(CGA)(4): parallel, anti-parallel, right-handed and left-handed homoduplexes of a trinucleotide repeat DNA.

Abstract Conformational properties of microsatellite DNA regions are the probable reason of their expansions in genomes which lead to serious genetic diseases in some cases. Using CD spectroscopy, UV absorption spectroscopy and polyacrylamide gel electrophoresis, we study in this paper conformational properties of (CGA) 4 and compare them with those of (CAG) 4 – a related repeat, connected with Huntington’s disease. We show that (CGA) 4 can adopt several distinct conformations in solution. Around neutral pH it forms a parallel-stranded homoduplex containing C + .C, G.G, and A.A base pairs. Under the same conditions (CAG) 4 forms a hairpin. At slightly alkaline pH values and low ionic strength, (CGA) 4 also folded into a hairpin which transformed into a bimolecular anti-parallel homoduplex at increasing salt concentrations. The duplex easily isomerized into left-handed Z-DNA, implying that the mismatched adenines between G.C pairs facilitate rather than hinder the B–Z transition. No similar changes took place with (CAG) 4 . Thus, the conformational repertoire of (CGA) 4 includes parallel, anti-parallel, right-handed, and left-handed homoduplexes. In contrast, (CAG) 4 invariably adopts only a single conformation, namely the very stable hairpin.