DNA octaplex formation with an I-motif of water-mediated A-quartets: Reinterpretation of the crystal structure of d(GCGAAAGC)

Journal of Biochemistry

Volumn 140, Issue 6, 2006, Pages 759-762

  Sato, Yoshiteru ^a   Mitomi, Kenta ^a   Sunami, Tomoko ^a   Kondo, Jiro ^b   Takénaka, Akio ^a  

^a TOKYO INSTITUTE OF TECHNOLOGY   (Japan)

^b INSTITUT DE BIOLOGIE MOLÉCULAIRE ET CELLULAIRE   (France)

Author keywords

A quartet; DNA octaplex; Non coding DNA; VNTR; X ray analysis

Indexed keywords

DNA FRAGMENT; MAGNESIUM ION; WATER; DNA; OLIGODEOXYRIBONUCLEOTIDE;

ARTICLE; CRYSTAL STRUCTURE; DNA REPLICATION; DNA SEQUENCE; DNA STRAND; DNA STRUCTURE; GENOME; HYDRATION; STRUCTURE ANALYSIS; VARIABLE NUMBER OF TANDEM REPEAT; BASE PAIRING; CHEMISTRY; CONFORMATION; X RAY CRYSTALLOGRAPHY;

BASE PAIRING; CRYSTALLOGRAPHY, X-RAY; DNA; MINISATELLITE REPEATS; NUCLEIC ACID CONFORMATION; OLIGODEOXYRIBONUCLEOTIDES; WATER;

EID: 34249055565     PISSN: 0021924X     EISSN: None     Source Type: Journal    
DOI: 10.1093/jb/mvj213     Document Type: Article

References (20)

1. International Human Genome Sequencing Consortium (2004) Finishing the euchromatic sequence of the human genome. Nature 431, 931-945
2. Jeffreys, A.J., Wilson, V., and Thein, S.L. (1985) Hypervariable 'minisatellite' regions in human DNA. Nature 314, 67-73
3. Jeffreys, A.J., Royle, N.J., Wilson, V., and Wong, Z. (1988) Spontaneous mutation rates to new length alleles at tandem-repetitive hypervariable loci in human DNA. Nature 332, 278-281
4. Inglehearn, C.F. and Cooke, H.J. (1990) A VNTR immediately adjacent to the human pseudoautosomal telomere. Nucleic Acids Res. 18, 471-476
5. Kondo, J., Adachi, W., Umeda, S., Sunami, T., and Takénaka, A. (2004) Crystal structures of a DNA octaplex with I-motif of G-quartets and its splitting into two quadruplexes suggest a folding mechanism of eight tandem repeats. Nucleic Acids Res. 32, 2541-2549
6. Sunami, T., Kondo, J., Hirao, I., Watanabe, K., Miura, K., and Takénaka, A. (2004) Structures of d(GCGAAGC) and d(GCGAAAGC) (tetragonal form): a switching of partners of the sheared G-A pairs to form a functional G·AxA·G crossing. Acta Crystallogr. D60, 422-431
7. Otwinowski, Z. and Minor, W. (1997) Processing of X-ray Diffraction Data Collected in Oscillation Mode in Methods in Enzymology (Carter, C.W. and Sweet, R.M., eds.) Vol. 276, pp. 307-326, Academic Press, New York
8. Brünger, A.T., Adams, P.D., Clore, G.M., DeLano, W.L., Gros, P., Grosse-Kunstleve, R.W., Jiang, J.S., Kuszewski, J., Nilges, M., Pannu, N.S., Read, R.J., Rice, L.M., Simonson, T., and Warren, G.L. (1998) Crystallography and NMR system: a new software suite for macromolecular structure determination. Acta Crystallogr. D54, 905-921
9. Murshudov, G.N., Vagin, A.A., and Dodson, E.J. (1997) Refinement of macromolecular structures by the maximum-likelihood method. Acta Crystallogr. D53, 240-255
10. Brünger, A.T. (1992) Free R value: a novel statistical quantity for assessing the accuracy of crystal structures. Nature 355, 472-475
11. Jones, T.A., Zou, J.Y., Cowan, S.W., and Kjeldgaard, M. (1991) Improved methods for building protein models in electron density maps and the location of errors in these models. Acta Crystallogr. A47, 110-119
12. Lu, X.J. and Olson, W.K. (2003) 3DNA: a software package for the analysis, rebuilding and visualization of three-dimensional nucleic acid structures. Nucleic Acids Res. 31, 5108-5121
13. Sayle, R.A. and Milner-White, E.J. (1995) RASMOL: biomolecular graphics for all. Trends Biochem. Sci. 20, 374
14. Williams, S., Hayes, L., Elsenboss, L., Williams, A., Andre, C., Abramson, R., Thompson, J.F., and Milos, P.M. (1997) Sequencing of the cholesteryl ester transfer protein 5′ regulatory region using artificial transposons. Gene 197, 101-107
15. n microsatellite in a canine Wilms tumor 1 (WT1) gene intron. Anim. Genet. 27, 59-60
16. De Luca, F., Reyes, A., Veronico, P., Di Vito, M., Lamberti, F., and De Giorgi, C. (2002) Characterization of the (GAAA) microsatellite region in the plant parasitic nematode Meloidogyne artiellia. Gene 293, 191-198
17. McCouch, S.R., Teytelman, L., Xu, Y., Lobos, K.B., Clare, K., Walton, M., Fu, B., Maghirang, R., Li, Z., Xing, Y., Zhang, Q., Kono, I., Yano, M., Fjellstrom, R., DeClerck, G., Schneider, D., Cartinhour, S., Ware, D., and Stein, L. (2002) Development and mapping of 2240 new SSR markers for rice (Oryza sativa L.). DNA Res. 9, 199-207
18. Hirao, I., Nishimura, Y., Tagawa, Y., Watanabe, K., and Miura, K. (1992) Extraordinarily stable mini-hairpins: electrophoretical and thermal properties of the various sequence variants of d(GCGAAAGC) and their effect on DNA sequencing. Nucleic Acids Res. 20, 3891-3896
19. Sunami, T., Kondo, J., Hirao, I., Watanabe, K., Miura, K., and Takénaka, A. (2004) Structure of d(GCGAAAGC) (hexagonal form): a base-intercalated duplex as a stable structure. Acta Crystallogr. D60, 90-96
20. Nakamura, Y., Leppert, M., O'Connell, P., Wolff, R., Holm, T., Culver, M., Martin, C., Fujimoto, E., Hoff, M., Kumlin, E., and White, R. (1987) Variable number of tandem repeat (VNTR) markers for human gene mapping. Science 235, 1616-1622