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Nucleic Acids Research, 2003, Vol. 31, No. 17 5134-5139
© 2003 Oxford University Press

Solution measurement of DNA curvature in papillomavirus E2 binding sites

Jeff M. Zimmerman and L. James Maher III*

Department of Biochemistry and Molecular Biology, Mayo Clinic-Rochester, 200 First Street SW, Rochester, MN 55905, USA

*To whom correspondence should be addressed. Tel: +1 507 284 9041; Fax: +1 507 284 2053; Email: maher{at}mayo.edu
Respectfully dedicated to the memory of Claude Hélène

‘Indirect readout’ refers to the proposal that proteins can recognize the intrinsic three-dimensional shape or flexibility of a DNA binding sequence apart from direct protein contact with DNA base pairs. The differing affinities of human papillomavirus (HPV) E2 proteins for different E2 binding sites have been proposed to reflect indirect readout. DNA bending has been observed in X-ray structures of E2 protein–DNA complexes. X-ray structures of three different E2 DNA binding sites revealed differences in intrinsic curvature. DNA sites with intrinsic curvature in the direction of protein-induced bending were bound more tightly by E2 proteins, supporting the indirect readout model. We now report solution measurements of intrinsic DNA curvature for three E2 binding sites using a sensitive electrophoretic phasing assay. Measured E2 site curvature agrees well the predictions of a dinucleotide model and supports an indirect readout hypothesis for DNA recognition by HPV E2.


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