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Nucleic Acids Research, 1989, Vol. 17, No. 19 7735-7748
© 1989

MOLECULAR BIOLOGY

Hydroxyl radical footprints reveal novel structural features around the NF I binding site in adenovirus DNA

Haralabos Zorbas, Lars Rogge, Michael Meisterernst and Ernst-Ludwig Winnacker

Institut für Biochcmie, Universität München Karlstraße 23, D-8000 Munich 2, FRG

Received June 28, 1989. Revised August 28, 1989. Accepted August 28, 1989.

We have identified a number of as yet unknown structural abnormalities of the NF I-DNA binding site within the inverted terminal repetition of adenovirus DNA by probing it with a hydroxyl radical footprinting technique. NF I binding alters the accessibility of the deoxyribose moieties to hydroxyl radicals both at the 3' and at the 5' side of the recognition sequence 5'-TGG(N)6GCCAA-3'. A smooth bend at the 5' side of the binding sequence is already present in naked linear DNA and it is further enhanced by protein binding. This could be demonstrated not only by hydroxyl radical footprinting but also by studying the temperature dependent mobility during gel electrophoresis of DNA fragments carrying the NF I binding site at circularly permutated positions. We propose that the bent conformation at this site is responsible for facilitating protein/DNA interactions.


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