Effect of Hydrodynamic Interactions on DNA Dynamics in Extensional Flow:  Simulation and Single Molecule Experiment

2004 ◽  
Vol 37 (24) ◽  
pp. 9242-9256 ◽  
Author(s):  
Charles M. Schroeder ◽  
Eric S. G. Shaqfeh ◽  
Steven Chu
Keyword(s):  
Single Molecule ◽  
Extensional Flow ◽  
Flow Simulation ◽  
Hydrodynamic Interactions ◽  
Dna Dynamics

scholarly journals Direct observation of DNA dynamics in semidilute solutions in extensional flow

2017 ◽  
Vol 61 (1) ◽  
pp. 151-167 ◽  
Author(s):  
Kai-Wen Hsiao ◽  
Chandi Sasmal ◽  
J. Ravi Prakash ◽  
Charles M. Schroeder
Keyword(s):  
Direct Observation ◽  
Extensional Flow ◽  
Dna Dynamics ◽  
Semidilute Solutions

scholarly journals Single-molecule sequence detection via microfluidic planar extensional flow at a stagnation point

Lab on a Chip ◽  
2010 ◽  
Vol 10 (12) ◽  
pp. 1543 ◽  
Author(s):  
Rebecca Dylla-Spears ◽  
Jacqueline E. Townsend ◽  
Linda Jen-Jacobson ◽  
Lydia L. Sohn ◽  
Susan J. Muller
Keyword(s):  
Stagnation Point ◽  
Single Molecule ◽  
Extensional Flow ◽  
Sequence Detection ◽  
Planar Extensional Flow

Single-molecule DNA dynamics in tapered contraction-expansion microchannels under electrophoresis

2009 ◽  
Vol 79 (4) ◽  
Author(s):  
Xin Hu ◽  
Shengnian Wang ◽  
L. James Lee
Keyword(s):  
Single Molecule ◽  
Dna Dynamics

scholarly journals DNA Dynamics and Single-Molecule Biology

2014 ◽  
Vol 114 (6) ◽  
pp. 3072-3086 ◽  
Author(s):  
Daniel Duzdevich ◽  
Sy Redding ◽  
Eric C. Greene
Keyword(s):  
Single Molecule ◽  
Dna Dynamics

scholarly journals Bridging the spatiotemporal scales of macromolecular transport in crowded biomimetic systems

2018 ◽  
Author(s):  
Kathryn Regan ◽  
Devynn Wulstein ◽  
Hannah Rasmussen ◽  
Ryan McGorty ◽  
Rae M. Robertson-Anderson
Keyword(s):  
Single Molecule ◽  
Biological Molecules ◽  
Biological Macromolecules ◽  
Dna Dynamics ◽  
Dna Transport ◽  
Macromolecular Transport ◽  
Dna Compaction ◽  
Biomimetic Systems ◽  
Conformational Properties ◽  
Spatiotemporal Scales

AbstractCrowding plays a key role in the transport and conformations of biological macromolecules. Gene therapy, viral infection and transfection require DNA to traverse the crowded cytoplasm, including a heterogeneous cytoskeleton of filamentous proteins. Given the complexity of cellular crowding, the dynamics of biological molecules can be highly dependent on the spatiotemporal scale probed. We present a powerful platform that spans molecular and cellular scales by coupling single-molecule conformational tracking (SMCT) and selective-plane illumination differential dynamic microscopy (SPIDDM). We elucidate the transport and conformational properties of large DNA, crowded by custom-designed networks of actin and microtubules, to link single-molecule conformations with ensemble DNA transport and cytoskeleton structure. We show that actin crowding leads to DNA compaction and suppression of fluctuations, combined with anomalous subdiffusion and heterogeneous transport, whereas microtubules have much more subdued impact across all scales. Interestingly, in composite networks of both filaments, microtubules primarily govern single-molecule DNA dynamics whereas actin governs ensemble transport.

scholarly journals Influence of the Experimental Set-Up on Single Molecule DNA Dynamics When Analyzed by Tethered Particle Motion

2010 ◽  
Vol 98 (3) ◽  
pp. 184a
Author(s):  
Catherine Tardin ◽  
Manoel Manghi ◽  
Julien Baglio ◽  
Laurence Salome ◽  
Nicolas Destainville
Keyword(s):  
Single Molecule ◽  
Particle Motion ◽  
Dna Dynamics ◽  
Tethered Particle Motion ◽  
Set Up

Anomalous pressure drop behaviour of mixed kinematics flows of viscoelastic polymer solutions: a multiscale simulation approach

2009 ◽  
Vol 631 ◽  
pp. 231-253 ◽  
Author(s):  
ANANTHA P. KOPPOL ◽  
RADHAKRISHNA SURESHKUMAR ◽  
ARASH ABEDIJABERI ◽  
BAMIN KHOMAMI
Keyword(s):  
Pressure Drop ◽  
Newtonian Fluid ◽  
Flow Rate ◽  
Extensional Flow ◽  
Flow Simulation ◽  
Multiscale Simulation ◽  
Excess Pressure ◽  
Micromechanical Models ◽  
Polymeric Solutions ◽  
Corner Vortex

