Abstract
A-DNA is a high-energy conformation of the double helix under physiological conditions. However, it can be stabilized by a decrease in water activity in drying fibers or by the presence of alcohols in aqueous solutions. This conformation may be biologically interesting. First, it is a stable form of double helical fragments of RNA, and thereby DNA–RNA hybrid duplexes. Second, the local B–A transition of DNA has been repeatedly suggested to occur during transcription. Third, proteins exist (e.g., a protein from sporulating bacteria) that transform DNA into the A form when complexed. This chapter discusses the problem of sequence effect on the B–A transition. The flow method for studying the B–A transition is based on the change in the hydrodynamic properties of DNA. The B–A junctions, whose existence is a direct consequence of the cooperativity, appear as a distortion of the regular helix and have an increased energy. Hence, DNA is expected to have increased flexibility at these sites and, probably, a bend. Experimentally this can be studied by observing changes in specific viscosity, sedimentation, and gel electrophoresis.
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