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1.
ACS Appl Mater Interfaces ; 12(18): 20722-20732, 2020 May 06.
Artigo em Inglês | MEDLINE | ID: mdl-32286786

RESUMO

Biohybrid molecules are a versatile class of materials for controlling the assembly behavior and functional properties of electronically active organics. In this work, we study the effect of the size of the π-conjugated core on the assembly and phase behavior for a series of π-conjugated peptides consisting of oligothiophene cores of defined lengths flanked by sequence-defined peptides (OTX, where X = 4, 5, 6 is the number of thiophene core units). Interestingly, we find that π-conjugated peptides with relatively short OT4 cores assemble into ordered, high aspect ratio, one-dimensional (1D) structures, whereas π-conjugated peptides with longer OT5 and OT6 cores assemble into disordered structures or lower aspect ratio 1D structures depending on assembly conditions. Phase diagrams for assembled materials are experimentally determined as a function of ionic strength, pH, temperature, and peptide concentration, revealing the impact of molecular sequence and π-conjugated core length on assembled morphologies. Molecular dynamics (MD) simulations are further used to probe the origins of microscale differences in assembly that arise from subtle changes in molecular identity. Broadly, our work elucidates the mechanisms governing the assembly of π-conjugated peptides, which will aid in efficient materials processing for soft electronic applications. Overall, these results highlight the complex phase behavior of biohybrid materials, including the impact of molecular sequence on assembly behavior and morphology.

2.
J Am Chem Soc ; 142(10): 4852-4861, 2020 Mar 11.
Artigo em Inglês | MEDLINE | ID: mdl-32069403

RESUMO

A major challenge in synthetic polymers lies in understanding how primary monomer sequence affects materials properties. In this work, we show that charge transport in single molecule junctions of conjugated oligomers critically depends on the primary sequence of monomers. A series of sequence-defined oligomers ranging from two to seven units was synthesized by an iterative approach based on the van Leusen reaction, providing conjugated oligomers with backbones consisting of para-linked phenylenes connected to oxazole, imidazole, or nitro-substituted pyrrole. The charge transport properties of these materials were characterized using a scanning tunneling microscope-break junction (STM-BJ) technique, thereby enabling direct measurement of molecular conductance for sequence-defined dimers, trimers, pentamers, and a heptamer. Our results show that oligomers with specific monomer sequences exhibit unexpected and distinct charge transport pathways that enhance molecular conductance more than 10-fold. A systematic analysis using monomer substitution patterns established that sequence-defined pentamers containing imidazole or pyrrole groups in specific locations provide molecular attachment points on the backbone to the gold electrodes, thereby giving rise to multiple conductance pathways. These findings reveal the subtle but important role of molecular structure including steric hindrance and directionality of heterocycles in determining charge transport in these molecular junctions. This work brings new understanding for designing molecular electronic components.

3.
Soft Matter ; 16(2): 337-347, 2020 Jan 02.
Artigo em Inglês | MEDLINE | ID: mdl-31802095

RESUMO

Lipid vesicles play a key role in fundamental biological processes. Despite recent progress, we lack a complete understanding of the non-equilibrium dynamics of vesicles due to challenges associated with long-time observation of shape fluctuations in strong flows. In this work, we present a flow-phase diagram for vesicle shape and conformational transitions in planar extensional flow using a Stokes trap, which enables control over the center-of-mass position of single or multiple vesicles in precisely defined flows [A. Shenoy, C. V. Rao and C. M. Schroeder, Proc. Natl. Acad. Sci. U. S. A., 2016, 113(15), 3976-3981]. In this way, we directly observe the non-equilibrium conformations of lipid vesicles as a function of reduced volume ν, capillary number Ca, and viscosity contrast λ. Our results show that vesicle dynamics in extensional flow are characterized by the emergence of three distinct shape transitions, including a tubular to symmetric dumbbell transition, a spheroid to asymmetric dumbbell transition, and quasi-spherical to ellipsoid transition. The experimental phase diagram is in good agreement with recent predictions from simulations [V. Narsimhan, A. P. Spann and E. S. Shaqfeh, J. Fluid Mech., 2014, 750, 144]. We further show that the phase boundary of vesicle shape transitions is independent of the viscosity contrast. Taken together, our results demonstrate the utility of the Stokes trap for the precise quantification of vesicle stretching dynamics in precisely defined flows.

