Difference in conformational diversity between nucleic acids with a six-membered 'sugar' unit and natural 'furanose' nucleic acids

Nucleic Acids Research

Volumn 31, Issue 12, 2003, Pages 2975-2989

  Lescrinier, Eveline ^a   Froeyen, Matheus ^a   Herdewijn, Piet ^a  

^a REGA INSTITUTE FOR MEDICAL RESEARCH   (Belgium)

Author keywords

[No Author keywords available]

Indexed keywords

DNA A; DNA B; DNA Z; DOUBLE STRANDED DNA; DOUBLE STRANDED RNA; NUCLEIC ACID; OLIGONUCLEOTIDE; PHOSPHATE; SUGAR; ALPHA HOMO DNA; ALPHA-HOMO-DNA; DNA; HEXOSE; RIBOSE; RNA; SUGAR ALCOHOL;

ARTICLE; BASE PAIRING; CHEMICAL STRUCTURE; CONTROLLED STUDY; CRYSTALLOGRAPHY; DNA CONFORMATION; DNA HELIX; DNA RESTRICTION; DNA RNA HYBRIDIZATION; DNA SEQUENCE; GEOMETRY; MOLECULAR RECOGNITION; NUCLEAR MAGNETIC RESONANCE SPECTROSCOPY; NUCLEIC ACID STRUCTURE; PRIORITY JOURNAL; RNA CONFORMATION; CHEMISTRY; CONFORMATION;

BASE PAIRING; DNA; HEXOSES; MODELS, MOLECULAR; MOLECULAR STRUCTURE; NUCLEIC ACID CONFORMATION; NUCLEIC ACIDS; OLIGONUCLEOTIDES; PHOSPHATES; RIBOSE; RNA; RNA, DOUBLE-STRANDED; SUGAR ALCOHOLS;

EID: 0038239273     PISSN: 03051048     EISSN: None     Source Type: Journal    
DOI: 10.1093/nar/gkg407     Document Type: Article

References (43)

