A non-Watson-Crick motif of base-pairing on surfaces for untethered oligonucleotides

Ka Yiu Wong, Arnold Vainrub, Tom Powdrill, Michael Hogan, Bernard Pettitt

Research output: Contribution to journalArticle

11 Citations (Scopus)

Abstract

A structural view of DNA association/hybridization to a target oligonucleotide molecule near a surface has been developed. Recent experiments have showed a kinetically rapid hybridization between large target DNA fragments and oligonucleotides electrostatically immobilized (untethered) to a surface. Theory and computer simulations have been used to investigate the nature of the specificity and affinity in such a system. Simulations were performed for a modified silicon dioxide surface with positively charged groups at neutral pH. The dosing of a surface with unattached oligonucleotide was simulated. The oligonucleotide was found to associate with the surface in salt water in a way that some of the bases remained stacked, and most of the bases near the surface on average pointed preferentially toward the solution, away from the surface. Use of an analytic solution to the linear Poisson-Boltzmann (PB) theory of the electric double layer interaction between DNA and a hard surface predicts tight binding in this system. The simulation thus gives a mechanism for specificity and the theory a mechanism for affinity. The geometry is such that only non-helical base pairs would be accommodated with an irregular backbone.

Original languageEnglish (US)
Pages (from-to)121-129
Number of pages9
JournalMolecular Simulation
Volume30
Issue number2-3
DOIs
StatePublished - Feb 15 2004
Externally publishedYes

Fingerprint

oligonucleotides
Oligonucleotides
Pairing
DNA
deoxyribonucleic acid
Specificity
Affine transformation
affinity
Immobilized Nucleic Acids
Target
Tight-binding
simulation
Saline water
Backbone
Ludwig Boltzmann
Analytic Solution
Salt
Silicon Dioxide
Irregular
Siméon Denis Poisson

Keywords

  • Non-Watson-Crick motif
  • Oligonucleotide
  • Poisson-Boltzmann theory
  • Thermodynamics

ASJC Scopus subject areas

  • Atomic and Molecular Physics, and Optics

Cite this

A non-Watson-Crick motif of base-pairing on surfaces for untethered oligonucleotides. / Wong, Ka Yiu; Vainrub, Arnold; Powdrill, Tom; Hogan, Michael; Pettitt, Bernard.

In: Molecular Simulation, Vol. 30, No. 2-3, 15.02.2004, p. 121-129.

Research output: Contribution to journalArticle

Wong, Ka Yiu ; Vainrub, Arnold ; Powdrill, Tom ; Hogan, Michael ; Pettitt, Bernard. / A non-Watson-Crick motif of base-pairing on surfaces for untethered oligonucleotides. In: Molecular Simulation. 2004 ; Vol. 30, No. 2-3. pp. 121-129.
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