4.
Soft Matter ; 16(1): 152-161, 2020 Jan 07.
Artigo em Inglês | MEDLINE | ID: mdl-31774103

RESUMO

Blends of polymers of different topologies, such as ring and supercoiled, naturally occur in biology and often exhibit emergent viscoelastic properties coveted in industry. However, due to their complexity, along with the difficulty of producing polymers of different topologies, the dynamics of topological polymer blends remains poorly understood. We address this void by using both passive and active microrheology to characterize the linear and nonlinear rheological properties of blends of relaxed circular and supercoiled DNA. We characterize the dynamics as we vary the concentration from below the overlap concentration c* to above (0.5c* to 2c*). Surprisingly, despite working at the dilute-semidilute crossover, entanglement dynamics, such as elastic plateaus and multiple relaxation modes, emerge. Finally, blends exhibit an unexpected sustained elastic response to nonlinear strains not previously observed even in well-entangled linear polymer solutions.

5.
Nucleic Acids Res ; 48(3): 1406-1422, 2020 02 20.
Artigo em Inglês | MEDLINE | ID: mdl-31863586

RESUMO

Recent advances in gene editing have been enabled by programmable nucleases such as transcription activator-like effector nucleases (TALENs) and CRISPR-Cas9. However, several open questions remain regarding the molecular machinery in these systems, including fundamental search and binding behavior as well as role of off-target binding and specificity. In order to achieve efficient and specific cleavage at target sites, a high degree of target site discrimination must be demonstrated for gene editing applications. In this work, we studied the binding affinity and specificity for a series of TALE proteins under a variety of solution conditions using in vitro fluorescence methods and molecular dynamics (MD) simulations. Remarkably, we identified that TALEs demonstrate high sequence specificity only upon addition of small amounts of certain divalent cations (Mg2+, Ca2+). However, under purely monovalent salt conditions (K+, Na+), TALEs bind to specific and non-specific DNA with nearly equal affinity. Divalent cations preferentially bind to DNA over monovalent cations, which attenuates non-specific interactions between TALEs and DNA and further stabilizes specific interactions. Overall, these results uncover new mechanistic insights into the binding action of TALEs and further provide potential avenues for engineering and application of TALE- or TALEN-based systems for genome editing and regulation.


Assuntos
Cálcio/química , Cátions Bivalentes/química , DNA/química , Magnésio/química , Nucleases dos Efetores Semelhantes a Ativadores de Transcrição/química , Sistemas CRISPR-Cas/genética , Proteínas de Ligação a DNA/química , Edição de Genes , Potássio/química , Ligação Proteica , Sódio/química , Soluções/química , Nucleases dos Efetores Semelhantes a Ativadores de Transcrição/metabolismo
6.
J Am Chem Soc ; 141(40): 16079-16084, 2019 Oct 09.
Artigo em Inglês | MEDLINE | ID: mdl-31514499

RESUMO

Charge transport in single molecule junctions critically depends on the chemical identity of anchor groups used to connect molecular wires to electrodes. In this work, we report the charge transport properties of conjugated oligomers with oxazole anchors, focusing on the role of the heteroatom substitution position in terminal oxazole groups. Our results show that oxazole serves as an efficient anchor group to form stable gold-molecule-gold junctions. We further observe quantum interference (QI) effects in oxazole-terminated phenylene molecular junctions, including destructive QI in meta-substituted phenyl rings and constructive QI in para-substituted phenyl rings containing terminal oxazole groups with the same chemical constitution on both termini (i.e., O5O5 (5-oxazolyl) or O4O4 (4-oxazolyl) linkages on both termini). Surprisingly, meta-substituted phenyl rings with nonequivalent constitutions (i.e., O4O5 oxazole terminal linkages) show unexpectedly higher conductance as compared to para-substituted analogues. These results suggest that charge transport in oxazole-terminated molecules is determined by the heteroatom substitution position of the oxazole anchor in addition to the aryl substitution pattern of the π-conjugated core. Our results further show that conjugated molecules with homogeneous oxazole linkages obey a quantum circuit rule such that GO4-p-O4/GO4-m-O4 = GO5-p-O5/GO5-m-O5, where G is molecular conductance. Overall, our work provides key insight into the development of new chemistries for molecular circuitry in the rapidly advancing field of single molecule electronics.

