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Title: DNA molecules deviate from shortest trajectory when driven through hydrogel

Abstract

Dynamic fluorescence-based single-molecule imaging of $λ$-DNA molecules driven through agarose hydrogels by DC electric fields reveals that passage through the hydrogel (98.5% water content) induces mobility orthogonal to the external field. Tortuous paths followed by the DNA molecules, which are heavily entangled in the hydrogel mesh as their contour length is nearly 100 times the hydrogel mesh size of 200 nm, cause them to appear to diffuse orthogonal to the driving force. The higher the driving field, from 2 to 16 V/cm, the higher the off-axis dispersion is, over the same time interval. In this work we measure the off-axis displacement distribution over 3 orders of magnitude of probability density and find a master curve after normalizing for time (t) elapsed, but the power of time for normalizing increases with the external field, from t0.25 to t0.6 with increasing field. Comparing trajectories over the same distance traveled in the electric field direction, we observe whereas for the highest field strengths DNA molecules come closest to taking the shortest trajectory between two points in space, deviations from the shortest trajectory grow larger and larger (up to 40% larger) as one approaches the case of small yet finite external field strength.

Authors:
 [1];  [2];  [3]; ORCiD logo [4]
  1. Inst. for Basic Science (IBS), Ulsan (South Korea). Center for Soft and Living Matter; Univ. of California, San Francisco, CA (United States)
  2. Google, Inc., Mountain View, CA (United States)
  3. Inst. for Basic Science (IBS), Ulsan (South Korea). Center for Soft and Living Matter
  4. Inst. for Basic Science (IBS), Ulsan (South Korea). Center for Soft and Living Matter; Ulsan National Institute of Science and Technology, Ulsan (South Korea)
Publication Date:
Research Org.:
Univ. of Illinois at Urbana-Champaign, IL (United States)
Sponsoring Org.:
USDOE Office of Science (SC), Basic Energy Sciences (BES) (SC-22). Materials Sciences & Engineering Division
OSTI Identifier:
1609407
Alternate Identifier(s):
OSTI ID: 1463063
Grant/Contract Number:  
FG02-02ER46019
Resource Type:
Accepted Manuscript
Journal Name:
Journal of Chemical Physics
Additional Journal Information:
Journal Volume: 149; Journal Issue: 16; Journal ID: ISSN 0021-9606
Publisher:
American Institute of Physics (AIP)
Country of Publication:
United States
Language:
English
Subject:
37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CHEMISTRY; 71 CLASSICAL AND QUANTUM MECHANICS, GENERAL PHYSICS; Chemistry; Physics; Molecule imaging; Polyelectrolytes; Electrophoresis; Stochastic processes; Random walks; Brownian motion; DNA studies; Nonequilibrium statistical mechanics; External energy source

Citation Formats

Guan, Juan, Chen, Kejia, Jee, Ah-Young, and Granick, Steve. DNA molecules deviate from shortest trajectory when driven through hydrogel. United States: N. p., 2018. Web. doi:10.1063/1.5033990.
Guan, Juan, Chen, Kejia, Jee, Ah-Young, & Granick, Steve. DNA molecules deviate from shortest trajectory when driven through hydrogel. United States. doi:10.1063/1.5033990.
Guan, Juan, Chen, Kejia, Jee, Ah-Young, and Granick, Steve. Mon . "DNA molecules deviate from shortest trajectory when driven through hydrogel". United States. doi:10.1063/1.5033990. https://www.osti.gov/servlets/purl/1609407.
@article{osti_1609407,
title = {DNA molecules deviate from shortest trajectory when driven through hydrogel},
author = {Guan, Juan and Chen, Kejia and Jee, Ah-Young and Granick, Steve},
abstractNote = {Dynamic fluorescence-based single-molecule imaging of $λ$-DNA molecules driven through agarose hydrogels by DC electric fields reveals that passage through the hydrogel (98.5% water content) induces mobility orthogonal to the external field. Tortuous paths followed by the DNA molecules, which are heavily entangled in the hydrogel mesh as their contour length is nearly 100 times the hydrogel mesh size of 200 nm, cause them to appear to diffuse orthogonal to the driving force. The higher the driving field, from 2 to 16 V/cm, the higher the off-axis dispersion is, over the same time interval. In this work we measure the off-axis displacement distribution over 3 orders of magnitude of probability density and find a master curve after normalizing for time (t) elapsed, but the power of time for normalizing increases with the external field, from t0.25 to t0.6 with increasing field. Comparing trajectories over the same distance traveled in the electric field direction, we observe whereas for the highest field strengths DNA molecules come closest to taking the shortest trajectory between two points in space, deviations from the shortest trajectory grow larger and larger (up to 40% larger) as one approaches the case of small yet finite external field strength.},
doi = {10.1063/1.5033990},
journal = {Journal of Chemical Physics},
number = 16,
volume = 149,
place = {United States},
year = {2018},
month = {8}
}

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