1. Arnott,S. (1999) Polynucleotide secondary structures: an historical perspective. In Neidle,S. (ed.), Oxford Handbook of Nucleic Acid Structure. Oxford University Press, pp. 1-38.
2. Blackburn,G.M. and Gait,M.J. (1996) DNA and RNA structure. In Blackburn,G.M. and Gait,M.J. (eds), Nucleic Acids in Chemistry and Biology. Oxford University Press, pp. 28-39.
3. Wahl,M.C. and Sundaralingam,M. (1999) A-DNA duplexes in the crystal. In Neidle,S. (ed.), Oxford Handbook of Nucleic Acid Structure. Oxford University Press, pp. 117-144.
4. Eschenmoser,A. and Dobler,M. (1992) ) Warum Pentose- und nicht Hexose-Nucleinsauren? Teil I) Einleitung und Problemstellung, Konformationsanalyse fur Oligonucleotid-Ketten aus 2′,3′-Dideoxyglucopyranosyl-Bausteinen ('Homo-DNS') sowie Betrachtungen zur Konformation von A- und B-DNS. Helv. Chim. Acta, 75, 218-259.
5. Lavery,R. and Zakrzewska,K. (1999) Base and base pair morphologies, helical parameters and definitions. In Neidle,S. (ed.), Oxford Handbook of Nucleic Acid Structure. Oxford University Press, pp. 39-76.
6. Federoff,O.Y., Salazar,M. and Reid,B.R. (1993) Structure of a DNA:RNA hybrid: why RNase H does not cleave pure RNA. J. Mol. Biol., 233, 509-523.
7. Gonzales,C., Stec,W., Reynolds,M.A. and James,T.L. (1995) Structure and dynamics of a DNA-RNA hybrid duplex with a chiral phosphorothioate moiety: NMR and MD with conventional and time-averaged restraints. Biochemistry, 34, 4969-4982.
8. Saenger,W. (1984) Principles of Nucleic Acid Structure. Springer-Verlag, New York.
9. vanDam,L. and Levitt,M.H. (2000) BII nucleotides in the B and C forms of natural-sequence polymeric DNA: a new model for the C form of DNA. J. Mol. Biol., 304, 541-561.
10. Lavery,R. and Sklenar H.J. (1988) The definition of generalized helicoidal parameters and of axis curvature for irregular nucleic acids. J. Biomol. Struct. Dyn., 6, 63-91.
11. Lancelot,G., Guesnet,J.L. and Vovelle,F. (1989) Solution structure of the parallel-stranded duplex oligonucleotide α-d(TCTAAAC)-β-d(AGATTTG) via complete relaxation matrix analysis of the NOE effects and molecular mechanics calculations. Biochemistry, 28, 7871-7878.
12. Arnott,S., Chandrasekaran,R., Hukins,D.W.L., Smith,P.J.C. and Watts,L. (1974) Structural details of a double-helix observed for DNAs containing alternating purine and pyrimidine sequences. J. Mol. Biol., 88, 523-533.
13. Froeyen,M., Lescrinier,E., Kerremans,L., Rosemeyer,H., Seela,F., Verbeure,B., Lagoja,I., Rozenski,J., Van Aerschot,A., Busson,R. and Herdewijn,P. (2001) α-HOMO-DNA and RNA form a parallel oriented non-A, non-B-type double helical structure. Chem. Eur. J., 7, 5183-5194.
14. Otting,G., Billeter,M., Wuthrich,K., Roth,H.J., Leumann,C. and Eschenmoser,A. (1993) Warum Pentose- und nicht Hexose-Nucleinsauren? IV) 'Homo-DNS': 1H-, 13C, 31P-, und 15N-NMR-spektroskopische Untersuchung von ddG1c(AAAAATTTTT) in wassriger Losung. Helv. Chim. Acta, 76, 2701-2756.
15. Groebke,K., Hunziker,J., Fraser,W., Peng,L., Diederichsen,U., Zimmermann,K., Holzner,A., Leumann,C. and Eschenmoser,A. (1988) Warum Pentose- und nicht Hexose-Nucleinesauren? Teil V (Purin-Purin)-Basenpaarung in der homo-DNS-Reihe: Guanin, Isoguanin, 2,6-Diaminopurin and Xanthin. Helv. Chim. Acta, 81, 375-474.
16. Wippo,H., Reck,F., Kudick,R., Ramaseshan,M., Ceulemans,G., Bolli,M., Krishnamurthy,R. and Eschenmoser,A. (2001) Pentopyranosyl oligonucleotide systems. Part 11: systems with shortened backbones: (D)-β-ribopyranosyl-(4′→3′)- and (L)-α-lyxopyranosyl-(4′→3′)-oligonucleotides. Bioorg. Med. Chem., 9, 2411-2428.
17. Kerremans,L., Schepers,G., Rozenski,J., Buson,R., Van Aerschot,A. and Herdewijn,P. (2001) Hybridization between 'six-membered' nucleic acids: RNA as a universal information system. Org. Lett., 3, 4129-4132.
18. Lescrinier,E., Esnouf,R., Schraml,J., Busson,R., Heus,H.A., Hilbers,C.W. and Herdewijn,P. (2000) Solution structure of a HNA-RNA hybrid. Chem. Biol., 7, 719-731.
19. Froeyen,M., Wroblowski,B., Esnouf,R., De Winter,H., Allart,B., Lescrinier,E. and Herdewijn,P. (2000) Molecular-dynamics studies of single-stranded hexitol, altritol, mannitol and ribose nucleic acids (HNA, MNA, ANA and RNA, resp.) and of the stability of HNARNA, ANARNA and MNARNA duplexes. Helv. Chim. Acta, 83, 2153-2182.
20. Declercq,R., Van Aerschot,A., Read,R.J., Herdewijn,P. and Van Meervelt,L. (2001) Crystal structure of double helical hexitol nucleic acids. J. Am. Chem. Soc., 124, 928-933.
21. Lescrinier,E., Esnouf,R.M., Schraml,J., Busson,R. and Herdewijn,P. (2000) Solution structure of a hexitol nucleic acid duplex with four consecutive T·T base pairs. Helv. Chim. Acta, 83, 1291-1310.
