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Title: Coarse-grained modeling of DNA oligomer hybridization: Length, sequence, and salt effects

Abstract

A recently-published coarse-grained DNA model [Hinckley, D. M. et al, J. Chem. Phys. 139, 144903 (2013)] is used to study the hybridization mechanism of DNA oligomers. Forward flux sampling is used to construct ensembles of reactive trajectories from which the effects of sequence, length, and ionic strength are revealed. Heterogeneous sequences are observed to hybridize via the canonical zippering mechanism. In contrast, homogeneous sequences hybridize through a slithering mechanism, while more complex base pair displacement processes are observed for repetitive sequences. In all cases the formation of non-native base pairs leads to an increase in the observed hybridization rate constants beyond those observed in sequence where only native base pairs are permitted. The scaling of rate constants with length is captured by extending existing hybridization theories to account for the formation of non-native base pairs. Furthermore, that scaling is found to be similar for oligomeric and polymeric systems, suggesting that similar physics are involved.

Authors:
; ;
Publication Date:
Research Org.:
Argonne National Lab. (ANL), Argonne, IL (United States)
Sponsoring Org.:
USDOE Office of Science - Office of Basic Energy Sciences - Materials Sciences and Engineering Division; National Science Foundation (NSF)
OSTI Identifier:
1395017
DOE Contract Number:  
AC02-06CH11357
Resource Type:
Journal Article
Resource Relation:
Journal Name: Journal of Chemical Physics; Journal Volume: 141; Journal Issue: 3
Country of Publication:
United States
Language:
English
Subject:
59 BASIC BIOLOGICAL SCIENCES

Citation Formats

Hinckley, Daniel M., Lequieu, Joshua P., and de Pablo, Juan J.. Coarse-grained modeling of DNA oligomer hybridization: Length, sequence, and salt effects. United States: N. p., 2014. Web. doi:10.1063/1.4886336.
Hinckley, Daniel M., Lequieu, Joshua P., & de Pablo, Juan J.. Coarse-grained modeling of DNA oligomer hybridization: Length, sequence, and salt effects. United States. doi:10.1063/1.4886336.
Hinckley, Daniel M., Lequieu, Joshua P., and de Pablo, Juan J.. Mon . "Coarse-grained modeling of DNA oligomer hybridization: Length, sequence, and salt effects". United States. doi:10.1063/1.4886336.
@article{osti_1395017,
title = {Coarse-grained modeling of DNA oligomer hybridization: Length, sequence, and salt effects},
author = {Hinckley, Daniel M. and Lequieu, Joshua P. and de Pablo, Juan J.},
abstractNote = {A recently-published coarse-grained DNA model [Hinckley, D. M. et al, J. Chem. Phys. 139, 144903 (2013)] is used to study the hybridization mechanism of DNA oligomers. Forward flux sampling is used to construct ensembles of reactive trajectories from which the effects of sequence, length, and ionic strength are revealed. Heterogeneous sequences are observed to hybridize via the canonical zippering mechanism. In contrast, homogeneous sequences hybridize through a slithering mechanism, while more complex base pair displacement processes are observed for repetitive sequences. In all cases the formation of non-native base pairs leads to an increase in the observed hybridization rate constants beyond those observed in sequence where only native base pairs are permitted. The scaling of rate constants with length is captured by extending existing hybridization theories to account for the formation of non-native base pairs. Furthermore, that scaling is found to be similar for oligomeric and polymeric systems, suggesting that similar physics are involved.},
doi = {10.1063/1.4886336},
journal = {Journal of Chemical Physics},
number = 3,
volume = 141,
place = {United States},
year = {Mon Jul 21 00:00:00 EDT 2014},
month = {Mon Jul 21 00:00:00 EDT 2014}
}