Rupture force between the third strand and the double strand within a triplex DNA

J Am Chem Soc. 2004 Nov 3;126(43):13992-7. doi: 10.1021/ja046341k.

Abstract

The rupture force to separate the third strand and the duplex within a triplex DNA was measured by means of atomic force spectroscopy. The tip and the sample surfaces were functionalized by oligodeoxyribonucleotides 5'-TTCTTCTTTCTTTTCCTTTTCTTTCTTCTTACTTCTCTCTCTC TCTCTCT-SH-3'. The sample surface was hybridized with 5'-AAGAAGAAAGAAAAGGAAAAGAAAGAAGAA-3' to form a double strand DNA on the surface prior to the force measurements. These sequences form triple helices with 30 base pairs under a pH of 5.8 and in the presence of 2.0 mM spermine. Signals of rupture of single and multiple triplex DNA were observed in the force distance curves. Rupture force histograms revealed a force of 42.6 +/- 1.9 pN from 24 independent measurements at a tip velocity of 400 nm/s to separate the third strand from duplex DNA. The velocity dependence of the rupture force quantum indicates a thermal dissociation process similar to that of rupturing a ds-DNA. The number of rupture events was controlled by adding oligonucleotides 5'-AAGAAGAAAGAAAAGGAAAAGAAAGAAGAA-3' either to reduce or to initiate triplex formation.

MeSH terms

  • Base Sequence
  • DNA / chemical synthesis
  • DNA / chemistry*
  • DNA, Single-Stranded / chemical synthesis
  • DNA, Single-Stranded / chemistry
  • Gold / chemistry
  • Microscopy, Atomic Force
  • Nucleic Acid Conformation
  • Oligonucleotides / chemical synthesis
  • Oligonucleotides / chemistry
  • Thermodynamics

Substances

  • DNA, Single-Stranded
  • Oligonucleotides
  • triplex DNA
  • Gold
  • DNA