Crystal structures of a DNA octaplex with I-motif of G-quartets and its splitting into two quadruplexes suggest of a folding mechanism of eight tandem repeats

Nucleic Acids Research

Volumn 32, Issue 8, 2004, Pages 2541-2549

  Kondo, Jiro ^a   Adachi, Wataru ^a   Umeda, Shun Ichi ^a   Sunami, Tomoko ^a   Takénaka, Akio ^a  

^a TOKYO INSTITUTE OF TECHNOLOGY   (Japan)

Author keywords

[No Author keywords available]

Indexed keywords

DNA FRAGMENT; GUANINE; POTASSIUM ION; DNA; POTASSIUM; QUADRUPLEX DNA; WATER;

ARTICLE; CONCENTRATION (PARAMETERS); CONTROLLED STUDY; CRYSTAL STRUCTURE; DNA REPLICATION; DNA STRUCTURE; GENE FUNCTION; GENE SEQUENCE; PRIORITY JOURNAL; PROTEIN FOLDING; STRUCTURE ANALYSIS; TANDEM REPEAT; X RAY ANALYSIS; CHEMICAL STRUCTURE; CHEMISTRY; CONFORMATION; DRUG EFFECT; GENETICS; METABOLISM; NUCLEOTIDE SEQUENCE; THERMODYNAMICS; VARIABLE NUMBER OF TANDEM REPEAT; X RAY CRYSTALLOGRAPHY;

BASE SEQUENCE; CRYSTALLOGRAPHY, X-RAY; DNA; MINISATELLITE REPEATS; MODELS, MOLECULAR; NUCLEIC ACID CONFORMATION; POTASSIUM; TANDEM REPEAT SEQUENCES; THERMODYNAMICS; WATER;

EID: 2442657982     PISSN: 03051048     EISSN: None     Source Type: Journal    
DOI: 10.1093/nar/gkh575     Document Type: Article

References (36)