22. Pitsch,S., Krishnamurthy,R., Bolli,M., Wendeborn,S., Holzner,A., Minton,M., Lesueur,C., Schlonvogt,I., Jaun,B. and Eschenmoser,A. (1995) Pyranosyl-RNA ('p-RNA'): base-pairing selectivity and potential to replicate. Helv. Chim. Acta, 78, 1621-1635.
23. Schlonvogt,I., Pitsch,S., Lesueur,C., Eschenmoser,A. and Jaun,B. (1996) 188. Pyranosyl-RNA ('p-RNA'): NMR and MD study of the duplex formed by self-pairing of ribopyranosyl-(C-G-A-A-T-T-C-G). Helv. Chim. Acta, 79, 2316-2345.
24. Micura,R., Kudick,R., Pitch,S. and Eschenmoser,A. (1999) Opposite orientation of backbone inclination in pyranosyl-RNA and homo-DNA correlates with opposite directionallity of duplex properties. Angew. Chem. Int. Ed., 38, 680-683.
25. Pitsch,S., Wendeborn,S., Jaun,B. and Eschenmoser,A. (1993) Why pentose- and not hexose-nucleic acids? Part VII. Pyranosyl-RNA ('p'-RNA). Helv. Chim. Acta, 76, 2161-2183.
26. Reck,F., Wippo,H., Kudick,R., Krishnamurthy,R. and Eschenmoser,A. (2001) Pentopyranosyl oligonucleotide systems. The α-L-lyxopyranosyl-(4′→2′)-oligonucleotide system. Helv. Chim. Acta, 84, 1778-1804.
27. Wagner,T., Huynh,H.K., Krishnamurthy,R. and Eschenmoser,A. (2002) Pentopyranosyl oligonucleotide systems. The β-D-xylopyranosyl-(4′→2′)-oligonucleotide system. Helv. Chim. Acta, 85, 399-416.
28. Ebert,M.O., Luther,A., Huynh,H.K., Krishnamurthy,R., Eschenmoser,A. and Jaun,B. (2002) NMR solution structure of the duplex formed by self-pairing of L-α-arabinopyranosyl-(4′→2′)-(C-G-A-A-T-T-C-G). Helv. Chim. Acta, 85, 4055-4073.
29. Herdewijn,P. (2001) TNA as a potential alternative to natural nucleic acids. Angew. Chem. Int. Ed., 40, 2249-2251.
30. Kozlov,I.A., Politis P.K., Van Aerschot,A., Busson,R., Herdewijn,P. and Orgel,L.E. (1999) Nonenzymatic synthesis of RNA and DNA oligomers on hexitol nucleic acid templates: the importance of A structure. J. Am. Chem. Soc., 121, 2653-2656.
31. Maurinsh,Y., Rosenmeyer,H., Esnouf,R., Medvedovici,A., Wang,J., Ceulemans,G., Lescrinier,E., Hendrix,C., Busson,R., Sandra,P., Seela,F., Van Aerschot,A. and Herdewijn,P. (1999) Synthesis and pairing properties of oligonucleotides containing 3-hydroxy-4-hydroxymethyl-1-cyclohexanyl nucleosides. Chem. Eur. J., 5, 2139-2150.
32. Wang,J., Verbeure,B., Luyten,I., Lescrinier,E., Froeyen,M., Hendrix,C., Rosemeyer,H., Seela,F., Van Aerschot,A. and Herdewijn,P. (2002) Cyclohexene nucleic acids (CeNA): serum stable oligonucleotides that activate RNase H and increase duplex stability with complementary RNA. J. Am. Chem. Soc., 122, 8595-8602.
33. Roberts,C., Bandaru,R. and Switzer,C. (1997) Theoretical and experimental study of isoguanine and isocytosine: base pairing in an expanded genetic system. J. Am. Chem. Soc., 119, 4640-4649.
34. Lehn,J.M. (2002) Towards complex matter: supramolecular chemistry and self-organization. Proc. Natl Acad. Sci. USA, 99, 4763-4768.
35. Weiner,P., Kollman,P.A., Nguyen,D.T. and Case,D.A. (1986) An all atom force field for simulations of proteins and nucleic acids. J. Comp. Chem., 7, 230-252.
36. Wang,J., Cieplak,P. and Kollman,P.A. (2000) How well does a restrained electrostatic potential (RESP) model perform in calculating conformational energies of organic and biological molecules? J. Comp. Chem., 21, 1049-1074.
37. Schmidt,M.W., Baldridge,K.K., Boatz,J.A., Elbert,S.T., Gordon,M.S., Jensen,J.H., Koseki,S., Matsunaga,N., Nguyen,K.A., Su,S., Windus,T.L., Dupuis,M. and Montgomery,M.A. (1993) General atomic and molecular electronic structure system. J. Comp. Chem., 14, 1347-1363.
38. Cieplak,P., Cornell,W.D., Bayly,C.I. and Kollman,P.A. (1995) Application of the multimolecule and multiconformational RESP methodology to biopolymers: charge derivation for DNA, RNA and protein. J. Comp. Chem., 16, 1357-1377.
39. Zhang,X.J. and Matthews,B.W. (1995) EDPDB: a multifunctional tool for protein structure analysis. J. Appl. Crystallogr., 28, 624-630.
40. Bohringer,M., Roth,H.J., Hunziker,J., Gobel,M., Krishnan,R., Giger,A., Schweizer,B., Schreiber,J., Leumann,C. and Eschenmoser,A. (1992) Warum Pentose- und nicht Hexose-Nucleinsauren? Teil II) Oligonucleotide aus 2′,3′-Dideoxy-β-D-glucopyranosyl-Bausteinen ('Homo-DNS' ): Herstellung. Helv. Chim. Acta, 75, 1416-1477.
41. Heisterberg,D.J. (1991) Quatfit program in CCL software archives, the Ohio Supercomputer Center Columbus, Ohio 43212, http://www.ccl.net/
42. Kraulis,P.J. (1991) MOLSCRIPT: a program to produce both detailed and schematic plots of protein structure. J. Appl. Crystallogr., 24, 946-950.
43. Esnouf,R.M. (1999) Further additions to Molscript 1.4, including reading and contouring of electron-density maps. Acta Crystallogr. D, 55, 938-940.