex fluids are fundamental quantities that can be used to determine a wide array of system properties. Recently, we demonstrated the direct determination of the equilibrium free energy landscape and corresponding elasticity of polymer chains from work calculations in highly nonequilibrium fluid flows.1 In the present study, we further demonstrate the generality of this formalism by applying this method to polymeric systems driven by fluid flows with vorticity and for molecules with dominant intramolecular hydrodynamic interactions (HI). We employ Brownian dynamics simulations of double stranded DNA with fluctuating HI, and we analyze polymer dynamics and the resultant free energy calculations in the context of the nonequilibrium work relations. Furthermore, we investigate the role of HI on the work and housekeeping power required to maintain a polymer chain at a nonequilibrium steady-state in flow, and we consider the relationship between housekeeping power and polymer chain size. On the basis of the results in this study, nonequilibrium work relations appear to be a powerful set of tools that can be used to understand the behavior of polymeric systems and soft materials.
- M. Tanyeri and C. M. Schroeder, “Manipulation and Confinement of Single Particles using a Fluid Flow”, Nano Letters, 13, 2357-2364 (2013).
High precision control of micro- and nanoscale objects in aqueous media is an essential technology for nanoscience and engineering. Existing methods for particle trapping primarily depend on optical, magnetic, electrokinetic, and acoustic fields. In this work, we report a new hydrodynamic flow based approach that allows for fine-scale manipulation and positioning of single micro- and nanoscale particles using automated fluid flow. As a proof-of-concept, we demonstrate trapping and two-dimensional (2D) manipulation of 500 nm and 2.2 μm diameter particles with a positioning precision as small as 180 nm during confinement. By adjusting a single flow parameter, we further show that the shape of the effective trap potential can be efficiently controlled. Finally, we demonstrate two distinct features of the flow-based trapping method, including isolation of a single particle from a crowded particle solution and active control over the surrounding medium of a trapped object. The 2D flow-based trapping method described here further expands the micro/nanomanipulation toolbox for small particles and holds strong promise for applications in biology, chemistry, and materials research.
- R. Mohan*, A. Mukherjee*, S. E. Sevgen, C. Sanpitakseree, J. Lee, C. M. Schroeder, P. J. A. Kenis, “A Multiplexed Microfluidic Platform for Rapid Antibiotic Susceptibility Testing”, Biosensors and Bioelectronics, 49, 118-125 (2013). * These authors contributed equally to the publication.
Effective treatment of clinical infections is critically dependent on the ability to rapidly screen patient samples to identify antibiograms of infecting pathogens. Existing methods for antibiotic susceptibility testing suffer from several disadvantages, including long turnaround times, excess sample and reagent consumption, poor detection sensitivity, and limited combinatorial capabilities. Unfortunately, these factors preclude the timely administration of appropriate antibiotics, complicating management of infections and exacerbating the development of antibiotic resistance. Here, we seek to address these issues by developing a microfluidic platform that relies on fluorescence detection of bacteria that express green fluorescent protein for highly sensitive and rapid antibiotic susceptibility testing. This platform possesses several advantages compared to conventional methods: (1) analysis of antibiotic action in two to four hours, (2) enhanced detection sensitivity (≈1 cell), (3) minimal consumption of cell samples and antibiotic reagents (<6 µL), and (4) improved portability through the implementation of normally closed valves. We employed this platform to quantify the effects of four antibiotics (ampicillin, cefalexin, chloramphenicol, tetracycline) and their combinations on Escherichia coli. Within four hours, the susceptibility of bacteria to antibiotics can be determined by detecting variations in maxima of local fluorescence intensity over time. As expected, cell density is a major determinant of antibiotic efficacy. Our results also revealed that combinations of three or more antibiotics are not necessarily better for eradicating pathogens compared to pairs of antibiotics. Overall, this microfluidic based biosensor technology has the potential to provide rapid and precise guidance in clinical therapies by identifying the antibiograms of pathogens.
- A. Mukherjee, J. Walker, K. B. Weyant, C. M. Schroeder, “Characterization of Flavin-based Fluorescent Proteins: An Emerging Class of Powerful Fluorescent Reporters”, PLOS ONE, 8, e64753 (2013).
