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Title: Evaluating the role of coherent delocalized phonon-like modes in DNA cyclization

Abstract

The innate flexibility of a DNA sequence is quantified by the Jacobson-Stockmayer’s J-factor, which measures the propensity for DNA loop formation. Recent studies of ultra-short DNA sequences revealed a discrepancy of up to six orders of magnitude between experimentally measured and theoretically predicted J-factors. These large differences suggest that, in addition to the elastic moduli of the double helix, other factors contribute to loop formation. We develop a new theoretical model that explores how coherent delocalized phonon-like modes in DNA provide single-stranded ”flexible hinges” to assist in loop formation. We also combine the Czapla-Swigon-Olson structural model of DNA with our extended Peyrard-Bishop-Dauxois model and, without changing any of the parameters of the two models, apply this new computational framework to 86 experimentally characterized DNA sequences. Our results demonstrate that the new computational framework can predict J-factors within an order of magnitude of experimental measurements for most ultra-short DNA sequences, while continuing to accurately describe the J-factors of longer sequences. Furthermore, we demonstrate that our computational framework can be used to describe the cyclization of DNA sequences that contain a base pair mismatch. Overall, our results support the conclusion that coherent delocalized phonon-like modes play an important role in DNA cyclization.

Authors:
ORCiD logo [1];  [2];  [2]; ORCiD logo [1]
  1. Los Alamos National Lab. (LANL), Los Alamos, NM (United States); Univ. of New Mexico, Albuquerque, NM (United States). Comprehensive Cancer Center
  2. Los Alamos National Lab. (LANL), Los Alamos, NM (United States)
Publication Date:
Research Org.:
Los Alamos National Lab. (LANL), Los Alamos, NM (United States)
Sponsoring Org.:
USDOE National Nuclear Security Administration (NNSA)
OSTI Identifier:
1412857
Report Number(s):
LA-UR-16-28857
Journal ID: ISSN 2045-2322
Grant/Contract Number:  
AC52-06NA25396
Resource Type:
Journal Article: Accepted Manuscript
Journal Name:
Scientific Reports
Additional Journal Information:
Journal Volume: 7; Journal Issue: 1; Journal ID: ISSN 2045-2322
Publisher:
Nature Publishing Group
Country of Publication:
United States
Language:
English
Subject:
59 BASIC BIOLOGICAL SCIENCES; computational biophysics; computational science

Citation Formats

Alexandrov, Ludmil B., Rasmussen, Kim Ø., Bishop, Alan R., and Alexandrov, Boian S. Evaluating the role of coherent delocalized phonon-like modes in DNA cyclization. United States: N. p., 2017. Web. doi:10.1038/s41598-017-09537-y.
Alexandrov, Ludmil B., Rasmussen, Kim Ø., Bishop, Alan R., & Alexandrov, Boian S. Evaluating the role of coherent delocalized phonon-like modes in DNA cyclization. United States. doi:10.1038/s41598-017-09537-y.
Alexandrov, Ludmil B., Rasmussen, Kim Ø., Bishop, Alan R., and Alexandrov, Boian S. Tue . "Evaluating the role of coherent delocalized phonon-like modes in DNA cyclization". United States. doi:10.1038/s41598-017-09537-y. https://www.osti.gov/servlets/purl/1412857.
@article{osti_1412857,
title = {Evaluating the role of coherent delocalized phonon-like modes in DNA cyclization},
author = {Alexandrov, Ludmil B. and Rasmussen, Kim Ø. and Bishop, Alan R. and Alexandrov, Boian S.},
abstractNote = {The innate flexibility of a DNA sequence is quantified by the Jacobson-Stockmayer’s J-factor, which measures the propensity for DNA loop formation. Recent studies of ultra-short DNA sequences revealed a discrepancy of up to six orders of magnitude between experimentally measured and theoretically predicted J-factors. These large differences suggest that, in addition to the elastic moduli of the double helix, other factors contribute to loop formation. We develop a new theoretical model that explores how coherent delocalized phonon-like modes in DNA provide single-stranded ”flexible hinges” to assist in loop formation. We also combine the Czapla-Swigon-Olson structural model of DNA with our extended Peyrard-Bishop-Dauxois model and, without changing any of the parameters of the two models, apply this new computational framework to 86 experimentally characterized DNA sequences. Our results demonstrate that the new computational framework can predict J-factors within an order of magnitude of experimental measurements for most ultra-short DNA sequences, while continuing to accurately describe the J-factors of longer sequences. Furthermore, we demonstrate that our computational framework can be used to describe the cyclization of DNA sequences that contain a base pair mismatch. Overall, our results support the conclusion that coherent delocalized phonon-like modes play an important role in DNA cyclization.},
doi = {10.1038/s41598-017-09537-y},
journal = {Scientific Reports},
number = 1,
volume = 7,
place = {United States},
year = {Tue Aug 29 00:00:00 EDT 2017},
month = {Tue Aug 29 00:00:00 EDT 2017}
}

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