IR and UV Studies on Stability and Conformations of Short DNA Duplexes Containing a No-Base Residue: Coexistence of B and Z Conformations

Abstract

Tridecamers containing a central no-base residue (X) have been synthesized and hybridized to their complementary strands, so as to constitute duplexes consisting of two hexamers separated by central mismatched X-A or X-T pairs. The effect of the introduction of this deoxyribose derivative on duplex stability was investigated by measuring UV absorbance as a function of salt concentration and temperature. As expected, the duplexes containing the abnormal base pairs (X-T and X-A) are less stable when compared to the totally complementary duplexes (A-T and T-A). The X-T mismatched duplex shows the most unstable thermodynamical behaviour. The conformational changes of these duplexes were studied by IR spectroscopy in condensed phase as a function of water content. At high relative humidity, the IR spectra show that these tridecamers form B-type double stranded duplex structures. If the water content is decreased, only the duplexes m5CGm5CGCTXAGCTTC GCGCGAATCGAAG and, to a lesser degree, m5CGm5CGCTXAGCTTC GCGGCATTCGAAG undergo a partial B---Z transition involving the methylated hexamer, the conformation of the second segment remaining of the B type. These results show that only one apurinic residue leads to a flexible junction between B and Z forms in a short duplex containing 5-methyl-2'-deoxycytidines.

High-resolution NMR studies of chimeric DNA-RNA-DNA duplexes, heteronomous base pairing, and continuous base stacking at junctions

“…Arnott et al (1983) were able to construct models of B-DNA embedded within a patch of Z-DNA as well as of B-DNA embedded within a patch of A-DNA, with only one base pair adopting a different conformation; both of these models were found to involve bending or kinking at the junction region. Subsequently, a B-Z junction has been observed in both natural DNA (Rich et al, 1984) and synthetic DNA oligomers (Sheardy, 1988;Adam et al, 1988), and a cell protein capable of binding to Z-DNA has also been reported (Leith et al, 1988). The possibility of a B-DNA/A-DNA junction in vivo was suggested by Rhodes and Klug (1986), who proposed that the DNA-binding site for transcriptional factor IIIA (TFIIIA) in the Xenopus 5S RNA gene region has an A-like structure on the basis of the observation that TFIIIA can bind to its target site in the double-stranded DNA structural gene as well as to the RNA transcript.…”