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DNA End-to-End Distance Change Due to Divalent Counterion Condensation Studffid by Pulse Gel Electrophoresis

Published online by Cambridge University Press:  10 February 2011

Anzhi Z. Li ,
Haiyan Huang  and
Kenneth A. Marx
Anzhi Z. Li
Affiliation:
Department of Chemistry, University of Massachusetts Lowell, Lowell, MA 01854
Haiyan Huang
Affiliation:
Department of Chemistry, University of Massachusetts Lowell, Lowell, MA 01854
Kenneth A. Marx*
Affiliation:
Department of Chemistry, University of Massachusetts Lowell, Lowell, MA 01854
*
Author for correspondence
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Abstract

The conformation change of DNA fragments due to divalent counterion condensation onto DNA was investigated by pulse gel electrophoresis, and interpreted by gel models (Reptation and Henry model) and Manning's counterion condensation theory. The measured mobility reductions μ/μ0 of λ-DNA-Hind III fragments, ranging from 23.13 to 2.027 kilobase pairs, due to interaction with divalent cation Mg2+ (1–400 μμ), and Ca2+(0–40 μM) in tris-borate buffer were well fit by Manning's Counterion Condensation (CC) theory. We observed the normalized mobility reduction to be shifted by a small amount Δ(μ/μ0) relative to the CC prediction value. Δ(μ/μ0) is a function of DNA length, and the ion environment (divalent concentration C2 and ionic strength). The ‘shift’ phenomena only occurred close to where C2 began dominating the counterion binding, a condition described by the monovalent/divalent cation isocompetition point. Combining our observation with theoretical considerations, we conclude that the divalent counterion condensation changes the DNA fragments' conformation, resulting in an end-to-end distance decrease which is molecular weight dependent. The effect was enhanced by an increase of divalent ion concentration and a decrease of the ionic strength.

Type
Research Article
Information
MRS Online Proceedings Library (OPL) , Volume 463: Symposia EE – Statistical Mechanics in Physics and Biology , 1996 , 67
Copyright
Copyright © Materials Research Society 1997

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References

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