NMR studies of fully modified locked nucleic acid (LNA) hybrids: Solution structure of an LNA:RNA hybrid and characterization of an LNA:DNA hybrid

Bioconjugate Chemistry

Volumn 15, Issue 3, 2004, Pages 449-457

  Nielsen, Katrine E ^a   Rasmussen, Jill ^a   Kumar, Ravindra ^a   Wengel, Jesper ^a   Jacobsen, Jens Peter ^a   Petersen, Michael ^a  

^a UNIVERSITY OF SOUTHERN DENMARK   (Denmark)

Author keywords

[No Author keywords available]

Indexed keywords

DNA; LOCKS (FASTENERS); NUCLEAR MAGNETIC RESONANCE SPECTROSCOPY; OLIGONUCLEOTIDES;

FURANOSE RING; HELIX AXIS; HIGH-RESOLUTION STRUCTURES; HYBRID SOLUTION; LOCKED NUCLEIC ACID; NMR STUDIES; NONAMERS; NUCLEIC ACID ANALOGUES; SOLUTION STRUCTURES; STRUCTURAL CHARACTERIZATION;

RNA;

BICYCLIC NUCLEIC ACID DERIVATIVE; BICYCLO COMPOUND; COMPLEMENTARY RNA; DEOXYRIBOSE; DNA HYBRID; LOCKED NUCLEIC ACID; NUCLEIC ACID; OLIGONUCLEOTIDE; RNA; UNCLASSIFIED DRUG;

ARTICLE; CONFORMATIONAL TRANSITION; DNA RNA HYBRIDIZATION; DRUG CONFORMATION; DRUG STRUCTURE; GEOMETRY; NUCLEAR MAGNETIC RESONANCE; NUCLEAR OVERHAUSER EFFECT; NUCLEIC ACID STRUCTURE; RNA HYBRIDIZATION; STRUCTURE ANALYSIS;

EID: 2442695613     PISSN: 10431802     EISSN: None     Source Type: Journal    
DOI: 10.1021/bc034145h     Document Type: Article

References (48)

