313D

Z-DNA HEXAMER WITH 5' OVERHANGS THAT FORM A REVERSE HOOGSTEEN BASE PAIR

Summary for 313D

• Entry DOI: 10.2210/pdb313d/pdb
• Descriptor: DNA (5'-D(*GP*(5CM)P*GP*CP*GP*CP*G)-3'), MAGNESIUM ION, COBALT HEXAMMINE(III), ... (4 entities in total)
• Functional Keywords: z-dna, double helix, modified, overhanging base, flipped-out base, dna
• Total number of polymer chains: 2
• Total formula weight: 4492.30

Authors

Mooers, B.H.M.,Eichman, B.F.,Ho, P.S. (deposition date: 1997-02-04, release date: 1997-08-05, Last modification date: 2024-02-21)

Primary citation

Mooers, B.H.,Eichman, B.F.,Ho, P.S.
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.
J.Mol.Biol., 269:796-810, 1997

PubMed Abstract: 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.

PubMed: 9223642
DOI: 10.1006/jmbi.1997.1100

Experimental method

X-RAY DIFFRACTION (1.68 Å)