Orientation of DNA on a Surface from Simulation

Ka Yiu Wong, Bernard Pettitt

Research output: Contribution to journalArticle

54 Citations (Scopus)

Abstract

DNA orientation near surfaces determines many properties related to hybridization efficiency. We performed a 40-ns molecular dynamics simulation to study the structure and orientation of a 12-base-pair DNA duplex tethered to a neutral, epoxide-coated silica surface. Starting with a canonical B-form tethered in an up-right position, normal to the surface, the DNA tilted to over 55° and back. The time scale was a few nanoseconds for tilting events. The linker between the DNA and the surface went from standing upright to tilted, and finally collapsed on the surface. Although the DNA conformation fluctuated, it remained closed to B-form for the entire 40 ns. Calculations of helical parameters of the DNA show that the tethered end of the DNA changed its conformation noticeably when attracted to the surface.

Original languageEnglish (US)
Pages (from-to)570-578
Number of pages9
JournalBiopolymers
Volume73
Issue number5
DOIs
StatePublished - Apr 5 2004
Externally publishedYes

Fingerprint

DNA
Conformations
Nucleic Acid Conformation
Epoxy Compounds
Molecular Dynamics Simulation
Base Pairing
Silicon Dioxide
Molecular dynamics
Silica
Computer simulation

Keywords

  • DNA chip
  • DNA orientation
  • Hybridization
  • Molecular dynamics

ASJC Scopus subject areas

  • Biochemistry, Genetics and Molecular Biology(all)
  • Biochemistry
  • Biophysics

Cite this

Orientation of DNA on a Surface from Simulation. / Wong, Ka Yiu; Pettitt, Bernard.

In: Biopolymers, Vol. 73, No. 5, 05.04.2004, p. 570-578.

Research output: Contribution to journalArticle

Wong, Ka Yiu ; Pettitt, Bernard. / Orientation of DNA on a Surface from Simulation. In: Biopolymers. 2004 ; Vol. 73, No. 5. pp. 570-578.
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