skip to main content
OSTI.GOV title logo U.S. Department of Energy
Office of Scientific and Technical Information

Title: Sub-diffusion and trapped dynamics of neutral and charged probes in DNA-protein coacervates

Abstract

The physical mechanism leading to the formation of large intermolecular DNA-protein complexes has been studied. Our study aims to explain the occurrence of fast coacervation dynamics at the charge neutralization point, followed by the appearance of smaller complexes and slower coacervation dynamics as the complex experiences overcharging. Furthermore, the electrostatic potential and probe mobility was investigated to mimic the transport of DNA / DNA-protein complex in a DNA-protein complex coacervate medium [N. Arfin and H. B. Bohidar, J. Phys. Chem. B 116, 13192 (2012)] by assigning neutral, negative, or positive charge to the probe particle. The mobility of the neutral probe was maximal at low matrix concentrations and showed random walk behavior, while its mobility ceased at the jamming concentration of c = 0.6, showing sub-diffusion and trapped dynamics. The positively charged probe showed sub-diffusive random walk followed by trapped dynamics, while the negatively charged probe showed trapping with occasional hopping dynamics at much lower concentrations. Sub-diffusion of the probe was observed in all cases under consideration, where the electrostatic interaction was used exclusively as the dominant force involved in the dynamics. For neutral and positive probes, the mean square displacement 〈R{sup 2}〉 exhibits a scaling with time as 〈R{supmore » 2}〉 ∼ t{sup α}, distinguishing random walk and trapped dynamics at α = 0.64 ± 0.04 at c = 0.12 and c = 0.6, respectively. In addition, the same scaling factors with the exponent β = 0.64 ± 0.04 can be used to distinguish random walk and trapped dynamics for the neutral and positive probes using the relation between the number of distinct sites visited by the probe, S(t), which follows the scaling, S(t) ∼ t{sup β}/ln (t). Our results established the occurrence of a hierarchy of diffusion dynamics experienced by a probe in a dense medium that is either charged or neutral.« less

Authors:
 [1];  [2]
  1. Polymer and Biophysics Laboratory, School of Physical Sciences, Jawaharlal Nehru University, New Delhi-110067 (India)
  2. Nonlinear Dynamics Laboratory, School of Physical Sciences, Jawaharlal Nehru University, New Delhi-110067 (India)
Publication Date:
OSTI Identifier:
22251951
Resource Type:
Journal Article
Journal Name:
AIP Advances
Additional Journal Information:
Journal Volume: 3; Journal Issue: 11; Other Information: (c) 2013 Author(s); Country of input: International Atomic Energy Agency (IAEA); Journal ID: ISSN 2158-3226
Country of Publication:
United States
Language:
English
Subject:
36 MATERIALS SCIENCE; DIFFUSION; DNA; INTERACTIONS; PROBES; PROTEINS

Citation Formats

Arfin, Najmul, Yadav, Avinash Chand, Bohidar, H. B., E-mail: bohi0700@mail.jnu.ac.in, and Special Centre for Nanosciences, Jawaharlal Nehru University, New Delhi-110067. Sub-diffusion and trapped dynamics of neutral and charged probes in DNA-protein coacervates. United States: N. p., 2013. Web. doi:10.1063/1.4830281.
Arfin, Najmul, Yadav, Avinash Chand, Bohidar, H. B., E-mail: bohi0700@mail.jnu.ac.in, & Special Centre for Nanosciences, Jawaharlal Nehru University, New Delhi-110067. Sub-diffusion and trapped dynamics of neutral and charged probes in DNA-protein coacervates. United States. https://doi.org/10.1063/1.4830281
Arfin, Najmul, Yadav, Avinash Chand, Bohidar, H. B., E-mail: bohi0700@mail.jnu.ac.in, and Special Centre for Nanosciences, Jawaharlal Nehru University, New Delhi-110067. 2013. "Sub-diffusion and trapped dynamics of neutral and charged probes in DNA-protein coacervates". United States. https://doi.org/10.1063/1.4830281.
@article{osti_22251951,
title = {Sub-diffusion and trapped dynamics of neutral and charged probes in DNA-protein coacervates},
author = {Arfin, Najmul and Yadav, Avinash Chand and Bohidar, H. B., E-mail: bohi0700@mail.jnu.ac.in and Special Centre for Nanosciences, Jawaharlal Nehru University, New Delhi-110067},
abstractNote = {The physical mechanism leading to the formation of large intermolecular DNA-protein complexes has been studied. Our study aims to explain the occurrence of fast coacervation dynamics at the charge neutralization point, followed by the appearance of smaller complexes and slower coacervation dynamics as the complex experiences overcharging. Furthermore, the electrostatic potential and probe mobility was investigated to mimic the transport of DNA / DNA-protein complex in a DNA-protein complex coacervate medium [N. Arfin and H. B. Bohidar, J. Phys. Chem. B 116, 13192 (2012)] by assigning neutral, negative, or positive charge to the probe particle. The mobility of the neutral probe was maximal at low matrix concentrations and showed random walk behavior, while its mobility ceased at the jamming concentration of c = 0.6, showing sub-diffusion and trapped dynamics. The positively charged probe showed sub-diffusive random walk followed by trapped dynamics, while the negatively charged probe showed trapping with occasional hopping dynamics at much lower concentrations. Sub-diffusion of the probe was observed in all cases under consideration, where the electrostatic interaction was used exclusively as the dominant force involved in the dynamics. For neutral and positive probes, the mean square displacement 〈R{sup 2}〉 exhibits a scaling with time as 〈R{sup 2}〉 ∼ t{sup α}, distinguishing random walk and trapped dynamics at α = 0.64 ± 0.04 at c = 0.12 and c = 0.6, respectively. In addition, the same scaling factors with the exponent β = 0.64 ± 0.04 can be used to distinguish random walk and trapped dynamics for the neutral and positive probes using the relation between the number of distinct sites visited by the probe, S(t), which follows the scaling, S(t) ∼ t{sup β}/ln (t). Our results established the occurrence of a hierarchy of diffusion dynamics experienced by a probe in a dense medium that is either charged or neutral.},
doi = {10.1063/1.4830281},
url = {https://www.osti.gov/biblio/22251951}, journal = {AIP Advances},
issn = {2158-3226},
number = 11,
volume = 3,
place = {United States},
year = {Fri Nov 15 00:00:00 EST 2013},
month = {Fri Nov 15 00:00:00 EST 2013}
}