Fluorescent reporter proteins based on flavin-binding photosensors were recently developed as a new class of genetically encoded probes characterized by small size and oxygen-independent maturation of fluorescence. Flavin-based fluorescent proteins (FbFPs) address two major limitations associated with existing fluorescent reporters derived from the green fluorescent protein (GFP)–namely, the overall large size and oxygen-dependent maturation of fluorescence of GFP. However, FbFPs are at a nascent stage of development and have been utilized in only a handful of biological studies. Importantly, a full understanding of the performance and properties of FbFPs as a practical set of biological probes is lacking. In this work, we extensively characterize three FbFPs isolated from Pseudomonas putida, Bacillus subtilis, and Arabidopsis thaliana, using in vitro studies to assess probe brightness, oligomeric state, maturation time, fraction of fluorescent holoprotein, pH tolerance, redox sensitivity, and thermal stability. Furthermore, we validate FbFPs as stable molecular tags using in vivo studies by constructing a series of FbFP-based transcriptional constructs to probe promoter activity in Escherichia coli. Overall, FbFPs show key advantages as broad-spectrum biological reporters including robust pH tolerance (4–11), thermal stability (up to 60°C), and rapid maturation of fluorescence (<3 min.). In addition, the FbFP derived from Arabidopsis thaliana (iLOV) emerged as a stable and nonperturbative reporter of promoter activity in Escherichia coli. Our results demonstrate that FbFP-based reporters have the potential to address key limitations associated with the use of GFP, such as pH-sensitive fluorescence and slow kinetics of fluorescence maturation (10–40 minutes for half maximal fluorescence recovery). From this view, FbFPs represent a useful new addition to the fluorescent reporter protein palette, and our results constitute an important framework to enable researchers to implement and further engineer improved FbFP-based reporters with enhanced brightness and tighter flavin binding, which will maximize their potential benefits.
- A. B. Marciel and C. M. Schroeder, “New Directions in Single Polymer Dynamics”, Journal of Polymer Science: Polymer Physics, 51, 556-566 (2013).
Single polymer techniques are a powerful set of molecular-level tools that enable the direct observation of polymer chain dynamics under highly non-equilibrium conditions. In this way, single polymer methods have been used to uncover fundamentally new information regarding the static and dynamic properties of polymeric materials. However, to achieve the full potential of these new methods, single polymer techniques must be further advanced to enable the study of polymers with complex architectures, heterogeneous chemistries, flexible backbones, and intermolecular interactions in entangled solutions, which reaches far beyond the current state-of-the-art. In this article, we explore recent developments in the area of single polymer physics, including single molecule force spectroscopy and fluorescence microscopy, and we further highlight exciting new directions in the field.
- U. Agrawal, D. Reilly, C. M. Schroeder, “Zooming in on Biological Processes with Fluorescence Nanoscopy”, Current Opinion in Biotechnology, 24 (2013).
Fluorescence nanoscopy enables the study of biological phenomena at nanometer scale spatial resolution. Recent biological studies using fluorescence nanoscopy have showcased the ability of these techniques to directly observe protein organization, subcellular molecular interactions, structural dynamics, electrical signaling, and diffusion of cytosolic proteins at unprecedented spatial resolution. Super-resolution imaging techniques critically rely on bright fluorescent probes such as organic dyes or fluorescent proteins. Recently, these methods have been extended to live cells and multicolor, three-dimensional imaging, thereby providing exquisite spatiotemporal resolutions of the order of 10–20 nm and 1–2 s for subcellular imaging. Further improvements in image processing algorithms, labeling techniques, correlative microscopy, and development of advanced fluorescent probes will be required to achieve true molecular-scale resolution using these techniques.
- Y. Kim, S. Kim, M. Tanyeri, J. A. Katzenellenbogen, C. M. Schroeder, “Dendrimer Probes for Enhanced Photostability and Localization in Fluorescence Imaging”, accepted to Biophysical Journal (2013).
News: This article was highlighted in a “New and Notable” article: Biophysical Journal, 104, 1394 (2013).
