Journal Article

The intrinsic structure and stability of out-of-alternation base pairs in Z-DNA

Brandt F. Eichman, Gary P. Schroth, Beth E. Basham and P. Shing Ho

in Nucleic Acids Research

Volume 27, issue 2, pages 543-550
Published in print January 1999 | ISSN: 0305-1048
Published online January 1999 | e-ISSN: 1362-4962 | DOI: http://dx.doi.org/10.1093/nar/27.2.543
The intrinsic structure and stability of out-of-alternation base pairs in Z-DNA

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  • Chemistry
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Alternating pyrimidine-purine sequences typically form Z-DNA, with the pyrimidines in the anti and purines in the syn conformations. The observation that dC and dT nucleotides can also adopt the syn conformation (i.e. the nucleotides are out-of-alternation) extends the range of sequences that can convert to this left-handed form of DNA. Here, we study the effects of placing two adjacent d(G·C) base pairs as opposed to a single d(G·C) base pair or two d(A·T) base pairs out-of-alternation by comparing the structure of d(m5CGGCm5CG)2 with the previously published structures of d(m5CGGGm5CG)·d(m5CGCCm5CG) and d(m5CGATm5CG)2. A high buckle and loss of stacking interactions are observed as intrinsic properties of the out-of-alternation base pairs regardless of sequence and the context of the dinucleotide. From solution titrations, we find that the destabilizing effect of out-of-alternation d(G·C) base pairs are identical whether these base pairs are adjacent or isolated. We can therefore conclude that it is these intrinsic distortions in the structure of the base pairs and not neighboring effects that account for the inability of out-of-alternation base pairs to adopt the left-handed Z conformation.

Journal Article.  5177 words.  Illustrated.

Subjects: Chemistry ; Biochemistry ; Bioinformatics and Computational Biology ; Genetics and Genomics ; Molecular and Cell Biology

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