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Crystal structure of d(GCGCGCG) with 5'-overhang G residues
- Source :
- ResearcherID
- Publisher :
- The Biophysical Society. Published by Elsevier Inc.
-
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.
- Subjects :
- 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
Subjects
Details
- Language :
- English
- ISSN :
- 00063495
- Issue :
- 3
- Database :
- OpenAIRE
- Journal :
- Biophysical Journal
- Accession number :
- edsair.doi.dedup.....ea2c17596e24b59d0ac5dbce1c5bbb1e
- Full Text :
- https://doi.org/10.1016/S0006-3495(97)78187-6