QCM-based rupture force measurement as a tool to study DNA dehybridization and duplex stability

Fedor N. Dultsev, Eugeny A. Kolosovsky, Alexander A. Lomzov, Dmitrii V. Pyshnyi

Research output: Contribution to journalArticlepeer-review

6 Citations (Scopus)

Abstract

The stability of double-stranded DNA (dsDNA) was assessed on the basis of unwinding force measurement. Unwinding force was measured directly with a quartz crystal microbalance (QCM). The amplitude of its surface oscillations was controlled by supplying variable alternate voltage. Under smoothly increasing amplitude of QCM surface oscillations, dsDNA fixed on QCM surface through one of its ends got unwound. This procedure allows reliable measurement of rupture force as small as 5-10 pN. It was demonstrated that oscillations of the surface, with dsDNA bound through one of its ends to this surface, at a frequency of 14 MHz, cause helix unwinding to form two complementary parts due to viscous forces of the liquid medium. Unwinding starts at the upper end. This was proven using oligonucleotide duplexes containing mismatches in different positions. For duplexes containing complementary 20 base pairs, the helix unwinding force is equal to 30-40 pN, which is in agreement with the data obtained by means of atomic-force microscopy (AFM) for the case of unzipping mode.

Original languageEnglish
Pages (from-to)891-901
Number of pages11
JournalAnalytical and Bioanalytical Chemistry
Volume409
Issue number4
DOIs
Publication statusPublished - 1 Jan 2017

Keywords

  • Bond rupture
  • DNA duplex
  • QCM
  • MECHANICAL STABILITY
  • SINGLE
  • SPECTROSCOPY
  • SURFACE
  • HYBRIDIZATION
  • MELTING TEMPERATURES
  • OLIGOMERS
  • MOLECULES
  • Viscosity
  • Nucleic Acid Denaturation
  • Nucleic Acid Hybridization
  • Quartz Crystal Microbalance Techniques/methods
  • DNA/chemistry
  • Base Sequence

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