Recent advances in fluorescence microscopy have enabled high-resolution imaging and tracking of single proteins and biomolecules in cells. To achieve high spatial resolutions in the nanometer range, bright and photostable fluorescent probes are critically required. From this view, there is a strong need for development of advanced fluorescent probes with molecular-scale dimensions for fluorescence imaging. Polymer-based dendrimer nanoconjugates hold strong potential to serve as versatile fluorescent probes due to an intrinsic capacity for tailored spectral properties such as brightness and emission wavelength. In this work, we report a new, to our knowledge, class of molecular probes based on dye-conjugated dendrimers for fluorescence imaging and single-molecule fluorescence microscopy. We engineered fluorescent dendritic nanoprobes (FDNs) to contain multiple organic dyes and reactive groups for target-specific biomolecule labeling. The photophysical properties of dye-conjugated FDNs (Cy5-FDNs and Cy3-FDNs) were characterized using single-molecule fluorescence microscopy, which revealed greatly enhanced photostability, increased probe brightness, and improved localization precision in high-resolution fluorescence imaging compared to single organic dyes. As proof-of-principle demonstration, Cy5-FDNs were used to assay single-molecule nucleic acid hybridization and for immunofluorescence imaging of microtubules in cytoskeletal networks. In addition, Cy5-FDNs were used as reporter probes in a single-molecule protein pull-down assay to characterize antibody binding and target protein capture. In all cases, the photophysical properties of FDNs resulted in enhanced fluorescence imaging via improved brightness and/or photostability.
2012 Back to Top
- A. Mukherjee and C. M. Schroeder, “Directed Evolution of Bright Mutants of a Flavin-Dependent Anaerobic Fluorescent Protein from Pseudomonas putida“, Journal of Biological Engineering, 6, 20, (2012).
Fluorescent reporter proteins have revolutionized our understanding of cellular bioprocesses by enabling live cell imaging with exquisite spatio-temporal resolution. Existing fluorescent proteins are predominantly based on the green fluorescent protein (GFP) and related analogs. However, GFP-family proteins strictly require molecular oxygen for maturation of fluorescence, which precludes their application for investigating biological processes in low-oxygen environments. A new class of oxygen-independent fluorescent reporter proteins was recently reported based on flavin-binding photosensors from Bacillus subtilis and Pseudomonas putida. However, flavin-binding fluorescent proteins show very limited brightness, which restricts their utility as biological imaging probes. In this work, we report the discovery of bright mutants of a flavin-binding fluorescent protein from P. putida using directed evolution by site saturation mutagenesis. We discovered two mutations at a chromophore-proximal amino acid (F37S and F37T) that confer a twofold enhancement in brightness relative to the wild type fluorescent protein through improvements in quantum yield and holoprotein fraction. In addition, we observed that substitution with other aromatic amino acids at this residue (F37Y and F37W) severely diminishes fluorescence emission. Therefore, we identify F37 as a key amino acid residue in determining fluorescence. To increase the scope and utility of flavin-binding fluorescent proteins as practical fluorescent reporters, there is a strong need for improved variants of the wild type protein. Our work reports on the application of site saturation mutagenesis to isolate brighter variants of a flavin-binding fluorescent protein, which is a first-of-its-kind approach. Overall, we anticipate that the improved variants will find pervasive use as fluorescent reporters for biological studies in low-oxygen environments.
- Y. Kim, S. Kim, J. A. Katzenellenbogen, C. M. Schroeder, “Specific Labeling of Zinc Finger Proteins using Non-canonical Amino Acids and Copper-free Click Chemistry”, Bioconjugate Chemistry, DOI:10.1021/bc300262h (2012).
Zinc finger proteins (ZFPs) play a key role in transcriptional regulation and serve as invaluable tools for gene modification and genetic engineering. Development of efficient strategies for labeling metalloproteins such as ZFPs is essential for understanding and controlling biological processes. In this work, we engineered ZFPs containing cysteine-histidine (Cys2-His2) motifs by metabolic incorporation of the unnatural amino acid azidohomoalanine (AHA), followed by specific protein labeling via click chemistry. We show that cyclooctyne promoted [3 + 2] dipolar cycloaddition with azides, known as copper-free click chemistry, provides rapid and specific labeling of ZFPs at high yields as determined by mass spectrometry analysis. We observe that the DNA-binding activity of ZFPs labeled by conventional copper-mediated click chemistry was completely abolished, whereas ZFPs labeled by copper-free click chemistry retain their sequence-specific DNA-binding activity under native conditions, as determined by electrophoretic mobility shift assays, protein microarrays, and kinetic binding assays based on Förster resonance energy transfer (FRET). Our work provides a general framework to label metalloproteins such as ZFPs by metabolic incorporation of unnatural amino acids followed by copper-free click chemistry.
- D. J. Mai, C. A. Brockman, C. M. Schroeder, “Microfluidic Systems for Single DNA Dynamics”, Soft Matter, DOI: 10.1039/c2sm26036k (2012).
