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Nucleic Acids Research, 2002, Vol. 30, No. 23 5244-5252
© 2002 Oxford University Press

A Hoogsteen base pair embedded in undistorted B-DNA

Jun Aishima1, Rossitza K. Gitti2,3, Joyce E. Noah4, Hin Hark Gan2,4,5, Tamar Schlick2,4,5 and Cynthia Wolberger*,1,2

1 Department of Biophysics and Biophysical Chemistry and 2 Howard Hughes Medical Institute, Johns Hopkins University School of Medicine, Baltimore, MD 21205-2185, USA, 3 Department of Chemistry and Biochemistry, University of Maryland Baltimore County, Baltimore, MD 21250, USA, 4 Department of Chemistry and 5 Courant Institute of Mathematical Sciences, New York University, 31 Washington Place, Room 1021 Main, New York, NY 10003, USA

*To whom correspondence should be addressed at 7 Johns Hopkins University School of Medicine, Baltimore, MD 21205-2185, USA. Tel: +1 410 955 0728; Fax: +1 410 614 8648; Email: cwolberg{at}jhmi.edu
Present address:
Jun Aishima, Lawrence Berkeley National Laboratory, 1 Cyclotron Road, Mail Stop 4-230, Berkeley, CA 94720, USA

Hoogsteen base pairs within duplex DNA typically are only observed in regions containing significant distortion or near sites of drug intercalation. We report here the observation of a Hoogsteen base pair embedded within undistorted, unmodified B-DNA. The Hoogsteen base pair, consisting of a syn adenine base paired with an anti thymine base, is found in the 2.1 Å resolution structure of the MAT{alpha}2 homeodomain bound to DNA in a region where a specifically and a non-specifically bound homeodomain contact overlapping sites. NMR studies of the free DNA show no evidence of Hoogsteen base pair formation, suggesting that protein binding favors the transition from a Watson–Crick to a Hoogsteen base pair. Molecular dynamics simulations of the homeodomain–DNA complex support a role for the non-specifically bound protein in favoring Hoogsteen base pair formation. The presence of a Hoogsteen base pair in the crystal structure of a protein–DNA complex raises the possibility that Hoogsteen base pairs could occur within duplex DNA and play a hitherto unrecognized role in transcription, replication and other cellular processes.


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