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Computational Studies of the Mechanical Stability for Single-Strand Break DNA.

Accepted version
Peer-reviewed

Type

Article

Change log

Authors

Sieradzan, Adam K 

Abstract

The stability of DNA is crucial for the existence of most living organisms. Even a single DNA break can lead to serious problems, including cell death. In this work the position specificity of single strand breaks (SSB) and the stability of short DNA fragments of various lengths and sequence repetitions (d(AT)30, d(ATGC)15, d(GC)30, d(TTAGG)12, d(TTAGGG)10, and d(TTTAGGG)9 with SSBs and d(GC) with 2-60 repetitions without SSBs) were examined, by performing a series of steered molecular dynamics simulations using the coarse-grained NARES-2P force field. Our results show that the stability of DNA with a SSB strongly depends on the position of the break, and that the minimum length of DNA required for stability is sequence dependent. d(GC)30 with an SSB in position x was found to be less resistant to stretching than d(GC) x without SSB, where x is the number of d(GC) repetitions. DNA sequences with longer repeated fragments (such as telomeres) exhibit greater stability in the presence of breaks positioned at the beginning of the chain, which could constitute a cellular defense mechanism against DNA damage.

Description

Keywords

Biochemical Phenomena, DNA, DNA Breaks, Single-Stranded, Hydrogen Bonding, Mechanical Phenomena, Molecular Dynamics Simulation, Molecular Structure

Journal Title

J Phys Chem B

Conference Name

Journal ISSN

1520-6106
1520-5207

Volume Title

122

Publisher

American Chemical Society (ACS)
Sponsorship
Engineering and Physical Sciences Research Council (EP/N035003/1)