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Chain length and oligonucleotide stability at high pressure

R B Macgregor1

  • 1Faculty of Pharmacy, University of Toronto, Ontario, Canada.

Biopolymers
|March 1, 1996
PubMed
Summary

Hydrostatic pressure increases DNA helix-coil transition temperature (Tm), but this effect weakens with shorter DNA oligomers. Terminal base pairs may cause a negative volume change, influencing pressure sensitivity.

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Area of Science:

  • Biophysics
  • Molecular Biology
  • Thermodynamics

Background:

  • DNA duplex stability is crucial for biological processes.
  • Hydrostatic pressure is known to influence DNA conformational transitions.
  • Previous studies have examined pressure effects on DNA polymers.

Purpose of the Study:

  • To investigate the effect of hydrostatic pressure on the helix-coil transition temperature (Tm) of DNA oligomers ((dA)n(dT)n).
  • To analyze how chain length affects the pressure dependence of Tm and thermodynamic parameters.
  • To elucidate the role of terminal base pairs in pressure-induced DNA transitions.

Main Methods:

  • Synthesized and characterized DNA oligomers ((dA)n(dT)n) for n = 11, 15, 19.
  • Measured helix-coil transition temperature (Tm) under varying hydrostatic pressures in 50 mM NaCl.
  • Analyzed van't Hoff enthalpy (DeltaHvH) from the transition half-width.
  • Compared oligomer data with existing polymer data.

Main Results:

  • Increasing hydrostatic pressure increased Tm for all DNA oligomers.
  • The pressure effect on Tm diminished with decreasing DNA chain length.
  • The van't Hoff enthalpy (DeltaHvH) decreased with shorter chains.
  • Shorter oligomers showed a small, negative pressure dependence for DeltaHvH, unlike the polymer.

Conclusions:

  • Terminal base pairs likely contribute a negative volume change to the helix-coil transition, explaining the chain-length dependence of pressure effects.
  • Internal base pairs behave similarly to polymer DNA, exhibiting a positive volume change.
  • Imperfect water interactions at terminal base pairs may drive the observed pressure-induced dissociation.

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