Computational Studies of the Mechanical Stability for Single-Strand Break DNA.
The journal of physical chemistry. B
American Chemical Society
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Krupa, P., Wales, D., & Sieradzan, A. K. (2018). Computational Studies of the Mechanical Stability for Single-Strand Break DNA.. The journal of physical chemistry. B, 122 (34), 8166-8173. https://doi.org/10.1021/acs.jpcb.8b05417
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.
DNA, Biochemical Phenomena, Molecular Structure, Hydrogen Bonding, DNA Breaks, Single-Stranded, Mechanical Phenomena, Molecular Dynamics Simulation
External DOI: https://doi.org/10.1021/acs.jpcb.8b05417
This record's URL: https://www.repository.cam.ac.uk/handle/1810/288551