Recent advances in microfluidics have enabled the molecular-level study of polymer dynamics using single DNA chains. Single polymer studies based on fluorescence microscopy allow for the direct observation of non-equilibrium polymer conformations and dynamical phenomena such as diffusion, relaxation, and molecular stretching pathways in flow. Microfluidic devices have enabled the precise control of model flow fields to study the non-equilibrium dynamics of soft materials, with device geometries including curved channels, cross slots, and microfabricated obstacles and structures. This review explores recent microfluidic systems that have advanced the study of single polymer dynamics, while identifying new directions in the field that will further elucidate the relationship between polymer microstructure and bulk rheological properties.
- M.-H. Lai, J. H. Jeong, R. Devolder, C. Brockman, C. M. Schroeder, H. Kong, “Ellipsoidal Polyaspartamide Polymersomes with Enhanced Cell-Targeting Ability”, Advanced Functional Materials, DOI 10.1002/adfm.201102664 (2012).
Nanosized polymersomes functionalized with peptides or proteins are being increasingly studied for targeted delivery of diagnostic and therapeutic molecules. Earlier computational studies have suggested that ellipsoidal nanoparticles, compared to spherical ones, display enhanced binding efficiency with target cells, but this has not yet been experimentally validated. Here, it is hypothesized that hydrophilic polymer chains coupled to vesicle-forming polymers would result in ellipsoidal polymersomes. In addition, ellipsoidal polymersomes modified with cell adhesion peptides bind with target cells more actively than spherical ones. This hypothesis is examined by substituting polyaspartamide with octadecyl chains and varying numbers of poly(ethylene glycol) (PEG) chains. Increasing the degree of substitution of PEG drives the polymer to self-assemble into an ellipsoidal polymersome with an aspect ratio of 2.1. Further modification of these ellipsoidal polymersomes with peptides containing an Arg-Gly-Asp sequence leads to a significant increase in the rate of association and decrease in the rate of dissociation with a substrate coated with αvβ3 integrins. The results will serve to improve the efficiency of targeted delivery of a wide array of polymersomes loaded with various biomedical modalities.
2011 Back to Top
- M. Tanyeri, M. Ranka, N. Sittipolkul, C. M. Schroeder, “Microfluidic Wheatstone Bridge for Rapid Sample Analysis”, Lab on a Chip, 11, 4181-4186 (2011).
We developed a microfluidic analogue of the classic Wheatstone bridge circuit for automated, real-time sampling of solutions in a flow-through device format. We demonstrate precise control of flow rate and flow direction in the “bridge” microchannel using an on-chip membrane valve, which functions as an integrated “variable resistor”. We implement an automated feedback control mechanism in order to dynamically adjust valve opening, thereby manipulating the pressure drop across the bridge and precisely controlling fluid flow in the bridge channel. At a critical valve opening, the flow in the bridge channel can be completely stopped by balancing the flow resistances in the Wheatstone bridge device, which facilitates rapid, on-demand fluid sampling in the bridge channel. In this article, we present the underlying mechanism for device operation and report key design parameters that determine device performance. Overall, the microfluidic Wheatstone bridge represents a new and versatile method for on-chip flow control and sample manipulation.
- F. Latinwo and C. M. Schroeder, “Model Systems for Single Molecule Polymer Dynamics”, Soft Matter, 7, 7907-7913 (2011), June (2011).
News: This article was selected as a “Hot Article” by the editor of Soft Matter.
Double stranded DNA (dsDNA) has long served as a model system for single molecule polymer dynamics. However, dsDNA is a semiflexible polymer, and the structural rigidity of the DNA double helix gives rise to local molecular properties and chain dynamics that differ from flexible chains, including synthetic organic polymers. Recently, we developed single stranded DNA (ssDNA) as a new model system for single molecule studies of flexible polymer chains. In this work, we discuss model polymer systems in the context of “ideal” and “real” chain behavior considering thermal blobs, tension blobs, hydrodynamic drag and force–extension relations. In addition, we present monomer aspect ratio as a key parameter describing chain conformation and dynamics, and we derive dynamical scaling relations in terms of this molecular-level parameter. We show that asymmetric Kuhn segments can suppress monomer–monomer interactions, thereby altering global chain dynamics. Finally, we discuss ssDNA in the context of a new model system for single molecule polymer dynamics. Overall, we anticipate that future single polymer studies of flexible chains will reveal new insight into the dynamic behavior of “real” polymers, which will highlight the importance of molecular individualism and the prevalence of non-linear phenomena.
