Temperature and salt dependence of the gel migration anomaly of curved DNA fragments

A series of oligonucleotides of different sequences have been cloned to study DNA curvature. Several DNA fragments containing these oligonucleotides in various numbers of repeats were analyzed in 10% polyacrylamide gels. A strong gel migration anomaly was found for dA4 sequences; a comparably very small but clearly detectable anomaly was observed for dA3 (both in a repeat length of 10 base-pairs). The temperature and salt (NaCl, MgCl2) dependence of the gel migration anomaly of these DNA fragments was measured. While a similar behaviour of all sequences is observed for the addition of NaCl, the temperature and MgCl2 dependence of the anomaly varies with the oligonucleotide sequence. These data are interpreted in terms of local DNA structure changes induced by changes in the temperature and the MgCl2 concentration which affect the planarity of the curved DNA fragments.