In certain curved DNA fragments without AA dinucleotides, the gel retardation anomaly associated with curvature passes through a maximum with fragment length, indicating length (and electric field) dependent structural transitions in the DNA We suggest that thermally induced stereochemical kinks in DNA are stabilized in the gel, thus relieving the effects of curvature. These kinks are shown to occur specifically at C A/TG and TA/TA stacks. Other physical and biological evidence points to frequent structural dislocations at CA and TA steps. These reversible sequence dependent kinks may therefore represent a novel class of structural protein-DNA recognition elements.
Bibliographical noteFunding Information:
Supported in part from research grants GM 33435 (REH) and NCI Cancer Training Grant T32CA09563 (PTM) from the National Institutes of Health and Hatch Project 102 from the UniversityofNevada Reno (REH). We thank Jane Button for help with synthesis and other laboratory procedures. Discussions with V. Zhurkin, Y. Lyubchenko and E. Charney are highly appreciated. We thank Drs. S. Schultz and T. Steitz for sharing, in advance of publication, their crystallographic results on the CAPDNA complex.
ASJC Scopus subject areas
- Molecular Biology
- Structural Biology