- C. A. Brockman, S. Kim, F. Latinwo, C. M. Schroeder, “Direct Observation of Single Flexible Polymers using Single Stranded DNA”, Soft Matter, 7, 8005-8012 (2011).
News: This article was selected as a “Hot Article” by the editor of Soft Matter.
Over the last 15 years, double stranded DNA (dsDNA) has been used as a model polymeric system for nearly all single polymer dynamics studies. However, dsDNA is a semiflexible polymer with markedly different molecular properties compared to flexible chains, including synthetic organic polymers. In this work, we report a new system for single polymer studies of flexible chains based on single stranded DNA (ssDNA). We developed a method to synthesize ssDNA for fluorescence microscopy based on rolling circle replication, which generates long strands (>65 kb) of ssDNA containing “designer” sequences, thereby preventing intramolecular base pair interactions. Polymers are synthesized to contain amine-modified bases randomly distributed along the backbone, which enables uniform labelling of polymer chains with a fluorescent dye to facilitate fluorescence microscopy and imaging. Using this approach, we synthesized ssDNA chains with long contour lengths (>30 μm) and relatively low dye loading ratios ([similar]1 dye per 100 bases). In addition, we used epifluorescence microscopy to image single ssDNA polymer molecules stretching in flow in a microfluidic device. Overall, we anticipate that ssDNA will serve as a useful model system to probe the dynamics of polymeric materials at the molecular level.
- M. Tanyeri, M. Ranka, N. Sittipolkul, C. M. Schroeder, “A Microfluidic-based Hydrodynamic Trap: Design and Implementation”, Lab on a Chip, 11, 1786-1794 (2011).
We report an integrated microfluidic device for fine-scale manipulation and confinement of micro- and nanoscale particles in free-solution. Using this device, single particles are trapped in a stagnation point flow at the junction of two intersecting microchannels. The hydrodynamic trap is based on active flow control at a fluid stagnation point using an integrated on-chip valve in a monolithic PDMS-based microfluidic device. In this work, we characterize device design parameters enabling precise control of stagnation point position for efficient trap performance. The microfluidic-based hydrodynamic trap facilitates particle trapping using the sole action of fluid flow and provides a viable alternative to existing confinement and manipulation techniques based on electric, optical, magnetic or acoustic force fields. Overall, the hydrodynamic trap enables non-contact confinement of fluorescent and non-fluorescent particles for extended times and provides a new platform for fundamental studies in biology, biotechnology and materials science.
- B. Schudel, M. Tanyeri, A. Mukherjee, C. M. Schroeder, P. J. A. Kenis, “Multiplexed Detection of Nucleic Acids in a Combinatorial Screening Chip”, Lab on a Chip, 11, 1916-1923 (2011).
Multiplexed diagnostic testing has the potential to dramatically improve the quality of healthcare. Simultaneous measurement of health indicators and/or disease markers reduces turnaround time and analysis cost and speeds up the decision making process for diagnosis and treatment. At present, however, most diagnostic tests only provide information on a single indicator or marker. Development of efficient diagnostic tests capable of parallel screening of infectious disease markers could significantly advance clinical and diagnostic testing in both developed and developing parts of the world. Here, we report the multiplexed detection of nucleic acids as disease markers within discrete wells of a microfluidic chip using molecular beacons and total internal reflection fluorescence microscopy (TIRFM). Using a 4 × 4 array of 200 pL wells, we screened for the presence of four target single stranded oligonucleotides encoding for conserved regions of the genomes of four common viruses: human immunodeficiency virus-1 (HIV-1), human papillomavirus (HPV), Hepatitis A (Hep A) and Hepatitis B (Hep B). Target oligonucleotides are accurately detected and discriminated against alternative oligonucleotides with different sequences. This combinatorial chip represents a versatile platform for the development of clinical diagnostic tests for simultaneous screening, detection and monitoring of a wide range of biological markers of disease and health using minimal sample size.
- E. M. Johnson-Chavarria , M. Tanyeri , C. M. Schroeder, “A Microfluidic-based Hydrodynamic Trap for Single Particles”, Journal of Visualized Experiments, 47, (2011).
In this article, we present a microfluidic-based method for particle confinement based on hydrodynamic flow. We demonstrate stable particle trapping at a fluid stagnation point using a feedback control mechanism, thereby enabling confinement and micromanipulation of arbitrary particles in an integrated microdevice.
