Alternative DNA Structures

Alternative DNA structures differ from regular double-stranded B-DNA. Everything interesting, ehether useful or harmful, that occurs with DNA, occurs when DNA changes from the normal regular B-form. For DNA to form an abnormal structure, its local sequence should be non-random, that is, contain certain order. Such ordered sequences include direct repeats, inverted repeats, and homopyrimidine-homopurine repeats (in particular, mirror repeats). Accordingly, the structures that can locally form due to these repetitions are: slipped-strand DNA, left-handed Z-DNA, cruciform DNA (four-way junctions), triple-stranded DNA. In stretches of adenines and some other nucleotide combinations certain parameters of B-DNA add up over a length of several base pairs to produce a permanently bent DNA helix. Fewer hydrogen bonds form in AT base pairs than in GC pairs, therefore, AT-rich sequences may form local stably unwound DNA structures. My group has studied physico-chemical properties of many unusual structures, their relations to the length instability of repeated DNA sequences, and structure-specific binding of poly(ADP-ribose)polymerase to DNA.

Some ideas of the biological significance of these and other structures are discussed in a recent review.
Potaman VN, Sinden RR. (2004) DNA: Alternative conformations and biology. In (T. Ohyama, Ed.) DNA Conformation and Transcription, pp.1-16. Landes Bioscience (Ohyama01Potaman.pdf).

Most of the work on alternative DNA structures in my group has been done in collaboration with Dr. Richard Sinden, Dr. Yuri Lyubchenko, Dr. Valery Soyfer, Dr. John Bissler.
There are several research resources frequently used by my group.

My current PubMed record