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Related Experiment Videos

Electrostatic forces at helix-coil boundaries in DNA.

R D Blake1, S G Delcourt

  • 1Department of Biochemistry, University of Maine, Orono 04469.

Biopolymers
|February 5, 1990
PubMed
Summary

The melting temperature (Tm) of DNA (dA.dT)N loops decreases with smaller loop sizes, indicating less sodium ion (Na+) release. This finding quantifies electrostatic forces at DNA helix-coil boundaries.

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Area of Science:

  • Molecular Biology
  • Biophysics
  • Physical Chemistry

Background:

  • DNA's melting temperature (Tm) is influenced by salt concentration.
  • Internal loop-forming (dA.dT)N domains in DNA exhibit unique thermodynamic properties.

Purpose of the Study:

  • To investigate the effect of sodium ion (Na+) concentration on the Tm of (dA.dT)N DNA domains.
  • To quantify the relationship between DNA loop size and counterion release during helix-coil transitions.

Main Methods:

  • Measurement of Tm for (dA.dT)N domains across a tenfold range of [Na+].
  • Analysis of the slopes (SN = dTm/d log [Na+]) in relation to loop size (N).
  • Application of a simple model for electrostatic forces at helix-coil boundaries.

Main Results:

  • SN values decrease linearly with increasing N-1, correlating with reduced Na+ release from finite loops compared to infinite ones.
  • The difference in counterion binding at helix-coil boundaries is constant and independent of loop size (71 bp < N < 350 bp).
  • The region of higher charge density at boundaries extends 18-50 Å into the coil.

Conclusions:

  • Finite DNA loops release less counterion per phosphate residue than infinite loops.
  • Electrostatic interactions at helix-coil boundaries are quantifiable and influence DNA thermodynamics.
  • A derived free energy equation for counterion binding accurately predicts Tm values.

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