Please use this identifier to cite or link to this item:
Title: Conformation-dependent DNA attraction
Authors: Nordenskiöld, Lars
Zhou, Ruhong
Mu, Yuguang
Li, Weifeng
Keywords: DRNTU::Science::Biological sciences
Issue Date: 2014
Source: Li, W., Nordenskiöld, L., Zhou, R., & Mu, Y. (2014). Conformation-dependent DNA attraction. Nanoscale, 6(12), 7085-7092.
Series/Report no.: Nanoscale
Abstract: Understanding 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.
DOI: 10.1039/c3nr03235c
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:].
Fulltext Permission: open
Fulltext Availability: With Fulltext
Appears in Collections:SBS Journal Articles

Files in This Item:
File Description SizeFormat 
Conformation dependent DNA attraction.pdf3.09 MBAdobe PDFThumbnail

Citations 20

Updated on Jul 24, 2020

Citations 20

Updated on Mar 4, 2021

Page view(s) 50

Updated on May 10, 2021

Download(s) 20

Updated on May 10, 2021

Google ScholarTM




Items in DR-NTU are protected by copyright, with all rights reserved, unless otherwise indicated.