1. Freier, S. M., and Altmann, K.-H. (1997). The ups and downs of nucleic acid duplex stability: structure-stability studies on chemically modified DNA:RNA duplexes. Nucleic Acids Res. 25, 4429-4443.
2. Manoharan, M. (1999). 2′-Carbohydrate modifications in antisense oligonucleotide therapy: importance of conformation, configuration and conjugation. Biochim. Biophys. Acta 1489, 117-130.
3. Kawasaki, A. M., Casper, M. D., Freier, S. M., Lesnik, E. A., Zounes, M. C., Cummins, L. L., Gonzalez, C., and Cook, P. D. (1993). Uniformly modified 2′-deoxy-2′-fluoro phosphorothioate oligonucleotides as nuclease-resistant antisense compounds with high affinity and specificity for RNA targets. J. Med. Chem. 36, 831-841.
4. Gryaznov, S. M. (1999). Oligonucleotide N3′-P5′ phosphoramidates as potential therapeutic agents. Biochim. Biophys. Acta 1489, 131-140.
5. Hendrix, C., Rosemeyer, H., De Bouvere, B., Van Aerschot, A., Seela, F., and Herdewijn, P. (1997). 1′,5′-Anhydrohexitol oligonucleotides: hybridisation and strand displacement with oligoribonucleotides, interaction with RNase H and HIV reverse transcriptase. Chem. Eur. J. 3, 1513-1520.
6. Koshkin, A. A., Singh, S. K., Nielsen, P., Rajwanshi, V. K., Kumar, R., Meldgaard, M., Olsen, C. E., and Wengel, J. (1998). LNA (locked nucleic acids): synthesis of the adenine, cytosine, guanine, 5-methylcytosine, thymine and uracil bicyclonucleoside monomers, oligomerisation, and unprecedented nucleic acid recognition. Tetrahedron 54, 3607-3630.
7. Obika, S., Nanbu, D., Hari, Y., Andoh, J., Morio, K., Doi, T., and Imanishi, T. (1998). Stability and structural features of the duplexes containing nucleoside analogues with a fixed N-type conformation, 2′-O, 4′-C-methyleneribonucleosides. Tetrahedron Lett. 39, 5401-5404.
8. Wengel, J. (1999). Synthesis of 3′-C- and 4′-C-branched oligonucleotides and the development of locked nucleic acid (LNA). Acc. Chem. Res. 32, 301-310.
9. Petersen, M., and Wengel, J. (2003). LNA: a versatile tool for therapeutics and genomics. Trends Biotechnol. 21, 74-81.
10. Kværnø, L., Kumar, R., Dahl, B. M., Olsen, C. E., and Wengel, J. (2000). Synthesis of abasic locked nucleic acid and two seco-LNA derivatives and evaluation of their hybridization properties compared with their more flexible DNA counterparts. J. Org. Chem. 65, 5167-5176.
11. Braasch, D. A., and Corey, D. R. (2001). Locked nucleic acid (LNA): fine-tuning the recognition of DNA and RNA. Chem. Biol. 8, 1-7.
12. Bondensgaard, K., Petersen, M., Singh, S. K., Rajwanshi, V. K., Wengel, J., and Jacobsen, J. P. (2000). Structural studies of LNA:RNA duplexes by NMR: conformations and implications for RNase H activity. Chem. Eur. J. 6, 2687-2695.
13. Kurreck, J., Wyszko, E., Gillen, C., and Erdmann, V. A. (2002). Design of antisense oligonucleotides stabilized by locked nucleic acids. Nucleic Acids Res. 30, 1911-1918.
14. Koshkin, A. A., Nielsen, P., Meldgaard, M., Rajwanshi, V. K., Singh, S. K., and Wengel, J. (1998). LNA (locked nucleic acid): an RNA mimic forming exceedingly stable LNA:LNA duplexes. J. Am. Chem. Soc. 120, 13252-13253.
15. Crinelli, R., Bianchi, M., Gentilini, L., and Magnani, M. (2002). Design and characterization of decoy oligonucleotides containing locked nucleic acids. Nucleic Acids Res. 30, 2435-2443.
16. Vester, B., Lundberg, L. B., Sørensen, M. D., Babu, B. R., Douthwaite, S., and Wengel, J. (2002). LNAzymes: incorporation of LNA-type monomers into DNAzymes markedly increases RNA cleavage. J. Am. Chem. Soc 124, 13682-13683.
17. Ørum, H., Jakobsen, M. H., Koch, T., Vuust, J., and Borre, M. (1999). Detection of the factor V Leiden mutation by direct allele-specific hybridization of PCR amplicons to photoimmobilized locked nucleic acids. Clin. Chem. 45, 1898-1905.
18. Simeonov, A., and Nikiforov, T. T. (2002). Single nucleotide polymorphism genotyping using short, fluorescently labeled locked nucleic acid (LNA) probes and fluorescence polarization detection. Nucleic Acids Res. 30, e91.
19. Petersen, M., Bondensgaard, K., Wengel, J., and Jacobsen, J. P. (2002). Locked nucleic acid (LNA) recognition of RNA: NMR solution structures of LNA: RNA hybrids. J. Am. Chem. Soc. 124, 5974-5982.
20. Singh, S. K., Nielsen, P., Koshkin, A. A., and Wengel, J. (1998). LNA (locked nucleic acids): synthesis and high-affinity nucleic acid recognition. Chem. Commun. 455-456.
21. Geen, H., and Freeman, R. (1991). Band-selective radiofrequency pulses. J. Magn. Reson. 93, 93-141.
22. Güntert, P., and Wüthrich, K. (1992). FLATT - a new procedure for high-quality baseline correction of multidimensional NMR spectra. J. Magn. Reson. 96, 403-407.
23. Wijmenga, S. S., and van Buuren, B. N. M. (1998). The use of NMR methods for conformational studies of nucleic acids. Prog. Nucl. Magn. Reson. Spectrosc. 32, 287-387.
