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dc.contributor.authorNordenskiöld, Larsen
dc.contributor.authorZhou, Ruhongen
dc.contributor.authorMu, Yuguangen
dc.contributor.authorLi, Weifengen
dc.identifier.citationLi, W., Nordenskiöld, L., Zhou, R., & Mu, Y. (2014). Conformation-dependent DNA attraction. Nanoscale, 6(12), 7085-7092.en
dc.description.abstractUnderstanding how DNA molecules interact with other biomolecules is related to how they utilize their functions and is therefore critical for understanding their structure-function relationships. For a long time, the existence of Z-form DNA (a left-handed double helical version of DNA, instead of the common right-handed B-form) has puzzled the scientists, and the definitive biological significance of Z-DNA has not yet been clarified. In this study, the effects of DNA conformation in DNA-DNA interactions are explored by molecular dynamics simulations. Using umbrella sampling, we find that for both B- and Z-form DNA, surrounding Mg(2+) ions always exert themselves to screen the Coulomb repulsion between DNA phosphates, resulting in very weak attractive force. On the contrary, a tight and stable bound state is discovered for Z-DNA in the presence of Mg(2+) or Na(+), benefiting from their hydrophobic nature. Based on the contact surface and a dewetting process analysis, a two-stage binding process of Z-DNA is outlined: two Z-DNA first attract each other through charge screening and Mg(2+) bridges to phosphate groups in the same way as that of B-DNA, after which hydrophobic contacts of the deoxyribose groups are formed via a dewetting effect, resulting in stable attraction between two Z-DNA molecules. The highlighted hydrophobic nature of Z-DNA interaction from the current study may help to understand the biological functions of Z-DNA in gene transcription.en
dc.format.extent9 p.en
dc.rights© 2014 The Royal Society of Chemistry. This is the author created version of a work that has been peer reviewed and accepted for publication by Nanoscale, The Royal Society of Chemistry. It incorporates referee’s comments but changes resulting from the publishing process, such as copyediting, structural formatting, may not be reflected in this document. The published version is available at: [Article DOI:].en
dc.subjectDRNTU::Science::Biological sciencesen
dc.titleConformation-dependent DNA attractionen
dc.typeJournal Articleen
dc.contributor.schoolSchool of Biological Sciencesen
dc.description.versionAccepted versionen
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