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 Research

Volumn 30, Issue 23, 2002, Pages 5253-5260

  Sunami, Tomoko ^e   Kondo, Jiro ^e   Kobuna, Tomonori ^e   Hirao, Ichiro ^a,b   Watanabe, Kimitsuna ^c   Miura, Kin Ichiro ^d   Takénaka, Aiko ^e  

^a RIKEN   (Japan)

^b UNIVERSITY OF TOKYO   (Japan)

^c UNIVERSITY OF TOKYO   (Japan)

^d GAKUSHUIN UNIVERSITY   (Japan)

^e TOKYO INSTITUTE OF TECHNOLOGY   (Japan)

Author keywords

[No Author keywords available]

Indexed keywords

ADENINE; CATION; COBALT; CYTOSINE; DNA FRAGMENT; DOUBLE STRANDED RNA; GUANINE; NUCLEOTIDE; OLIGOMER; RIBOSE; TYROSINE;

BASE PAIRING; CONTROLLED STUDY; CRYSTAL STRUCTURE; CRYSTALLIZATION; DNA STRAND; DNA STRUCTURE; PRIORITY JOURNAL; PROTEIN CONFORMATION; PROTON TRANSPORT; REVIEW;

BASE PAIRING; BASE SEQUENCE; CRYSTALLOGRAPHY, X-RAY; DNA; HYDROGEN BONDING; IONS; MODELS, MOLECULAR; MOLECULAR STRUCTURE; NUCLEIC ACID CONFORMATION; NUCLEIC ACID HETERODUPLEXES;

HOMO;

EID: 0036920556     PISSN: 03051048     EISSN: None     Source Type: Journal    
DOI: 10.1093/nar/gkf639     Document Type: Review

References (55)