1. Watson,J.D. and Crick,F.H. (1953) Molecular structure of nucleic acids: a structure for deoxyribose nucleic acid. Nature, 171, 737-738.
2. Fuller,W., Wilkins,M.H.F., Wilson,H.R. and Hamilton,L.D. (1965) The molecular configuration of deoxyribonucleic acid. IV. X-ray diffraction study of the A form. J. Mol. Biol., 12, 60-80.
3. Leslie,A.G.W., Arnott,S., Chandrasekaran,R. and Ratliff,R.L. (1980) Polymorphism of DNA double helices. J. Mol. Biol., 143, 49-72.
4. Wang,A.H.-J., Quigley,G.J., Kolpak,F.J., Crawford,J.L., van Boom,J.H., van der Marel,G. and Rich,A. (1979) Molecular structure of a left-handed double helix DNA fragment at atomic resolution. Nature, 282, 680-686.
5. Drew,H., Takano,T., Tanaka,S., Itakura,K. and Dickerson,R.E. (1980) High-salt d(CpGpCpG): a left-handed double helix. Nature, 286, 567-573.
6. Brown,B.A.,2nd and Rich,A. (2001) The left-handed double helical nucleic acids. Acta Biochim. Pol., 48, 295-312.
7. Sunami,T., Kondo,J., Kobuna,T., Hirao,I., Watanabe,K., Miura,K. and Takénaka,A. (2002) Crystal structure of d(GCGAAAGCT) containing a parallel-stranded duplex with homo base pairs and an anti-parallel duplex with Watson-Crick base pairs. Nucleic Acids Res., 30, 5253-5260.
8. Wang,E. and Feigon,J. (1999) Structures of nucleic acid triplexes. In Neidle,S. (ed.), Nucleic Acid Structure. Oxford University Press, Oxford, UK, pp. 355-388.
9. Patel,D.J., Bouaziz,A., Kettani,A. and Wang,Y. (1999) Structures of guanine-rich and cytosine-rich quadruplexes formed in vitro by telomeric, centromeric and triplet repeat disease DNA sequences. In Neidle,S. (ed.), Nucleic Acid Structure. Oxford University Press, Oxford, UK, pp. 389-453.
10. International Human Genome Sequencing Consortium. (2001) Initial sequencing and analysis of the human genome. Nature, 409, 860-921.
11. 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.
12. Jeffreys,A.J., Wilson,V. and Thein,S.L. (1985) Hypervariable 'minisatellite' regions in human DNA. Nature, 314, 67-73.
13. Jeffreys,A.J., Wilson,V. and Thein,S.L. (1985) Individual-specific 'fingerprints' of human DNA. Nature, 316, 76-79.
14. Wahls,W.P., Wallace,L.J. and Moore,P.D. (1990) Hypervariable, minisatellite DNA is a hotspot for homologous recombination in human cells. Cell, 60, 95-103.
15. Lucassen,A.M., Julier,C., Beressi,J.P., Boitard,C., Froguel,P., Lathrop,M. and Bell,J.I. (1993) Susceptibility to insulin dependent diabetes mellitus maps to a 4.1 kb segment of DNA spanning the insulin gene and associated VNTR. Nature Genet., 4, 305-310.
16. Virtaneva,K., D'Amato,E., Miao,J., Koskiniemi,M., Norio,R., Avanzini,G., Franceschetti,S., Michelucci,R., Tassinari,C.A., Omer,S., Pennacchio,L.A., Myers,R.M., Dieguez-Lucena,J.L., Krahe,R., de la Chapelle,A. and Lehesjoki,A.E (1997) Unstable minisatellite expansion causing recessively inherited myoclonus epilepsy, EPM1. Nature Genet., 15, 393-396.
17. Nakamura,Y., Koyama,K. and Matsushima,M. (1998) VNTR (variable number of tandem repeat) sequences as transcriptional, translational, or functional regulators. J. Hum. Genet., 43, 149-152.
18. Inglehearn,C.F. and Cooke,H.J. (1990) A VNTR immediately adjacent to the human pseudoautosomal telomere. Nucleic Acids Res., 18, 471-476.
19. Kondo,J., Umeda,U., Fujita,K., Sunami,T. and Takénaka,A. (2004) X-Ray analyses of d(GCGAXAGC) containing G and T at X: the base-intercalated duplex is still stable even in point mutants at the fifth residue. J. Synchrotron Rad., 11, 117-120.
20. 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. D, 60, 90-96.
21. 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·A×A·G crossing. Acta Crystallogr. D, 60, 422-431.
22. Wandergem,R. (1982) Intracellular potassium activity during liver regeneration. In McKeehan,W., Boynton,A. and Whitfield,J. (eds), Ions, Cell Proliferation and Cancer. Academic Press, New York, pp. 175-186.
23. Leslie,A.G.W. (1992) Molecular data processing. In Moras,D., Podjarny,A.D. and Thierry,J.C. (eds), Crystallography Computing 5, From Chemistry to Biology. Oxford University Press, Oxford, UK, pp. 50-61.
24. Steller,I., Bolotovsky,R. and Rossmann,M.G. (1997) An algorithm for automatic indexing of oscillation images using Fourier analysis. J. Appl. Crystallogr., 30, 1036-1040.
25. Rossmann,M.G. and van Beek,C.G. (1999) Data processing. Acta Crystallogr. D, 55, 1631-1640.
26. Powell,H.R. (1999) The Rossmann Fourier autoindexing algorithm in MOSFLM. Acta Crystallogr. D, 55, 1690-1695.
27. Pflugrath,J.W. (1999) The finer things in X-ray diffraction data collection. Acta Crystallogr. D, 55, 1718-1725.
28. Collaborative Computational Project, Number 4 (1994) The CCP4 suite: programs for protein crystallography. Acta Crystallogr. D, 50, 760-763.
29. Terwilliger,T.C. and Berendzen,J. (1999) Automated structure solution for MIR and MAD. Acta Crystallogr. D, 55, 849-861.
30. Brünger,A.T., Adams,P.D., Clore,G.M., DeLano,W.L., Gros,P. and Grosse-Kunstleve,R.W. (1998) Crystallography and NMR system: a new software suite for macromolecular structure determination. Acta Crystallogr. D, 54, 905-921.
31. Navaza,J. (1994) AMoRe: an automated package for molecular replacement. Acta Crystallogr. A, 50, 157-163.
32. 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.
33. 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. A, 47, 110-119.
34. Sayle,R.A. and Milner-White,E.J. (1995) RASMOL: biomolecular graphics for all. Trends Biochem. Sci., 20, 374.
35. Armour,J.A., Wong,Z., Wilson,V., Royle,N.J. and Jeffreys,A.J. (1989) Sequences flanking the repeat arrays of human minisatellites: association with tandem and dispersed repeat elements. Nucleic Acids Res., 17, 4925-4935.
36. Brünger,A.T. (1992) Free R value: a novel statistical quantity for assessing the accuracy of crystal structure. Nature, 355, 472-475.