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Nucleic Acids Research, 2003, Vol. 31, No. 22 6663-6673
© 2003 Oxford University Press

Article

Molecular flip–flops formed by overlapping Fis sites

Paul N. Hengen, Ilya G. Lyakhov, Lisa E. Stewart1 and Thomas D. Schneider*,1

Intramural Research Support Program, SAIC and 1 Laboratory of Experimental and Computational Biology, NCI Frederick, Frederick, MD, USA

*To whom correspondence should be addressed at National Cancer Institute at Frederick, PO Box B, Building 469, Room 144, Frederick, MD 21702-1201, USA. Tel: +301 846 5581; Fax: +301 846 5598; Email: toms{at}ncifcrf.gov
Present addresses:
Paul N. Hengen, Applied Biosystems, 3833 North First Street, San Jose, CA, 95134-1701, USA
Lisa E. Stewart, Alkami Biosystems, Inc., PO Box 11216, Berkeley, CA 94712-2216, USA
The authors wish it to be known that, in their opinion, the first two authors should be regarded as joint First Authors.

The DNA-binding protein Fis frequently uses pairs of sites 7 or 11 base pairs (bp) apart. Two overlapping Fis sites separated by 11 bp are found in the Escherichia coli origin of chromosomal replication. Only one of these sites is bound by Fis at a time, so the structure is a molecular flip–flop that could direct alternative firing of replication complexes in opposite directions. Alternatively, the flip–flop could represent part of an on–off switch for replication. Because they can be used to create precise switched states, molecular flip–flops could be used as the basis of a novel molecular computer.


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