7.
Langmuir ; 35(33): 10947-10957, 2019 Aug 20.
Artigo em Inglês | MEDLINE | ID: mdl-31340647

RESUMO

Bioinspired materials have been developed with the aim of harnessing natural self-assembly for precisely engineered functionality. Microfluidics is poised to play a key role in the directed assembly of advanced materials with ordered nano and mesoscale features. More importantly, there is a strong need for understanding the kinetics of continuous assembly processes. In this work, we describe a continuous microfluidic system for the assembly and alignment of synthetic oligopeptides with π-conjugated cores using a three-dimensional (3D) flow focusing of inlet reactant streams. This system facilitates in situ confocal fluorescence microscopy and in situ fluorescence lifetime imaging microscopy (FLIM), which can be used in unprecedented capacity to characterize the integrity of peptides during the assembly process. To achieve continuous assembly, we integrate chevron patterns in the ceiling and floor of the microdevice to generate a 3D-focused sheath flow of the reactant peptide. Consequently, the peptide stream is directed toward an acidic triggering stream in a cross-slot geometry which mediates assembly into higher-order fiber-like structures. Using this approach, the focused peptide stream is assembled using a planar extensional flow, which ensures high degrees of microstructural alignment within the assembled material. We demonstrate the efficacy of this approach using three different synthetic oligopeptides, and in all cases, we observe the efficient and continuous assembly of oligopeptides. In addition, finite element simulations are used to guide device design and to validate 3D focusing. Overall, this approach presents an efficient and effective method for the continuous assembly and alignment of ordered materials using microfluidics.

8.
Nat Commun ; 10(1): 1753, 2019 04 15.
Artigo em Inglês | MEDLINE | ID: mdl-30988290

RESUMO

Understanding the dynamics of ring polymers is a particularly challenging yet interesting problem in soft materials. Despite recent progress, a complete understanding of the nonequilibrium behavior of ring polymers has not yet been achieved. In this work, we directly observe the flow dynamics of DNA-based rings in semidilute linear polymer solutions using single molecule techniques. Our results reveal strikingly large conformational fluctuations of rings in extensional flow long after the initial transient stretching process has terminated, which is observed even at extremely low concentrations (0.025 c*) of linear polymers in the background solution. The magnitudes and characteristic timescales of ring conformational fluctuations are determined as functions of flow strength and polymer concentration. Our results suggest that ring conformational fluctuations arise due to transient threading of linear polymers through open ring chains stretching in flow.

9.
Phys Rev Lett ; 120(26): 267801, 2018 Jun 29.
Artigo em Inglês | MEDLINE | ID: mdl-30004741

RESUMO

Stress relaxation following deformation of an entangled polymeric liquid is thought to be affected by transient reforming of chain entanglements. In this work, we use single molecule techniques to study the relaxation of individual polymers in the transition regime from unentangled to entangled solutions. Our results reveal the emergence of dynamic heterogeneity underlying polymer relaxation behavior, including distinct molecular subpopulations described by a single-mode and a double-mode exponential relaxation process. The slower double-mode timescale τ_{d,2} is consistent with a characteristic reptation time, whereas the single-mode timescale τ_{s} and the fast double-mode timescale τ_{d,1} are attributed to local regions of transient disentanglement due to deformation.

10.
ACS Appl Mater Interfaces ; 9(47): 41586-41593, 2017 Nov 29.
Artigo em Inglês | MEDLINE | ID: mdl-29112374

RESUMO

One-dimensional (1-D) supramolecular self-assembly offers a powerful strategy to achieve long-range unidirectional ordering of organic semiconducting materials via noncovalent interactions. Using a 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. Through use of 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), photoinduced force microscopy (PiFM), fluorescence polarization microscopy, and electron microscopy. These results reveal the 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.

11.
ACS Cent Sci ; 3(9): 986-994, 2017 Sep 27.
Artigo em Inglês | MEDLINE | ID: mdl-28979940

RESUMO

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 π-conjugated synthetic oligopeptides containing different π-conjugated cores (quaterthiophene and perylene diimide) using a combination of particle tracking microrheology, confocal fluorescence microscopy, optical spectroscopy, and electron microscopy. Our results show that π-conjugated oligopeptides self-assemble into ß-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 π-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 π-conjugated cores greatly influences the self-assembly process, such that oligopeptides appended to π-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 π-conjugated oligopeptides driven by concentration, which is controlled by a combination of enthalpic and entropic interactions between oligopeptide subunits.

