A study of DNA tethered to a surface by an all-atom molecular dynamics simulation

Ka Yiu Wong, Bernard Pettitt

Research output: Contribution to journalArticle

42 Citations (Scopus)

Abstract

In order to understand the structure of DNAs and their interactions when on microarray surfaces, we performed the first all-atom molecular dynamics simulation of DNA tethered to a surface. On the surface, the binding of the DNA was enhanced, and its average equilibrium conformation was the B form. The DNA duplex spontaneously tilted towards its nearest neighbor and settled in a leaning position with a interaxial distance of 2.2 nm. This close packing of the DNAs, which affects both in situ synthesis and deposition of probes on microarray surfaces, can thus be explained by salted-induced colloidlike DNA-DNA attractions.

Original languageEnglish (US)
Pages (from-to)233-235
Number of pages3
JournalTheoretical Chemistry Accounts
Volume106
Issue number3
DOIs
StatePublished - Jul 2001
Externally publishedYes

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Molecular dynamics
deoxyribonucleic acid
molecular dynamics
Atoms
DNA
Computer simulation
atoms
simulation
Microarrays
attraction
Conformations
probes
synthesis
interactions

ASJC Scopus subject areas

  • Physical and Theoretical Chemistry

Cite this

A study of DNA tethered to a surface by an all-atom molecular dynamics simulation. / Wong, Ka Yiu; Pettitt, Bernard.

In: Theoretical Chemistry Accounts, Vol. 106, No. 3, 07.2001, p. 233-235.

Research output: Contribution to journalArticle

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