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Nucleic Acids Research, 1990, Vol. 18, No. 13 3847-3851
© 1990

MOLECULAR BIOLOGY

DNA Conformational analysis in solution by uranyl mediated photocleavage

Peter E. Nielsen, Niels Erik Møllegaard and Claus Jeppesen

Research Center for Medical Biotechnology, Department of Biochemistry B, The Panum Institute, University of Copenhagen Blegdamsvej 3c, DK-2200 Copenhagen N, Denmark

Received March 29, 1990. Revised May 30, 1990. Accepted May 30, 1990.

Uranyl mediated photocleavage of double stranded DNA is proposed as a general probing for DNA helix conformation in terms of minor groove width/electronegative potential. Specifically, it is found that A/T-tracts known to constitute strong distamycin binding sites are preferentially photocleaved by uranyl in a way indicating strongest uranyl binding at the center of the minor groove of the AT-region. The A-tracts of kinetoplast DNA show the highest reactivity at the 3'-end of the tract— as opposed to cleavage by EDTA/Fell—in accordance with the minor groove being more narrow at this end. Finally, uranyl photocleavage of the internal control region (ICR) of the 5S-RNA gene yields a cleavage modulation pattern fully compatible with that obtained by DNase I which also— in a more complex way—senses DNA minor groove width.


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