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dc.contributor.authorKrupa, Pawełen
dc.contributor.authorWales, Daviden
dc.contributor.authorSieradzan, Adam Ken
dc.date.accessioned2019-01-30T11:19:44Z
dc.date.available2019-01-30T11:19:44Z
dc.date.issued2018-08-16en
dc.identifier.issn1520-6106
dc.identifier.urihttps://www.repository.cam.ac.uk/handle/1810/288551
dc.description.abstractThe 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.
dc.format.mediumPrint-Electronicen
dc.languageengen
dc.publisherAmerican Chemical Society
dc.subjectDNAen
dc.subjectBiochemical Phenomenaen
dc.subjectMolecular Structureen
dc.subjectHydrogen Bondingen
dc.subjectDNA Breaks, Single-Strandeden
dc.subjectMechanical Phenomenaen
dc.subjectMolecular Dynamics Simulationen
dc.titleComputational Studies of the Mechanical Stability for Single-Strand Break DNA.en
dc.typeArticle
prism.endingPage8173
prism.issueIdentifier34en
prism.publicationDate2018en
prism.publicationNameThe journal of physical chemistry. Ben
prism.startingPage8166
prism.volume122en
dc.identifier.doi10.17863/CAM.35836
dcterms.dateAccepted2018-08-06en
rioxxterms.versionofrecord10.1021/acs.jpcb.8b05417en
rioxxterms.versionAM*
rioxxterms.licenseref.urihttp://www.rioxx.net/licenses/all-rights-reserveden
rioxxterms.licenseref.startdate2018-08-16en
dc.contributor.orcidKrupa, Paweł [0000-0002-9710-7837]
dc.contributor.orcidWales, David [0000-0002-3555-6645]
dc.identifier.eissn1520-5207
rioxxterms.typeJournal Article/Reviewen
pubs.funder-project-idEPSRC (EP/N035003/1)
rioxxterms.freetoread.startdate2019-08-06


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