101. Crystal structure of d(GCGCGCG) with 5'-overhang G residues
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Markus C. Wahl, Muttaiya Sundaralingam, B. Pan, and Changill Ban
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Models, Molecular ,Circular dichroism ,Guanine ,Stereochemistry ,030303 biophysics ,Biophysics ,Guanosine ,Crystal structure ,Crystallography, X-Ray ,Cobalt hexammine ,03 medical and health sciences ,chemistry.chemical_compound ,Molecular replacement ,030304 developmental biology ,Base Composition ,0303 health sciences ,Base Sequence ,Hydrogen bond ,Circular Dichroism ,Hydrogen Bonding ,Cobalt ,DNA ,Crystallography ,Oligodeoxyribonucleotides ,chemistry ,Nucleic Acid Conformation ,Research Article - Abstract
The crystal structure of the DNA heptamer d(GCGCGCG) has been solved at 1.65 A resolution by the molecular replacement method and refined to an R-value of 0.184 for 3598 reflections. The heptamer forms a Z-DNA d(CGCGCG)2 with 5'-overhang G residues instead of an A-DNA d(GCGCGC)2 with 3'-overhang G residues. The overhang G residues from parallel strands of two adjacent duplexes form a trans reverse Hoogsteen G x G basepair that stacks on the six Z-DNA basepairs to produce a pseudocontinuous helix. The reverse Hoogsteen G x G basepair is unusual in that the displacement of one G base relative to the other allows them to participate in a bifurcated (G1)N2 . . . N7(G8) and an enhanced (G8)C8-H . . . O6(G1) hydrogen bond, in addition to the two usual hydrogen bonds. The 5'-overhang G residues are anti and C2'-endo while the 3'-terminal G residues are syn and C2'-endo. The conformations of both G residues are different from the syn/C3'-endo for the guanosine in a standard Z-DNA. The two cobalt hexammine ions bind to the phosphate groups in both GpC and CpG steps in Z(I) and Z(II) conformations. The water structure motif is similar to the other Z-DNA structures.
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