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

Ka Yiu Wong, Arnold Vainrub, Tom Powdrill, Michael Hogan, B. Montgomery Pettitt

Research output: Contribution to journalArticlepeer-review

12 Scopus citations


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
Issue number2-3
StatePublished - Feb 15 2004
Externally publishedYes


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

ASJC Scopus subject areas

  • General Chemistry
  • Information Systems
  • Modeling and Simulation
  • General Chemical Engineering
  • General Materials Science
  • Condensed Matter Physics


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