12.
Annu Rev Chem Biomol Eng ; 8: 577-597, 2017 06 07.
Artigo em Inglês | MEDLINE | ID: mdl-28489428

RESUMO

Exciting new advances in genome engineering have unlocked the potential to radically alter the treatment of human disease. In this review, we discuss the application of single-molecule techniques to uncover the mechanisms behind two premier classes of genome editing proteins: transcription activator-like effector nucleases (TALENs) and the clustered regularly interspaced short palindromic repeats (CRISPR)/CRISPR-associated system (Cas). 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. Here, we discuss the DNA search and recognition process for TALEs and Cas9 that have been revealed by recent single-molecule experiments.


Assuntos
Sistemas CRISPR-Cas , Edição de Genes/métodos , Imagem Individual de Molécula/métodos , Nucleases dos Efetores Semelhantes a Ativadores de Transcrição/análise , Animais , Repetições Palindrômicas Curtas Agrupadas e Regularmente Espaçadas , DNA/análise , DNA/genética , DNA/metabolismo , Genoma , Humanos , Imagem Óptica/métodos , Espectrometria de Fluorescência/métodos , Análise Espectral/métodos , Nucleases dos Efetores Semelhantes a Ativadores de Transcrição/metabolismo
13.
ACS Appl Mater Interfaces ; 9(4): 3977-3984, 2017 Feb 01.
Artigo em Inglês | MEDLINE | ID: mdl-28067038

RESUMO

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 noncovalent interactions through hydrogen bonding in biopolymer subunits. Despite recent progress, there is a need to control and quantitatively understand assembly under nonequilibrium conditions. In this work, we study the nonequilibrium 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 nonequilibrium conditions, specifically showing that oligopeptide assembly is governed by a delicate balance between reaction kinetics and transport processes.

14.
Phys Rev Lett ; 119(12): 127801, 2017 Sep 22.
Artigo em Inglês | MEDLINE | ID: mdl-29341644

RESUMO

Bottle-brush polymers exhibit closely grafted side chains that interact by steric repulsion, thereby causing stiffening of the main polymer chain. 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.

15.
Nat Chem Biol ; 12(10): 831-7, 2016 10.
Artigo em Inglês | MEDLINE | ID: mdl-27526029

RESUMO

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 about 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 nonspecific search, despite remaining associated with DNA templates during the search process. Our results suggest that the protein helical structure enables TALEs to adopt a loosely wrapped conformation around DNA templates during nonspecific search, facilitating rapid one-dimensional (1D) 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 is unique among the broad class of sequence-specific DNA-binding proteins and supports efficient 1D search along DNA.


Assuntos
DNA/metabolismo , Rotação , Efetores Semelhantes a Ativadores de Transcrição/metabolismo , DNA/química , Modelos Moleculares , Conformação Proteica
16.
Lab Chip ; 16(16): 2974-6, 2016 08 02.
Artigo em Inglês | MEDLINE | ID: mdl-27447687
17.
Proc Natl Acad Sci U S A ; 113(15): 3976-81, 2016 Apr 12.
Artigo em Inglês | MEDLINE | ID: mdl-27035979

RESUMO

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.

18.
Anal Chem ; 87(21): 11048-57, 2015 Nov 03.
Artigo em Inglês | MEDLINE | ID: mdl-26461122

RESUMO

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.


Assuntos
Corantes Fluorescentes/química , Nanoconjugados , Fotoquímica
19.
Soft Matter ; 11(29): 5947-54, 2015 Aug 07.
Artigo em Inglês | MEDLINE | ID: mdl-26123827

RESUMO

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.

20.
Nat Commun ; 6: 7277, 2015 Jun 01.
Artigo em Inglês | MEDLINE | ID: mdl-26027871

RESUMO

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.


Assuntos
Proteínas de Ligação a DNA/metabolismo , DNA/metabolismo , Sítios de Ligação , Difusão , Escherichia coli , Polarização de Fluorescência , Microscopia de Fluorescência , Ligação Proteica , Streptomyces , Ativação Transcricional
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