Immobilization of nucleic acids at solid surfaces: effect of oligonucleotide length on layer assembly

Biophys J. 2000 Aug;79(2):975-81. doi: 10.1016/S0006-3495(00)76351-X.

Abstract

This report investigates the effect of DNA length and the presence of an anchoring group on the assembly of presynthesized oligonucleotides at a gold surface. The work seeks to advance fundamental insight into issues that impact the structure and behavior of surface-immobilized DNA layers, as in, for instance, DNA microarray and biosensor devices. The present study contrasts immobilization of single-stranded DNA (ssDNA) containing a terminal, 5' hexanethiol anchoring group with that of unfunctionalized oligonucleotides for lengths from 8 to 48 bases. Qualitatively, the results indicate that the thiol anchoring group strongly enhances oligonucleotide immobilization, but that the enhancement is reduced for longer strand lengths. Interestingly, examination of the probe coverage as a function of strand length suggests that adsorbed thiol-ssDNA oligonucleotides shorter than 24 bases tend to organize in end-tethered, highly extended configurations for which the long-term surface coverage is largely independent of oligonucleotide length. For strands longer than 24 bases, the surface coverage begins to decrease notably with probe length. The decrease is consistent with a less ordered arrangement of the DNA chains, presumably reflecting increasingly polymeric behavior.

Publication types

  • Research Support, U.S. Gov't, Non-P.H.S.

MeSH terms

  • Base Sequence
  • DNA / chemistry*
  • DNA, Single-Stranded / chemistry*
  • Gold
  • Models, Molecular
  • Nucleic Acid Conformation
  • Oligodeoxyribonucleotides / chemistry*
  • Structure-Activity Relationship
  • Surface Properties
  • Thionucleotides

Substances

  • DNA, Single-Stranded
  • Oligodeoxyribonucleotides
  • Thionucleotides
  • Gold
  • DNA