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Nucleic Acids Research, 2001, Vol. 29, No. 23 4881-4891
© 2001 Oxford University Press

Strong minor groove base conservation in sequence logos implies DNA distortion or base flipping during replication and transcription initiation

Thomas D. Schneider*

National Cancer Institute at Frederick, Laboratory of Experimental and Computational Biology, Building 469, PO Box B, Frederick, MD 21702-1201, USA

The sequence logo for DNA binding sites of the bacteriophage P1 replication protein RepA shows unusually high sequence conservation (~2 bits) at a minor groove that faces RepA. However, B-form DNA can support only 1 bit of sequence conservation via contacts into the minor groove. The high conservation in RepA sites therefore implies a distorted DNA helix with direct or indirect contacts to the protein. Here I show that a high minor groove conservation signature also appears in sequence logos of sites for other replication origin binding proteins (Rts1, DnaA, P4 {alpha}, EBNA1, ORC) and promoter binding proteins ({sigma}70, {sigma}D factors). This finding implies that DNA binding proteins generally use non-B-form DNA distortion such as base flipping to initiate replication and transcription.

* Tel: +1 301 846 5581; Fax: +1 301 846 5598; Email: toms{at}ncifcrf.gov


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