2010 Back to Top
- Y. Han, D. Dodd, C. M. Schroeder, R. I. Mackie, I. K. O. Cann, “Comparative Analysis of Two Thermophilic Enzymes Exhibiting both β-1,4-Mannosidic and β-1,4-Glucosidic Cleavage Activities fromCaldanaerobius polysaccharolyticus“, Journal of Bacteriology, 192, 4111-4121 (2010).
The hydrolysis of polysaccharides containing mannan requires endo-1,4-β-mannanase and 1,4-β-mannosidase activities. In the current report, the biochemical properties of two endo-β-1,4-mannanases (Man5A and Man5B) from Caldanaerobius polysaccharolyticus were studied. Man5A is composed of an N-terminal signal peptide (SP), a catalytic domain, two carbohydrate-binding modules (CBMs), and three surface layer homology (SLH) repeats, whereas Man5B lacks the SP, CBMs, and SLH repeats. To gain insights into how the two glycoside hydrolase family 5 (GH5) enzymes may aid the bacterium in energy acquisition and also the potential application of the two enzymes in the biofuel industry, two derivatives of Man5A (Man5A-TM1 [TM1 stands for truncational mutant 1], which lacks the SP and SLH repeats, and Man5A-TM2, which lacks the SP, CBMs, and SLH repeats) and the wild-type Man5B were biochemically analyzed. The Man5A derivatives displayed endo-1,4-β-mannanase and endo-1,4-β-glucanase activities and hydrolyzed oligosaccharides with a degree of polymerization (DP) of 4 or higher. Man5B exhibited endo-1,4-β-mannanase activity and little endo-1,4-β-glucanase activity; however, this enzyme also exhibited 1,4-β-mannosidase and cellodextrinase activities. Man5A-TM1, compared to either Man5A-TM2 or Man5B, had higher catalytic activity with soluble and insoluble polysaccharides, indicating that the CBMs enhance catalysis of Man5A. Furthermore, Man5A-TM1 acted synergistically with Man5B in the hydrolysis of β-mannan and carboxymethyl cellulose. The versatility of the two enzymes, therefore, makes them a resource for depolymerization of mannan-containing polysaccharides in the biofuel industry. Furthermore, on the basis of the biochemical and genomic data, a molecular mechanism for utilization of mannan-containing nutrients by C. polysaccharolyticus is proposed.
- M. Tanyeri, E. M. Johnson-Chavarria and C. M. Schroeder, “Hydrodynamic Trap for Single Particles and Cells”, Applied Physics Letters, 96, 224101 (2010).
News: This article was selected to appear in the June 14, 2010 issue of Virtual Journal of Nanoscale Science & Technology.
Trapping and manipulation of microscale and nanoscale particles is demonstrated using the sole action of hydrodynamic forces. We developed an automated particle trap based on a stagnation point flow generated in a microfluidic device. The hydrodynamic trap enables confinement and manipulation of single particles in low viscosity (1–10 cP) aqueous solution. Using this method, we trapped microscale and nanoscale particles (100 nm–15 μm) for long time scales (minutes to hours). We demonstrate particle confinement to within 1 μm of the trap center, corresponding to a trap stiffness of ∼10e−5 – 10e−4 pN/nm.
- S. Kim, C. M. Schroeder, X. S. Xie, “Single-Molecule Study of DNA Polymerization Activity of HIV-1 Reverse Transcriptase on DNA Templates”, Journal of Molecular Biology, 395, 995-1006 (2010).
HIV-1 RT (human immunodeficiency virus-1 reverse transcriptase) is a multifunctional polymerase responsible for reverse transcription of the HIV genome, including DNA replication on both RNA and DNA templates. During reverse transcription in vivo, HIV-1 RT replicates through various secondary structures on RNA and single-stranded DNA (ssDNA) templates without the need for a nucleic acid unwinding protein, such as a helicase. In order to understand the mechanism of polymerization through secondary structures, we investigated the DNA polymerization activity of HIV-1 RT on long ssDNA templates using a multiplexed single-molecule DNA flow-stretching assay. We observed that HIV-1 RT performs fast primer extension DNA synthesis on single-stranded regions of DNA (18.7 nt/s) and switches its activity to slow strand displacement synthesis at DNA hairpin locations (2.3 nt/s). Furthermore, we found that the rate of strand displacement synthesis is dependent on the GC content in hairpin stems and template stretching force. This indicates that the strand displacement synthesis occurs through a mechanism that is neither completely active nor passive: that is, the opening of the DNA hairpin is driven by a combination of free energy released during dNTP (deoxyribonucleotide triphosphate) hydrolysis and thermal fraying of base pairs. Our experimental observations provide new insight into the interchanging modes of DNA replication by HIV-1 RT on long ssDNA templates.
