313d
Z-DNA HEXAMER WITH 5' OVERHANGS THAT FORM A REVERSE HOOGSTEEN BASE PAIR
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OverviewOverview
We have solved the structures of the homoduplex d(Gm5CGCGCG)2, and the, heteroduplexes d(GCGCGCG)/d(TCGCGCG) and d(GCGCGCG)/d(CCGCGCG). The, structures form six base-pairs of identical Z-DNA duplexes with single, nucleotides overhanging at the 5'-ends. The overhanging nucleotide from, one strand remains stacked and sandwiched between the blunt-ends of two, adjacent Z-DNA duplexes, while the overhanging base of the opposing strand, is extra-helical. The stacked and the extra-helical bases from adjacent, duplexes pair to form a distorted d(G x G) reverse Hoogsteen base-pair in, the d(Gm5CGCGCG)2 homoduplex, and d(G x T) reverse wobble and d(G x C), reverse Watson-Crick base-pairs in the d(GCGCGCG)/d(TCGCGCG) and, d(GCGCGCG)/d(CCGCGCG) heteroduplexes, respectively. Interestingly, only, the d(G,T) and d(G x C) base-pairs were observed in the heteroduplexes, suggesting that both the d(G x T) reverse wobble and d(G x C) reverse, Watson-Crick base-pairs are more stable in this crystal environment than, the d(G x G) reverse Hoogsteen base-pair. To estimate the relative, stability of the three types of reverse base-pairs, crystals were grown, using various mixtures of sequences and their strand compositions analyzed, by mass spectrometry. The d(G x C) reverse Watson-Crick base-pair was, estimated to be more stable by approximately 1.5 kcal/mol and the d(G x T), reverse wobble base-pair more stable by approximately 0.5 kcal/mol than, the d(G x G) reverse Hoogsteen base-pair. The step during crystallization, responsible for discriminating between the strands in the crystal is, highly cooperative, suggesting that it occurs during the initial, nucleating event of crystal growth.
About this StructureAbout this Structure
313D is a Protein complex structure of sequences from [1] with and as ligands. Full crystallographic information is available from OCA.
ReferenceReference
The structures and relative stabilities of d(G x G) reverse Hoogsteen, d(G x T) reverse wobble, and d(G x C) reverse Watson-Crick base-pairs in DNA crystals., Mooers BH, Eichman BF, Ho PS, J Mol Biol. 1997 Jun 27;269(5):796-810. PMID:9223642
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