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Determination of the Effective Charge of DNA Fragments Containing Variable Numbers of Α-Tracts

Nancy C. Stellwagen, University of Iowa, 51 Newton Road, Iowa City, IA 52242 and Yongjun Lu, Internal Medicine, University of Iowa, 51 Newton Road, Iowa City, IA 52242.

A 199-bp DNA restriction fragment obtained from simian virus 40 (SV40) is intrinsically curved because it contains 5 closely spaced A-tracts, runs of 4-6 contiguous adenine or thymine residues, in the center of the fragment. Thirty derivatives were prepared, in which each of the A-tracts was mutated to another sequence and characterized by capillary electrophoresis (CE) and transient electric birefringence (TEB). The rotational relaxation times obtained from the TEB measurements were used to calculate the translational diffusion coefficients of each oligomer, using equations given in the literature. The translational friction coefficients, combined with the free solution mobilities, were then used to estimate the effective charge of each oligomer from the Nernst-Einstein equation. The effective charge of each oligomer depends on the number of A-tracts in the curvature module, suggesting that A-tracts preferentially bind monovalent counterions, reducing their effective net charge. On average, the effective charge of each DNA fragment is reduced by approximately one-half charge unit per A-tract.