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Nucleic Acids Research, 1990, Vol. 18, No. 23 6853-6856
© 1990

Articles

DNA-sequence recognition by CAP: role of the adenine N6 atom of base pair 6 of the DNA site

Angelo Gunasekera, Yon W. Ebright and Richard H. Ebright*

Department of Chemistry and Waksman Institute, Rutgers University New Brunswick, NJ 08855, USA

* To whom correspondence should be addressed

Received September 18, 1990. Revised November 6, 1990. Accepted November 6, 1990.

Two similar, but not identical, models have been proposed for the amino acid-base pair contacts in the CAP-DNA complex (‘Model I,’ Weber, I. and Steitz, T., Proc. Natl. Acad. Sci. USA, 81, 3973–3977, 1984; ‘Model II,’ Ebright, et al., Proc. Natl. Acad. Sci. USA, 81, 7274–7278, 1984). One difference between the two models involves Glu181 of CAP. Model I predicts that Glu181 of CAP makes two specificity determining contacts: one H-bond with the cytosine N4 atom of G:C at base pair 7 of the DNA half site, and one H-bond with the adenine N6 atom of T:A at base pair 6 of the DNA half site. In contrast, Model II predicts that Glu181 makes only one specificity determining contact: one H-bond with the cytosine N4 atom of G:C at base pair 7 of the DNA half site. In the present work, we show that replacement of T:A at base pair 6 of the DNA half site by T:N6-methyl-adenine has no, or almost no, effect on the binding of CAP. We conclude, contrary to Model I, that Glu181 of CAP makes no contact with the adenine N6 atom of base pair 6 of the DNA half site.


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