Conformational flexibility of DNA: polymorphism and handedness.

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Abstract
Left-handed duplexes are possible for A, B, and D forms of DNA. These duplexes are stereochemically satisfactory and are consistent with the observed X-ray intensity data. On scrutiny the refined right-handed models of B and D DNA by Arnott and coworkers are stereochemically unacceptable. A stereochemical guideline for molecular model building may be formulated based on theory and analysis of single-crystal structure data of dinucleoside monophosphate and higher oligomers. This led to both right- and left-handed DNA duplexes. The right-handed B and D DNA duplexes so obtained are stereochemically superior to earlier models, and agree well with the observed X-ray intensity data. The observation that DNA can exist in either handedness for all the polymorphous forms of DNA at once explained A .dblarw. B and B .dblarw. D transitions. Polymorphism of DNA is a reflection on the conformational flexibility inherent in DNA, the same cause that ultimately allows DNA in either handedness. The possibility of various types of right- and left-handed duplexes, generated by using dinucleoside monophosphate and trinucleoside diphosphate as repeating units, resulted in a variety of models called RL. All these models have alternating right and left helical segments and inverted stacking at the bend region as suggested by us earlier. The B-Z DNA model of Wang et al. is only an example of RL models.