DNase I susceptibility of bent DNA and its alteration by ditercalinium and distamycin

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Abstract
The bending of kinetoplast DNA from Crithidia fasciculata is thought to be related to the periodic distribution of AA or TT cluster sequences. The sensitivity to DNase I of the two strands of this DNA was analyzed at nucleotide resolution by sequencing gel electrophoresis. The effect on the DNase I cleavage pattern of two drugs, ditercalinium and distamycin, that are able to remove bending was analyzed. The same analysis was done on a pBR 322 DNA fragment of random sequence as a control. The periodic distribution of the AA or TT clusters in the bent DNA fragment was first analyzed by computing the autocorrelation function of the AA or TT clusters in the bent DNA fragment. It is shown that the AT tracts are on average 10.5 base pairs apart. This value is almost identical with that of the B-DNA helix pitch in solution [10.5 (Wang, 1979); 10.6 .+-. 0.1 (Rhodes and Klug, 1980)]. To reveal the periodic pattern of DNase I cleavage on this bent DNA, alone or in presence of drugs, the cross correlation between the different bands obtained from DNAse I cleavage and the presence of AA to TT sequences was computed. This shows that GC and mixed sequences are the most sensitive regions. These data also suggest that there is a periodic fluctuation in the width of the minor groove in the bent fragment. Ditercalinium and distamycin alter the DNase I cutting pattern of the bent DNA fragment but in an inverse fashion. Distamycin protects the AT tract from DNase I attack and enhances DNase I sensitivity of GC and mixed-sequence regions, whereas ditercalinium protects GC and mixed-sequence regions and enhances AT tract DNase I sensitivity. The behavior of the two strands is strikingly asymmetrical in the presence of ditercalinium. At several sequences DNase I sensitivity of the A-rich strand is strongly enhanced, whereas DNase I sensitivity of the corresponding sequence on the T-rich strand is completely protected.