- C. J. Yeoman, Y. Han, D. Dodd, C. M. Schroeder, R. I. Mackie, I. K. O. Cann, “Thermostable Enzymes as Biocatalysts in the Biofuel Industry”, Advances in Applied Microbiology, 70 (2010).
Lignocellulose is the most abundant carbohydrate source in nature and represents an ideal renewable energy source. Thermostable enzymes that hydrolyze lignocellulose to its component sugars have significant advantages for improving the conversion rate of biomass over their mesophilic counterparts. We review here the recent literature on the development and use of thermostable enzymes for the depolymerization of lignocellulosic feedstocks for biofuel production. Furthermore, we discuss the protein structure, mechanisms of thermostability, and specific strategies that can be used to improve the thermal stability of lignocellulosic biocatalysts.
2000s Back to Top
- S. Kim, P. C. Blainey, C. M. Schroeder, X. S. Xie, “Multiplexed Single-molecule Assay for Enzymatic Activity on Flow-stretched DNA”, Nature Methods, 4, 397-399 (2007).
We report a single-molecule assay for nucleic-acid enzymes on flow-stretched DNA templates. To facilitate the detection of slow or intermittent enzymatic activities, we developed the assay with 15 nm spatial resolution at a frame rate of 1 Hz and approximately 10 nm mechanical stability over the timescale of hours. With multiplexed data collection, we applied the assay to phi29 DNA polymerase, HIV-1 reverse transcriptase, lambda exonuclease and Escherichia coli RNA polymerase.
- C. M. Schroeder, R. E. Teixeira, E. S. G. Shaqfeh, S. Chu, “Characteristic Periodic Motion of Polymers in Shear Flow”, Physical Review Letters,95, 018301 (2005).
The motion of both free and tethered polymer molecules as well as rigid Brownian rods in unbound shear flow is found to be characterized by a clear periodicity or tumbling frequency. Periodicity is shown using a combination of single molecule DNA experiments and computer simulations. In all cases, we develop scaling laws for this behavior and demonstrate that the frequency of characteristic periodic motion scales sublinearly with flow rate.
- C. M. Schroeder, R. E. Teixeira, E. S. G. Shaqfeh, S. Chu, “Dynamics of DNA in the Flow-Gradient Plane of Steady Shear Flow: Observations and Simulations”, Macromolecules, 38, 1967-1978 (2005).
The dynamical behavior of DNA in steady shear flow has been elucidated using a combination of Brownian dynamics (BD) simulation and single molecule visualization using fluorescence microscopy. Observations of DNA motion in the flow-gradient plane of shear flow using a novel flow apparatus allow for measurement of the gradient-direction polymer thickness (δ2), a microscopic conformational property that has direct influence on macroscopic polymer solution properties. To complement experimental results for λ-phage DNA (22 μm in length) and 84 μm DNA, we present BD simulation results for DNA in terms of both free-draining bead−spring models and models including both intramolecular hydrodynamic interactions (HI) and excluded volume (EV) interactions. Good agreement between experiments and BD simulations is obtained for ensemble averaged measurements of polymer extension, δ2, and orientation angle over a wide range of flow strengths. Macroscopic solution properties, including the polymer contribution to the shear viscosity (ηp) and first normal stress coefficient (), are calculated in BD simulations. Power law scalings of ηp and from the single molecule experiment and BD simulation agree well with bulk rheological characterization of dilute polymer solutions. Histograms of polymer extension demonstrate good agreement between experiment and BD simulation, though histograms of δ2 from BD simulation slightly differ from experimental results. Cross-correlations of polymer extension and δ2 display rich dynamical polymer behavior, which we discuss on a physical basis. Finally, the power spectral density of polymer extension and δ2 is presented for DNA for both single molecule experiment and BD simulation.
- C. M. Schroeder, E. S. G. Shaqfeh, S. Chu, “Effect of Hydrodynamic Interactions on DNA Dynamics in Extensional Flow: Simulation and Single Molecule Experiment”, Macromolecules, 37, 9242-9256(2004).