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 Z' DNA 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. Cruse,W.B., Egert,E., Kennard,O., Sala,G.B., Salisbury,S.A. and Viswamitra,M.A. (1983) Self base pairing in a complementary deoxydinucleoside morrophosphate duplex: crystal and molecular structure of deoxycytidylyl-(3′-5′)-deoxyguanosine. Biochemistry, 12, 1833-1839.
8. Westhof,E. and Sundaralingam,M. (1980) X-ray-structure of a cytidylyl-3Pm,5′-adenosine-proflavine complex: a self-paired parallel-chain double helical dimer with an intercalated acridine dye. Proc. Natl Acad. Sci. USA, 77, 1852-1856.
9. Robinson,H., van der Marel,G.A., van Boom,J.H. and Wang,A.H.-J. (1992) Unusual DNA conformation at low pH revealed by NMR: parallel-stranded DNA duplex with homo base pairs. Biochemistry, 31, 10510-10517.
10. Robinson,H. and Wang,A.H.-J. (1993) 5′-CGA sequence is a strong motif for homo base-paired parallel-stranded DNA duplex as revealed by NMR analysis. Proc. Natl Acad. Sci. USA, 90, 5224-5228.
11. +.C,G.G and A.A pairs. J. Mol. Biol., 242, 508-526.
12. Parvathy,V.R., Bhaumik,S.R., Chary,K.V., Govil,G., Liu,K., Howard,F.B. and Miles,H.T. (2002) NMR structure of a parallel-stranded DNA duplex at atomic resolution. Nucleic Acids Res., 30, 1500-1511.
13. Soyfer,V.N. and Potaman,V.N. (1996) Triple-helical Nucleic Acids. Springer-Verlag, New York.
14. Keniry,M.A. (2000) Quadruplex structures in nucleic acids. Biopolymers, 56, 123-146.
15. 4). Biochemistry, 33, 13540-13546.
16. Snoussi,K., Nonin-Lecomte,S. and Leroy,J.L. (2001) The RNA i-motif. J. Mol. Biol., 309, 139-153.
17. Tchurikov,N.A., Chemov,B.K., Golova,Y.B. and Nechipurenko,Y.D. (1989) Parallel DNA: generation of a duplex between two Drosophila sequences in vitro. FEBS Lett., 257, 415-418.
18. Tchurikov,N.A., Shchyolkina,A.K., Borissova,O.F. and Chernov,B.K. (1992) Southern molecular hybridization experiments with parallel complementary DNA probes. FEBS Lett., 297, 233-236.
19. Borisova,O.F., Shchyolkina,A.K., Chernov,B.K. and Tchurikov,N.A. (1993) Relative stability of AT and GC pairs in parallel DNA duplex formed by a natural sequence. FEBS Lett., 322, 304-306.
20. Tchurikov,N.A., Chistyakova,L.G., Zavilgelsky,G.B., Manukhov,I.V., Chernov,B.K. and Golova,Y.B. (2000) Gene-specific silencing by expression of parallel complementary RNA in Escherichia coli. J. Biol. Chem., 275, 26523-26529.
21. Hirao,I., Naraoka,T., Kanamori,S., Nakamura,M. and Miura,K. (1988) Synthetic oligodeoxyribonucleofides showing abnormal mobilities on polyacrylamide gel electrophoresis. Biochem. Int., 16, 157-162.
22. Hirao,I., Nishimura,Y., Naraoka,T., Watanabe,K., Arata,Y. and Miura,K. (1989) Extraordinary stable structure of short single-stranded DNA fragments containing a specific base sequence: d(GCGAAAGC). Nucleic Acids Res., 17, 2223-2231.
23. 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.
24. Hirao,I., Ishida,M., Watanabe,K. and Miura,K. (1990) Unique hairpin structures occurring at the replication origin of phage G4 DNA. Biochim. Biophys. Acta, 1087, 199-204.
25. Shepard,W., Cruse,W.B., Fourme,R., de la Fortelle,E. and Prangé,T. (1998) A zipper-like duplex in DNA: the crystal structure of d(GCGAAAGCT) at 2.1 Å resolution. Structure, 6, 849-861.
26. Sunami,T., Kondo,J., Chatake,T., Hirao,I., Watanabe,K., Miura,K. and Takénaka,A. (2001) X-ray analyses of d(GCGAAAGC) and d(GXGAAAGCT), where X=2′-deoxy-5-iodocytidine. Nucleic Acids Symp. Ser., [Suppl 1], 191-192.
27. Berger,I., Kang,C., Sinha,N., Wolters,M. and Rich,A. (1996) A highly efficient 24-condition matrix for the crystallization of nucleic acid fragments. Acta Crystallogr., D52, 465-468.
28. Leslie,A.G.W. (1992) Molecular data processing. In Moras,D., Podjarny,A.D. and Thierry,J.-C. (eds), Crystallographic Computing 5, From Chemistry to Biology. Oxford University Press, Oxford, UK, pp. 50-61.
29. 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.
30. Rossmann,M.G. and van Beek,C.G. (1999) Data processing. Acta Crystallogr., D55, 1631-1640.
31. Powell,H.R. (1999) The Rossmann Fourier autoindexing algorithm in MOSFLM. Acta Crystallogr., D55, 1690-1695.
32. Collaborative Computational Project Number 4 (1994) The CCP4 suite: programs for protein crystallography. Acta Crystallogr., D50, 760-763.
33. Terwilliger,T.C. and Berendzen,J. (1999) Automated structure solution for MIR and MAD. Acta Crystallogr., D55, 849-861.
34. 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 & NMR System: a new software suite for macromolecular structure determination. Acta Crystallogr., D54, 905-921.
35. Bansal,M., Battacharyya,D. and Ravi,B. (1995) NUPARAM and NUCGEN: software for analysis and generation of sequence dependent nucleic acid structures. Comput. Appl. Biosci., 11, 281-287.
36. 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.
37. Kraulis,P.J. (1991) MOLSCRIPT a program to produce both detailed and schematic plots of protein structures. J. Appl. Crystallogr., 24, 946-950.
38. Sayle,R.A. and Milner-White,E.J. (1995) RASMOL biomolecular graphics for all. Trends Biochem. Sci., 20, 374-376.
39. Matthews,BW. (1968) Solvent content of protein crystals. J. Mol. Biol., 33, 491-497.
40. Takénaka,A., Matsumoto,O., Chen,Y., Hasegawa,S., Chatake,T., Tsunoda,M., Ohta,T., Komatsu,Y., Koizumi,M. and Ohtsuka,E. (1995) Structural composition of hammerhead ribozymes. J. Biochem., 117, 850-855.
41. 4-methoxycytosine residue at X: a characteristic pattern of sugar puckers in the crystalline state of the Dickerson-Drew type DNA dodecamers. Biophys. Chem., 95, 69-77.
42. Langridge,R. and Rich,A. (1963) Molecular structure of helical polycytidylic acid. Nature, 198, 725-728.
43. Shibata,M., Takénaka,A. and Sasada,Y. (1985) Structure of 9-(2-hydroxyethyl)guanine. Acta Crystallogr., C41, 1501-1503.
44. Takénaka,A. and Sasada,Y. (1982) Elementary patterns in protein-nucleic acid interactions. III. Crystal structure of adenine:phtbalic acid (3:1) complex hexahydrate. Bull. Chem. Soc. Jpn, 55, 680-686.
45. Suck,D., Manor,P.C. and Saenger,W. (1976) The structure of a trinucleoside diphosphate: Adenylyl-(3′,5′)-adenylyl-(3′,5′)-adenosine hexahydrate. Acta Crystallogr., B32, 1727-1737.
46. Arora,S.K. and Larson,S.B. (1987) Structure of arprinocid [9-(2-chloro-6-fluorobenzyl)adenine], a coccidiostat. Acta Crystallogr., C43, 912-914.
47. Ohki,M., Takénaka,A., Shimanouchi,H. and Sasada,Y. (1977) 3-(9-Adenyl)propionyltryptamine monohydrate. Acta Crystallogr., B33, 2954-2956.
48. Cai,L., Chen,L., Raghavan,S., Ratliff,R., Moyzis,R. and Rich,A. (1998) Intercalated cytosine motif and novel adenine clusters in the crystal structure of the Tetrahymena telomere. Nucleic Acids Res., 26, 4696-4705.
49. Saenger,W. (1984) Principles of Nucleic Acid Structure. Springer-Verlag, New York.
50. Sunami,T., Chatake,T., Hirao,I., Yokoyama,S., Watanabe,K., Miura,K. and Takénaka,T. (1998) X-Ray analysis of a deoxy-oligonucleotide containing a stable hairpin structure. The Annual Meeting 1998 of CrSJ, Abstract, 118. Yokohama, Nov., CrSJ, Tokyo.
51. Albert,A. (1973) Ionization constants of pyrimidines and purines. In Zorbach,W.W. and Tipson,S. (eds), Synthetic Procedures in Nucleic Acid Chemistry. John Wiley & Sons, Vol. 2, pp. 1-46.
52. + base pairs can form simultaneously in a novel multistranded DNA complex. Biochemistry, 29, 828-836.
53. Breaker,R.R. and Joyce,G.F. (1994) A DNA enzyme that cleaves RNA. Chem. Biol., 1, 223-229.
54. Sioud,M. (2001) Nucleic acid enzymes as a novel generation of anti-gene agents. Curr. Mol. Med., 1, 575-588.
55. Brünger,A.T. (1992) Free R value: a novel statistical quantity for assessing the accuracy of crystal structures. Nature, 355, 472-475.