Comparison of the electrophoretic and hydrodynamic properties of DNA and RNA oligonucleotide duplexes

Gordon F. Bonifacio, Tom Brown, Graeme L. Conn, Andrew N. Lane

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56 Scopus citations

Abstract

The electrophoretic behavior of defined DNA and RNA oligonucleotide duplexes from 10 to 20 bp in length has been investigated as a function of salt conditions, gel concentration, and temperature. The RNA oligomers migrated much more slowly than the DNA oligomers of the same sequence under all conditions. From sedimentation equilibrium and velocity measurements, the apparent partial specific volume in 0.1 M KCl, 20 mM NaP1, pH 7, was determined as 0.56 ± 0.015 ml g-1 for DNA and 0.508 ml g-1 for RNA. The translational friction coefficients were determined and compared with the values calculated for cylinders. Taking into account the shape factors, the solution density, and partial specific volumes, the effective degree of hydration was estimated as 0.8-1 g g-1 DNA. There was no significant difference in the frictional coefficients of the DNA and RNA oligomers, indicating that the effective sizes of DNA and RNA are very similar in solution. The differential electrophoretic mobility of DNA and RNA must arise from the differences in interaction with counterions, which is probably a global property of the oligonucleotides.

Original languageEnglish
Pages (from-to)1532-1538
Number of pages7
JournalBiophysical Journal
Volume73
Issue number3
DOIs
StatePublished - Sep 1997

Bibliographical note

Funding Information:
We thank Dr. T. A. Frenkiel for help with the NMR diffusion measure-ments. This work was supported by the Medical Research Council and a Royal Society of Edinburgh Caledonian Research Fellowship to GLC.

ASJC Scopus subject areas

  • Biophysics

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