Intramolecular hydrodynamic interactions (HI) in flexible polymer chains influence both the equilibrium and nonequilibrium physical properties of macromoecules. In this work, we utilize a combination of single molecule experimental techniques and Brownian dynamics (BD) simulation to investigate the role of HI and excluded-volume (EV) interactions for DNA molecules ranging in contour length from 150 to 1300 μm. Epifluorescence microscopy is used to directly observe the dynamics of DNA molecules in planar extensional flow, and a semiimplicit bead−spring BD algorithm with fluctuating HI and EV interactions is presented. Quantitatitative agreement between ensemble average transient molecular extension in experiment and BD simulation is shown for DNA with 150 μm contour length. Simulations show polymer conformation hysteresis for larger DNA chains (1300 μm in length) when HI and EV parameters are chosen such that simulation results match the experimental polymer relaxation time and polymer stretch at flow strengths below the coil−stretch transition. Furthermore, conformation-dependent resistivities are extracted from BD simulation for DNA chains 1300 μm in length, and this drag functionality is utilized in a coarse-grained Brownian dumbbell model with variable resistivity. Finally, steady-state molecular extension results from the coarse-grained model are compared to simple polymer kinetic theory for a dumbbell with variable resistivity.
- C. M. Schroeder, H. P. Babcock, E. S. G. Shaqfeh, S. Chu, “Observation of Polymer Conformation Hysteresis in Extensional Flow”, Science, 301, 1515-1519 (2003).
Highly extensible Escherichia coli DNA molecules in planar extensional flow were visualized in dilute solution by fluorescence microscopy. For a narrow range of flow strengths, the molecules were found in either a coiled or highly extended conformation, depending on the deformation history of the polymer. This conformation hysteresis persists for many polymer relaxation times and is due to conformation-dependent hydrodynamic forces. Polymer conformational free-energy landscapes were calculated from computer simulations and show two free-energy minima for flow strengths near the coil-stretch transition. Hysteresis cycles may directly influence bulk-solution stresses and the development of stress-strain relations for dilute polymer flows.
- S. J. Vinay, D. M. Phillips, Y. S. Lee, C. M. Schroeder, X. Ma, M. C. Kim, M. S. Jhon, “Simulation of Ultrathin Lubricant Films Spreading of Various Carbon Surfaces”, Journal of Applied Physics,87, 6164-6166 (2000).
The mathematical modeling of the dynamics of ultrathin perfluoropolyalkylether (PFPE) films, taking into consideration both the disk carbonsurface composition and lubricant endgroup functionality, is described. Theoretical development based on the Monte Carlo method was employed to emulate experimental spreading data. In this model, we construct a system Hamiltonian based on a lattice-gas model by explicitly incorporating four classes of interactions: molecule/molecule, molecule/surface, endgroup/endgroup, and endgroup/surface, where a molecule is denoted as a backbone in the absence of endgroups. Spreading properties are investigated by tuning the lubricant interactions to model PFPE Z (without polar endgroups) and PFPE Zdol (with polar endgroups) on several surfaces. The simulations qualitatively describe the spreading profiles for molecules with and without polar endgroups. Acquired from N-frame animations, L-t plots are constructed and provide a qualitative comparison with the experimental data obtained from scanning microellipsometry.
Book Chapters Back to Top
- C. M. Schroeder, P. C. Blainey, S. Kim, X. S. Xie, “Hydrodynamic Flow-stretching Assay for Single Molecule Studies of Nucleic Acid-Protein Interactions”, in Single Molecule Techniques: A Laboratory Manual, T. Ha and P. Selvin (eds.), Cold Spring Harbor Laboratory Press, 2007.
- A. Mukherjee and C. M. Schroeder, “Microfluidic Methods in Single Cell Biology”, in Microfluidic Methods in Molecular Biology , C. Lu and S. Verbridge (eds.), Springer, in press, 2016.
Patents Back to Top
- C. M. Schroeder, H. P. Babcock, E. S. G. Shaqfeh, S. Chu, “System and Method for Confining an Object to a Region of Fluid Flow Having a Stagnation Point”, United States Patent, No. 7,013,739 B2, March 21, 2006.
- Y. Kim, S. Kim, M. Tanyeri, J. A. Katzenellenbogen, C. M. Schroeder, “Dye-conjugated Dendrimers”, United States Patent, No. 13/385,828, University of Illinois at Urbana-Champaign, May 2016.