DNA A-tracts are not curved in solutions containing high concentrations of monovalent cations

Earle Stellwagen, Justin P. Peters, L James Maher III, Nancy C. Stellwagen

Research output: Contribution to journalArticle

8 Citations (Scopus)

Abstract

The intrinsic curvature of seven 98 bp DNA molecules containing up to four centrally located A6-tracts has been measured by gel and capillary electrophoresis as a function of the number and arrangement of the A-tracts. At low cation concentrations, the electrophoretic mobility observed in polyacrylamide gels and in free solution decreases progressively with the increasing number of phased A-tracts, as expected for DNA molecules with increasingly curved backbone structures. Anomalously slow electrophoretic mobilities are also observed for DNA molecules containing two pairs of phased A-tracts that are out of phase with each other, suggesting that out-of-phase distortions of the helix backbone do not cancel each other out. The mobility decreases observed for the A-tract samples are due to curvature, not cation binding in the A-tract minor groove, because identical free solution mobilities are observed for a molecule with four out-of-phase A-tracts and one with no A-tracts. Surprisingly, the curvature of DNA A-tracts is gradually lost when the monovalent cation concentration is increased to ∼200 mM, regardless of whether the cation is a hydrophilic ion like Na+, NH4 +, or Tris+ or a hydrophobic ion like tetrabutylammonium. The decrease in A-tract curvature with increasing ionic strength, along with the known decrease in A-tract curvature with increasing temperature, suggests that DNA A-tracts are not significantly curved under physiological conditions.

Original languageEnglish (US)
Pages (from-to)4138-4148
Number of pages11
JournalBiochemistry
Volume52
Issue number24
DOIs
StatePublished - Jun 18 2013

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Monovalent Cations
DNA
Cations
Electrophoretic mobility
Molecules
Ions
Capillary electrophoresis
Capillary Electrophoresis
Ionic strength
Osmolar Concentration
Gels
Temperature

ASJC Scopus subject areas

  • Biochemistry

Cite this

DNA A-tracts are not curved in solutions containing high concentrations of monovalent cations. / Stellwagen, Earle; Peters, Justin P.; Maher III, L James; Stellwagen, Nancy C.

In: Biochemistry, Vol. 52, No. 24, 18.06.2013, p. 4138-4148.

Research output: Contribution to journalArticle

Stellwagen, Earle ; Peters, Justin P. ; Maher III, L James ; Stellwagen, Nancy C. / DNA A-tracts are not curved in solutions containing high concentrations of monovalent cations. In: Biochemistry. 2013 ; Vol. 52, No. 24. pp. 4138-4148.
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