The mechanism of the emergence of distinct overstretched DNA states

The Journal of Chemical Physics
You-Liang ZhuZhao-Yan Sun

Abstract

Although multiple overstretched DNA states were identified in experiments, the mechanism of the emergence of distinct states is still unclear. Molecular dynamics simulation is an ideal tool to clarify the mechanism, but the force loading rates in stretching achieved by conventional all-atom DNA models are much faster, which essentially affect overstretching states. We employed a modified coarse-grained DNA model with an unprecedented low loading rate in simulations to study the overstretching transitions of end-opened double-stranded DNA. We observed two-strand peeling off for DNA with low stability and the S-DNA with high stability under tension. By introducing a melting-forbidden model which prevents base-pair breaking, we still observed the overstretching transition induced by the formation of S-DNA due to the change of dihedral angle. Hence, we confirmed that the competition between the two strain-softening manners, i.e., base-pair breaking and dihedral angle variation, results in the emergence of distinct overstretched DNA states.

References

Feb 9, 1996·Science·P CluzelF Caron
Jun 10, 1997·Proceedings of the National Academy of Sciences of the United States of America·C G BaumannC Bustamante
Apr 14, 1999·Nature Structural Biology·M RiefH E Gaub
Mar 29, 2000·Biophysical Journal·H Clausen-SchaumannH E Gaub
Feb 13, 2001·Biophysical Journal·I Rouzina, V A Bloomfield
Feb 13, 2001·Biophysical Journal·I Rouzina, V A Bloomfield
Jun 8, 2002·Journal of Molecular Biology·Nilesh K Banavali, Alexander D MacKerell
Aug 25, 2004·Physical Review. E, Statistical, Nonlinear, and Soft Matter Physics·Simona CoccoJohn F Marko
Mar 9, 2007·The Journal of Chemical Physics·Thomas A KnottsJuan J de Pablo
Oct 15, 2008·Physical Review Letters·Binquan Luan, Aleksei Aksimentiev
Mar 4, 2009·Biophysical Journal·E J SambriskiJ J de Pablo
Oct 21, 2009·Proceedings of the National Academy of Sciences of the United States of America·Joost van MamerenErwin J G Peterman
Oct 23, 2009·Proceedings of the National Academy of Sciences of the United States of America·Mark C WilliamsMicah J McCauley
May 4, 2010·Nucleic Acids Research·Hongxia FuJie Yan
Jan 7, 2011·Journal of the American Chemical Society·D Hern Paik, Thomas T Perkins
May 24, 2011·The Journal of Physical Chemistry. a·Alexander BalaeffDavid N Beratan
Nov 25, 2009·Journal of Physics. Condensed Matter : an Institute of Physics Journal·Szymon Niewieczerzał, Marek Cieplak
Sep 8, 2011·The Journal of Physical Chemistry. a·Mario WolterTomáš Kubař
Apr 26, 2012·Proceedings of the National Academy of Sciences of the United States of America·Xinghua ZhangJie Yan
Sep 6, 2012·Proceedings of the National Academy of Sciences of the United States of America·Niklas BosaeusBengt Nordén
Sep 18, 2012·The Journal of Chemical Physics·Chia Wei HsuEfthimios Kaxiras
Feb 23, 2013·Proceedings of the National Academy of Sciences of the United States of America·Xinghua ZhangJie Yan
Feb 23, 2013·Proceedings of the National Academy of Sciences of the United States of America·Graeme A KingErwin J G Peterman
Mar 8, 2013·The Journal of Chemical Physics·Flavio RomanoArd A Louis
Oct 19, 2013·Journal of Computational Chemistry·You-Liang ZhuZhong-Yuan Lu
Oct 23, 2014·Journal of the American Chemical Society·Xinghua ZhangJie Yan
Dec 4, 2014·The Journal of Physical Chemistry. B·Matúš RebičJozef Uličný

❮ Previous
Next ❯

Citations

Jan 14, 2020·Nucleic Acids Research·Jack W ShepherdMark C Leake
May 6, 2020·Journal of the American Chemical Society·Fengqin LiXiaolei Zuo

❮ Previous
Next ❯

Related Concepts

Trending Feeds

COVID-19

Coronaviruses encompass a large family of viruses that cause the common cold as well as more serious diseases, such as the ongoing outbreak of coronavirus disease 2019 (COVID-19; formally known as 2019-nCoV). Coronaviruses can spread from animals to humans; symptoms include fever, cough, shortness of breath, and breathing difficulties; in more severe cases, infection can lead to death. This feed covers recent research on COVID-19.

Blastomycosis

Blastomycosis fungal infections spread through inhaling Blastomyces dermatitidis spores. Discover the latest research on blastomycosis fungal infections here.

Nuclear Pore Complex in ALS/FTD

Alterations in nucleocytoplasmic transport, controlled by the nuclear pore complex, may be involved in the pathomechanism underlying multiple neurodegenerative diseases including Amyotrophic Lateral Sclerosis and Frontotemporal Dementia. Here is the latest research on the nuclear pore complex in ALS and FTD.

Applications of Molecular Barcoding

The concept of molecular barcoding is that each original DNA or RNA molecule is attached to a unique sequence barcode. Sequence reads having different barcodes represent different original molecules, while sequence reads having the same barcode are results of PCR duplication from one original molecule. Discover the latest research on molecular barcoding here.

Chronic Fatigue Syndrome

Chronic fatigue syndrome is a disease characterized by unexplained disabling fatigue; the pathology of which is incompletely understood. Discover the latest research on chronic fatigue syndrome here.

Evolution of Pluripotency

Pluripotency refers to the ability of a cell to develop into three primary germ cell layers of the embryo. This feed focuses on the mechanisms that underlie the evolution of pluripotency. Here is the latest research.

Position Effect Variegation

Position Effect Variagation occurs when a gene is inactivated due to its positioning near heterochromatic regions within a chromosome. Discover the latest research on Position Effect Variagation here.

STING Receptor Agonists

Stimulator of IFN genes (STING) are a group of transmembrane proteins that are involved in the induction of type I interferon that is important in the innate immune response. The stimulation of STING has been an active area of research in the treatment of cancer and infectious diseases. Here is the latest research on STING receptor agonists.

Microbicide

Microbicides are products that can be applied to vaginal or rectal mucosal surfaces with the goal of preventing, or at least significantly reducing, the transmission of sexually transmitted infections. Here is the latest research on microbicides.

Related Papers

Journal of the American Chemical Society
Xinghua ZhangJie Yan
Proceedings of the National Academy of Sciences of the United States of America
Xinghua ZhangJie Yan
Proceedings of the National Academy of Sciences of the United States of America
Mark C WilliamsMicah J McCauley
© 2022 Meta ULC. All rights reserved