Molecular dynamics simulations of end-tethered single-stranded DNA probes on a silica surface.

Content Provider	Semantic Scholar
Author	Wang, Zunliang Zeng, Xin Deng, Yan He, Nongyue Wang, Qiong Huang, Jianguo
Copyright Year	2011
Abstract	The structure of DNA molecules tethered to surfaces may significantly affect the efficiency of hybridization on the DNA microarray. Understanding the structure of single-stranded DNA (ssDNA) tethered to surfaces is critical for applying the molecular recognition function of DNA microarrays. Although a number of experimental methods have been applied to determine the structure of the DNA probe on surfaces, they can not provide enough information on the dynamical behavior of the ssDNAs on surfaces. Herein, we investigated the dynamics and interaction of seven DNA probes tethered on a silica surface by a molecular dynamics simulation. From the simulation results, we examined the structure and dynamics of the ssDNAs, by calculating the root-mean-square derivations, the tilt angles, the radius of gyration, and the distances of the neighboring ssDNAs. The data obtained from our simulation suggests the packing density has a significant effect on the overall structure and molecular orientation change of surface-tethered ssDNAs, which is complementary to the recent experimental reports. Our simulation provided a structural insight, which is helpful to better understand the behavior of ssDNA on surfaces and optimize the design of DNA microarray.
File Format	PDF HTM / HTML
Alternate Webpage(s)	http://or.nsfc.gov.cn/bitstream/00001903-5/92983/1/1000004535990.pdf
PubMed reference number	22400209v1
Volume Number	11
Issue Number	10
Journal	Journal of nanoscience and nanotechnology
Language	English
Access Restriction	Open
Subject Keyword	DNA Breaks, Single-Stranded DNA Microarray format DNA Probes DNA, Single-Stranded Distance Heparin, Low-Molecular-Weight Molecular Dynamics Nucleic Acid Hybridization Silicon Dioxide
Content Type	Text
Resource Type	Article