A long-standing unresolved problem in non-Newtonian fluid mechanics, namely, the relationship between friction drag and flow rate in inertialess complex kinematics flows of dilute polymeric solutions is investigated via self-consistent multiscale flow simulations. Specifically, flow of a highly elastic dilute polymeric solution, described by first principles micromechanical models, through a 4:1:4 axisymmetric contraction and expansion geometry is examined utilizing our recently developed highly efficient multiscale flow simulation algorithm (Koppol, Sureshkumar & Khomami, J. Non-Newtonian Fluid Mech., vol. 141, 2007, p. 180). Comparison with experimental measurements (Rothstein & McKinley, J. Non-Newtonian Fluid Mech., vol. 86, 1999, p. 61) shows that the pressure drop evolution as a function of flow rate can be accurately predicted when the chain dynamics is described by multi-segment bead-spring micromechanical models that closely capture the transient extensional viscosity of the experimental fluid. Specifically, for the first time the experimentally observed doubling of the dimensionless excess pressure drop at intermediate flow rates is predicted. Moreover, based on an energy dissipation analysis it has been shown that the variation of the excess pressure drop with the flow rate is controlled by the flow-microstructure coupling in the extensional flow dominated region of the flow. Finally, the influence of the macromolecular chain extensibility on the vortex dynamics, i.e. growth of the upstream corner vortex at low chain extensibility or the shrinkage of the upstream corner vortex coupled with the formation of a lip vortex that eventually merges with the upstream corner vortex at high chain extensibility is elucidated.

scholarly journals A molecular view of DNA flexibility

2021 ◽  
Vol 54 ◽  
Author(s):  
Alberto Marin-Gonzalez ◽  
J. G. Vilhena ◽  
Ruben Perez ◽  
Fernando Moreno-Herrero
Keyword(s):  
Mechanical Properties ◽  
Single Molecule ◽  
Base Pair ◽  
Molecular Mechanisms ◽  
Cytosine Methylation ◽  
Persistence Length ◽  
Dna Dynamics ◽  
Dna Mechanics ◽  
Future Design ◽  
Pair Level

Abstract DNA dynamics can only be understood by taking into account its complex mechanical behavior at different length scales. At the micrometer level, the mechanical properties of single DNA molecules have been well-characterized by polymer models and are commonly quantified by a persistence length of 50 nm (~150 bp). However, at the base pair level (~3.4 Å), the dynamics of DNA involves complex molecular mechanisms that are still being deciphered. Here, we review recent single-molecule experiments and molecular dynamics simulations that are providing novel insights into DNA mechanics from such a molecular perspective. We first discuss recent findings on sequence-dependent DNA mechanical properties, including sequences that resist mechanical stress and sequences that can accommodate strong deformations. We then comment on the intricate effects of cytosine methylation and DNA mismatches on DNA mechanics. Finally, we review recently reported differences in the mechanical properties of DNA and double-stranded RNA, the other double-helical carrier of genetic information. A thorough examination of the recent single-molecule literature permits establishing a set of general ‘rules’ that reasonably explain the mechanics of nucleic acids at the base pair level. These simple rules offer an improved description of certain biological systems and might serve as valuable guidelines for future design of DNA and RNA nanostructures.

scholarly journals Dynamics and rheology of ring-linear blend semidilute solutions in extensional flow: Single molecule experiments

2021 ◽  
Vol 65 (4) ◽  
pp. 729-744
Author(s):  
Yuecheng Zhou ◽  
Charles D. Young ◽  
Megan Lee ◽  
Sourya Banik ◽  
Dejie Kong ◽  
...  
Keyword(s):  
Single Molecule ◽  
Extensional Flow ◽  
Semidilute Solutions

scholarly journals Macromolecule Translocation in a Nanopore: Center of Mass Drift–Diffusion over an Entropic Barrier

2019 ◽  
Author(s):  
Z. E. Dell ◽  
M. Muthukumar
Keyword(s):  
Single Molecule ◽  
Theoretical Approach ◽  
Center Of Mass ◽  
Diffusion Constant ◽  
Hydrodynamic Interactions ◽  
Biological Processes ◽  
Theoretical Approaches ◽  
Direct Interpretation ◽  
Synthetic Macromolecules ◽  
A Chain

ABSTRACTMany fundamental biological processes involve moving macromolecules across membranes, through nanopores, in a process called translocation. Such motion is necessary for gene expression and regulation, tissue formation, and viral infection. Furthermore, in recent years nanopore technologies have been developed for single molecule detection of biological and synthetic macromolecules, which have been most notably employed in next generation DNA sequencing devices. Many successful theories have been established, which calculate the entropic barrier required to elongate a chain during translocation. However, these theories are at the level of the translocation coordinate (number of forward steps) and thus lack a clear connection to experiments and simulations. Furthermore, the proper diffusion coefficient for such a coordinate is unclear. In order to address these issues, we propose a center of mass (CM) theory for translocation. We start with the entropic barrier approach and show that the translocation coordinate is equivalent to the center of mass of the chain, providing a direct interpretation of previous theoretical studies. We thus recognize that the appropriate dynamics is given by CM diffusion, and calculate the appropriate diffusion constant (Rouse or Zimm) as the chain translocates. We illustrate our theoretical approach with a planar nanopore geometry and calculate some characteristic dynamical predictions. Our main result is the connection between the translocation coordinate and the chain CM, however, we also find that the translocation time is sped up by 1–2 orders of magnitude if hydrodynamic interactions are present. Our approach can be extended to include the details included in previous translocation theories. Most importantly this work provides a direct connection between theoretical approaches and experiments or simulations.SIGNIFICANCEMacromolecule motion through nanopores is critical for many biological processes, and has been recently employed for nucleic acid sequencing. Despite this, direct theoretical understandings of translocation are difficult to evaluate due to the introduction of the translocation coordinate. In this manuscript, we propose a theory for translocation written at the center of mass level of the polymer chain. This theoretical approach is more easily compared to experimental and simulation results, and additionally allows one to accurately account for hydrodynamic interactions on the macromolecule dynamics.

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