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Nucleic Acids Research, 1994, Vol. 22, No. 25 5753-5860
© 1994

Articles

Sequence determinants of DNA bending in the ilvlH promoter and regulatory region of Escherichia coli

Qing Wang+,, Fred G. Albert2, Daniel J. Fitzgerald2, Joseph M. Calvo1 and John N. Anderson2,*

Sections of Genetics and Development Cornell University Ithaca, NY 14853 1Molecular and Cell Biology, Cornell University Ithaca, NY 14853 2Department of Biological Sciences, Purdue University West Lafayette, IN 47907-1392, USA

*To whom correspondence should be addressed

+Present address: Department of Human Genetics, University of Utah, Health Sciences Center, Salt Lake City, UT 84112, USA

Received April 19, 1994. Revised September 29, 1994. Accepted September 29, 1994.

Previous studies have shown that the promoter/ regulatory region of the IlvlH operon displays intrinsic curvature, with the bend center located at position -120 relative to the transcription start site. In this report, a 57 bp sequence spanning the bend center was mutagenlzed In vitro In order to study the relationship between nucleotlde sequence and curvature measured by electrophoresis. The strategy used for analyzing the results consisted of determining the strengths of the relationships between electrophoretic anomaly and predicted curvature calculated by computer programs that differ in wedge angle composition. The results revealed that programs which assume that bending occurs only at AA/TT display good predictive value, with correlation coefficients between electrophoretic anomaly and predicted curvature as high as 0.93. In contrast, a program which assumes that bending occurs at all 16 dinucleotlde steps exhibited lower predictive value, while there were no significant relationships between the experimental data and curvature calculated by a program that was based on all non-AA/TT wedge values. These results show that the complete wedge model which incorporates values for all dinucleotlde steps does not adequately describe the electrophoretic data In this report.


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