Structural Basis of Stable Bending in DNA Containing AnTracts. Different Types of Bending

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Abstract
Structural determinants of DNA bending of different types have been studied by theoretical conformational analysis of duplexes. Their terminal parts were fixed either in an ordinary low-energy B-like conformation or in “anomalous” conformations with a narrowed minor groove typical of An tracts. The anomalous conformations had different negative tilt angles (up to about zero), different propeller twists and minor groove widths. Calculations have been performed for DNA fragments AnTm, TnAm, AnGCTm, AnCGTm, TmGCAn, TmCGAn which are the models of the junction of two anomalous structures on An and Tm tracts. On the AT step of the AnTm fragment the minor groove can be easily narrowed so that a whole unbent fragment of anomalous structure is formed on An Tm. According to our energy estimates, there should not be any reliable bending on AnTm. In contrast, in all other cases there was a pronounced roll-like bending into the major groove in the chemical symmetry region. Calculations of the junction between the anomalous and ordinary B-like structure for GnTm and CnAm have shown that there is an equilibrium bending with a tilt component towards the chain having the anomalous structure at the 5′-end. From our calculations it is impossible to determine precisely the direction of bending, though it can be suggested that the roll component of bending might be directed towards the major groove. The anomalous structure is the main reason of bending; alternations of pyrimidines and purines can modulate the value and the direction of equilibrium bending (only the value in the case of self-complemantary fragments). The results are consistent with the experimental data and promote a better understanding of the problem of DNA bending.