Methylation of the Z-DNA decamer d(GC)5 potentiates the formation of A-DNA: Crystal structure of d(Gm5CGm5CGCGCGC)

Journal of Molecular Biology

Volumn 270, Issue 2, 1997, Pages 247-258

  Tippin, D B ^b   Ramakrishnan, B ^b   Sundaralingam, M ^a  

^a OHIO STATE UNIVERSITY   (United States)

^b NONE

Author keywords

A DNA; Methylation; X ray structure; Z A transition; Z DNA

Indexed keywords

CELL NUCLEUS DNA; DNA A; DNA Z; DOUBLE STRANDED DNA; OLIGOMER; OLIGONUCLEOTIDE;

ARTICLE; CRYSTAL STRUCTURE; DNA CONFORMATION; DNA METHYLATION; NUCLEOTIDE SEQUENCE; PRIORITY JOURNAL; R FACTOR;

EID: 0030754556     PISSN: 00222836     EISSN: None     Source Type: Journal    
DOI: 10.1006/jmbi.1997.1102     Document Type: Article

References (36)

1. Ban C., Sundaralingam M. Crystal structure of the self-complementary 5′-purine start decamer d(GCACGCGTGC) in the A -DNA conformation. Biophys. J. 71:1996;1222-1227.
2. Ban C., Ramakrishnan B., Sundaralingam M. Crystal structure of the self- complementary 5′-purine start decamer d(GCGCGCGCGC) in the Z -DNA conformation. Biophys. J. 71:1996;1215-1221.
3. Berman H. M., Olson W. K., Beveridge D., Westbrook J., Galbin A., Demeny T., Hsieh S., Srinivasin A. R., Schneider B. The nucleic acid database: a comprehensive relational database of three dimensional structures of nucleic acids. Biophys. J. 63:1992;751-759.
4. Bingman C., Jain S., Zon G., Sundaralingam M. Crystal and molecular structure of the alternating dodecamer d(GCGTACGTACGC) in the A -DNA form: comparison with the isomorphous non-alternating dodecamer d(CCGTACGTACGG). Nucl. Acids Res. 20:1992a;6637-6647.
5. Bingman C., Li X., Zon G., Sundaralingam M. Crystal and molecular structure of d(GTGCGCAC): investigation of the effects of base sequence on the conformation of octamer duplexes. Biochemistry. 31:1992b;12803-12812.
6. 3+binding to the guanine. J. Biomol. Struct. Dynam. 3:1986;649-665.
7. Brunger A. T., Kuriyan J., Karplus M. Crystallographic R factor refinement by molecular dynamics. Science. 235:1987;458-460.
8. Calladine C. R. Mechanics of sequence dependent bases in B -DNA. J. Mol. Biol. 161:1982;343-352.
9. Chevrier B., Dock A. C., Hartmann B., Leng M., Moras D., Thuong M. T., Westhof E. Solvation of the left-handed hexamer d(5BrC-G-5BrC-G-5BrC-G) in crystals grown at two temperatures. J. Mol. Biol. 188:1986;707-719.
10. 2: combined x-ray and NMR study. Nucl. Acids Res. 18:1990;5521-5528.
11. Coll M., Fita I., Lloveras J., Subirana J. A., Bardella F., Huynh-Dinh T., Igolen J. Structure of d(CACGTG), Z -DNA hexamer containing A·T base-pairs. Nucl. Acids Res. 16:1988;8695-8705.
12. Drew H., Takano T., Itakura K., Dickerson R. E. High-salt d(CpGpCpG), a left-handed Z′ DNA double helix. Nature. 286:1980;567-573.
13. 3: the role of the methyl group on 5-methylcytosine in stabilizing Z -DNA. Nucl. Acids Res. 10:1982;7879-7892.
14. Fugii S., Wang A. H.-J., Quigley G. J., Westerink H., van der Marel G. A., van Boom J. H., Rich A. The octamers d(CGCGCGCG) and d(CGCATGCG) both crystallize as Z -DNA in the same hexagonal lattice. Biopolymers. 24:1985;243-250.
15. Furey, B. 1992, PHASES, V.A. Med. Center, Pittsburgh, PA.
16. Grubinska B., Laskiewicz I., Royland J., Wiggins R. C., Konat G. W. Differentiation-specific demethylation of myelin associated glycoprotein gene in cultured oligodendrocytes. J. Neurosci. Res. 39:1994;233-242.