24. Saenger, W. (1984) Principles of Nucleic Acid Structure, Springer-Verlag, New York.
25. Case, D. A., Pearlman, D. A., Caldwell, J. W., Cheatham, T. E., III., Ross, W. S., Simmerling, C. L., Darden, T. A., Merz, K. M., Stanton, R. V., Cheng, A. L., Vincent, J. J., Crowley, M., Tsui, V., Radmer, R. J., Duan, Y., Pitera, J., Massura, I., Seibel, G. L., Singh, U. C., Weiner, P., and Kollman, P. A. (2000) AMBER 6 University of California, San Francisco.
26. Bayly, C. I., Cieplak, P., Cornell, W. D., and Kollman, P. A. (1993). A well-behaved electrostatic potential based method using charge restraints for deriving atomic charges: the RESP model. J. Phys. Chem. 97, 10269-10280.
27. Macaya, R. F., Schultze, P., and Feigon, J. (1992). Sugar conformation in intramolecular DNA triplexes determined by coupling constants obtained by automated simulation of P.COSY cross-peaks. J. Am. Chem. Soc. 114, 781-783.
28. de Leeuw, F. A. A. M., and Altona, C. (1983). Computer-assisted pseudorotation analysis of five-membered rings by means of proton spin-spin coupling constants: program PSEUROT. J. Comput. Chem. 4, 428-437.
29. Woody, R. W. (1995). Circular dichroism. Methods Enzymol. 34-71.
30. Baase, W. A., and Johnson, W. C. (1979). Circular dichroism and DNA secondary structure. Nucleic Acids Res. 6, 797-814.
31. Hare, D. R., Wemmer, D. E., Chou, S.-H., Drobny, G., and Reid, B. R. (1983). Assignment of the nonexchangeable proton resonances of d(C-G-C-G-A-A-T-T-C-G-C-G) using two-dimensional nuclear magnetic resonance methods. J. Mol. Biol. 171, 319-336.
32. 2. Biochemistry 22, 5943-5951.
33. 1H NMR spectra by two-dimensional NOE spectroscopy. J. Am. Chem. Soc. 105, 2914-2916.
34. Wüthrich, K. (1986) NMR of Proteins and Nucleic Acids, John Wiley & Sons, New York.
35. Lavery, R., and Sklenar, H. (1988). The definition of generalized helicoidal parameters and of axis curvature of irregular nucleic acids. J. Biomol. Struct. Dyn. 6, 63-91.
36. Lavery, R., and Sklenar, H. (1989). Defining the structure of irregular nucleic acids: conventions and principles. J. Biomol. Struct. Dyn. 7, 655-667.
37. Jensen, G. A., Singh, S. K., Kumar, R., Wengel, J., and Jacobsen, J. P. (2001). A comparison of the solution structures of an LNA:DNA duplex and the unmodified DNA:DNA duplex. J. Chem. Soc., Perkin Trans. 2 1224-1232.
38. Petersen, M., Nielsen, C. B., Nielsen, K. E., Jensen, G. A., Bondensgaard, K., Singh, S. K., Rajwanshi, V. K., Koshkin, A. A., Dahl, B. M., Wengel, J., and Jacobsen, J. P. (2000). The conformations of locked nucleic acids (LNA). J. Mol. Recognit. 13, 44-53.
39. Gonzáles, C., Stec, W., Reynolds, M., and James, T. L. (1995). Structure and dynamics of a DNA. RNA hybrid duplex with a chiral phosphorothioate moiety: NMR and molecular dynamics with conventional and time-averaged restraints. Biochemistry 34, 4969-4982.
40. Bachelin, M., Hessler, G., Kurz, G., Hacia, J. G., Dervan, P. B., and Kessler, H. (1998). Structure of a stereoselective phosphorothioate DNA/RNA duplex. Nat. Struct. Biol. 5, 271-276.
41. Gyi, J. I., Lane, A. N., Conn, G. L., and Brown, T. (1998). Solution structures of DNA:RNA hybrids with purine-rich and pyrimidine-rich strands: comparison with the homologues DNA and RNA duplexes. Biochemistry 37, 73-80.
42. Aramini, J. M., and Germann, M. W. (1999). Solution structure of a DNA·RNA hybrid containing an α-anomeric thymidine and polarity reversals: d(ATGG-3′-3′-aT-5′-5′-GCTC)· r(gagcaccau). Biochemistry 38, 15448-15458.
43. Fedoroff, O. Y., Salazar, M., and Reid, B. R. (1993). Structure of a DNA: RNA hybrid duplex. Why RNase H does not cleave pure DNA. J. Mol. Biol. 233, 509-523.
44. Fedoroff, O. Y., Ge, Y., and Reid, B. R. (1997). Solution structure of r(gaggacug):d(CAGTCCTC) hybrid: implications for the initiation of HIV-1 (+)-strand synthesis. J. Mol. Biol. 269, 225-239.
45. Cheatham, T. E., III., and Kollman, P. A. (1997). Molecular dynamics simulations highlight the structural differences among DNA:DNA, RNA:RNA, and DNA:RNA hybrid duplexes. J. Am. Chem. Soc. 119, 4805-4825.
46. Denisov, A. Y., Noronha, A. M., Wilds, C. J., Trempe, J.-F., Pon, R. T., Gehring, K., and Damha, M. J. (2001). Solution structure of an arabinonucleic acid (ANA)/RNA duplex in a chimeric hairpin: comparison with 2′-fluor-ANA/RNA and DNA/RNA hybrids. Nucleic Acids Res. 29, 4284-4293.
47. Brameld, K. A., and Goddard, W. A., III. (1999). Ab initio quantum mechanical study of the structure and energies for the pseudorotation of 5′-dehydroxy analogues of 2′-deoxyribose and ribose sugars. J. Am. Chem. Soc. 121, 985-993.
48. Sørensen, M. D., Kværnø, L., Bryld, T., Håkansson, A. E., Verbeure, B., Gaubert, G., Herdewijn, P., and Wengel, J. (2002). α-L-ribo-Configured locked nucleic acid (α-L-LNA): synthesis and properties. J. Am. Chem. Soc. 124, 2164-2176.