Nucleic Acids Research Advance Access published online on March 10, 2009
Nucleic Acids Research, doi:10.1093/nar/gkp134
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Structural Biology |
Direct demonstration and quantification of long-range DNA looping by the 
bacteriophage repressor
1Physics Department, 400 Dowman Dr., 2Cell Biology Department, 615 Michael St, Emory University, Atlanta, GA 30322 and 3Laboratory of Molecular Biology, NCI, NIH, 37 Convent Drive, Bethesda, MD 20892-4264, USA
*To whom correspondence should be addressed. Tel: +1 (404) 727 4930; Fax: +1 (404) 727 0873; Email: lfinzi{at}emory.edu
Received September 23, 2008. Revised February 13, 2009. Accepted February 17, 2009.
Recently, it was proposed that DNA looping by the 
repressor (CI protein) strengthens repression of lytic genes during lysogeny and simultaneously ensures efficient switching to lysis. To investigate this hypothesis, tethered particle motion experiments were performed and dynamic CI-mediated looping of single DNA molecules containing the repressor binding sites separated by 2317 bp (the wild-type distance) was quantitatively analyzed. DNA containing all three intact operators or with mutated o3 operators were compared. Modeling the thermodynamic data established the free energy of CI octamer-mediated loop formation as 1.7 kcal/mol, which decreased to –0.7 kcal/mol when supplemented by a tetramer (octamer+tetramer-mediated loop). These results support the idea that loops secured by an octamer of CI bound at oL1, oL2, oR1 and oR2 operators must be augmented by a tetramer of CI bound at the oL3 and oR3 to be spontaneous and stable. Thus the o3 sites are critical for loops secured by the CI protein that attenuate cI expression.
The authors wish it to be known that, in their opinion, the first two authors should be regarded as joint First Authors.