17. Ho P. S., Frederick C. A., Quigley G. A., van der Marel G. A., van Boom J. H., Wang A. H.-J., Rich A. GT wobble base-pairing in Z -DNA at 1.0 angstrom atomic resolution: the crystal structure of d(CGCGTG). EMBO J. 4:1985;3617-3623.
18. Ho P. S., Quigley G. J., Tilton R. F. Jr, Rich A. Hydration of methylated and nonmethylated B-DNA and Z -DNA. J. Phys. Chem. 92:1988;939-945.
19. Jain S. C., Zon G., Sundaralingam M. The potentially Z -DNA-forming sequence d(GTGTACAC) crystallizes as A -DNA. J. Mol. Biol. 197:1987;141-145.
20. Jovin T. M., McIntosh L. P., Arndt-Jovin D. J., Zarling A., Eckstein F. Left-handed DNA: from synthetic polymers to chromosomes. J. Biomol. Struct. Dynam. 1:1983;21-52.
21. Kagawa T. F., Stoddard D., Zhou G., Ho P. S. Quantitative analysis of DNA secondary structure from solvent-accessible surfaces: the B- to Z -transition as a model. Biochemistry. 28:1989;6642-6651.
22. Kim J. L., Nikolov D. B., Burley S. K. Co-crystal structure of TBP recognizing the minor groove of a TATA element. Nature. 365:1993;520-528.
23. Kim Y., Geiger J. H., Hahn S., Sigler P. B. Crystal structure of a yeast TBP/TATA-box complex. Nature. 365:1993;512-519.
24. Kumar V. D., Harrison R. W., Andrews L. C., Weber I. T. Crystal structure at 1.5 angstroms resolution of d(CGCICICG), an octanucleotide containing inosine, and its comparison with d(CGCG) and d(CGCGCG) structures. Biochemistry. 31:1992;1541-1550.
25. Langlois D. B., Dautant A., Courseille C., Precigoux G. Orthorhombic crystal structure of the A -DNA octamer d(GTACGTAC). Comparison with the tetragonal structure. Eur. J. Biochem. 213:1993;673-682.
26. Moores B. H. M., Schroth G. P., Baxter W. W., Ho P. S. Alternating and non-alternating dG-dC hexanucleotides crystallize as canonical A -DNA. J. Mol. Biol. 249:1995;772-784.
27. Peticolas W. L., Wang Y., Thomas G. A. Some rules for predicting the base-sequence dependence of DNA conformation. Proc. Natl Acad. Sci. USA. 85:1988;2579-2583.
28. Pohl F. M., Jovin T. M. Salt-induced co-operative conformational change of a synthetic DNA: equilibrium and kinetic studies with poly (dG-dC). J. Mol. Biol. 67:1972;375-396.
29. nsequence do not assume left-handed conformation in high salt conditions. J. Mol. Biol. 175:1984;419-423.
30. 5C base-pair. Biophys. J. 69:1995;553-558.
31. 5CG). Biochemistry. 32:1993;13381-13392.
32. Sadasivan C., Gautham N. Sequence-dependent microheterogeneity of Z -DNA: the crystal and molecular structures of d(CACGCG)·d(CGCGTG) and d(CGCACG)·d(CGTGCG). J. Mol. Biol. 248:1995;918-930.
33. Takusagawa T. The crystal structure of d(GTACGTAC) at 2.25 angstroms resolution. Are the A -DNA's always unwound approximately 10 degrees at the C-G steps? J. Biomol. Struct. Dynam. 7:1990;795-809.
34. Wang A. H.-J., Quigley G. J., Kolpak F. J., Crawford J. L., van Boom J. H., van der Marel G. A., Rich A. Molecular structure of a left-handed double helical DNA fragment at atomic resolution. Nature. 282:1979;680-686.
35. Yoon C., Prive G. G., Goodsell D. S., Dickerson R. E. Structure of an alternating B -DNA helix and its relationship to A -tract DNA. Proc. Natl Acad. Sci. USA. 85:1988;6332-6336.
36. 5CG). Biochemistry. 29:1990;7229-7236.