LNA (Locked Nucleic Acid): High-affinity targeting of complementary RNA and DNA

Biochemistry

Volumn 43, Issue 42, 2004, Pages 13233-13241

  Vester, Birte ^a   Wengel, Jesper ^a  

^a UNIVERSITY OF SOUTHERN DENMARK   (Denmark)

Author keywords

[No Author keywords available]

Indexed keywords

DIAGNOSIS; DNA; MONOMERS; OLIGOMERS; RESEARCH; SUGARS;

HYBRIDIZATION AFFINITY; LOCKED NUCLEIC ACID (LNA); MIMICKING SUGAR CONFORMATION; OLIGONUCLEOTIDES;

RNA;

CARBOHYDRATE DERIVATIVE; COMPLEMENTARY DNA; COMPLEMENTARY RNA; DOUBLE STRANDED DNA; FURANOSE; LOCKED NUCLEIC ACID; MONOMER; NUCLEIC ACID; OLIGONUCLEOTIDE; SINGLE STRANDED DNA; UNCLASSIFIED DRUG;

ARTICLE; BINDING AFFINITY; CONFORMATION; GENE SILENCING; GENE STRUCTURE; GENE TARGETING; HYBRIDIZATION; MEDICAL RESEARCH; PRIORITY JOURNAL;

EID: 6344277190     PISSN: 00062960     EISSN: None     Source Type: Journal    
DOI: 10.1021/bi0485732     Document Type: Article

References (58)

1. Petersen, M., and Wengel, J. (2003) LNA: a versatile tool for therapeutics and genomics, Trends Biotechnol. 21, 74-81.
2. Jepsen, J. S., and Wengel, J. (2004) Locked Nucleic Acid: a potent nucleic acid analogue in therapeutics and biotechnology, Curr. Opin. Drug Discovery Dev. 7, 188-194.
3. 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. 4, 455-456.
4. 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.
5. Obika, S., Nanbu, D., Hari, Y., Morio, K., In, Y., Ishida, T., and Imanishi, T. (1997) Synthesis of 2′-O,4′-C-methyleneuridine and -cytidine novel bicyclic nucleosides having a fixed C3′-endo sugar puckering, Tetrahedron Lett. 38, 8735-8738.
6. 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.
7. Sørensen, M. D., Kvaernø, 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.
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. Kumar, R., Singh, S. K., Koshkin, A. A., Rajwanshi, V. K., Meldgaard, M., and Wengel, J. (1998) The first analogues of LNA (locked nucleic acids): Phosphorothioate-LNA and 2′-thio-LNA, Biorg. Med. Chem. Lett. 8, 2219-2222.
10. McTigue, P. M., Peterson, R. J., and Kahn, J. D. (2004) Sequence-dependent thermodynamic parameters for locked nucleic acid (LNA)-DNA duplex formation, Biochemistry 43, 5388-5405.
11. 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.
12. Nielsen, K. E., Rasmussen, J., Kumar, R., Wengel, J., Jacobsen, J. P., and Petersen, M. (2004) 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 Chem. 15, 449-457.
13. 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.
14. Nielsen, K. M. E., Petersen, M., Håkansson, A. E., Wengel, J., and Jacobsen, J. P. (2002) α-L-LNA (α-L-ribo Configured Locked Nucleic Acid) Recognition of DNA: An NMR Spectroscopic Study, Chem. - Eur. J. 8, 3001-3009.
15. Nielsen, J. T., Stein, P. C., and Petersen, M. (2003) NMR structure of an α-L-LNA:RNA hybrid: structural implications for RNase H recognition, Nucleic Acids Res. 31, 5858-5867.
16. 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.
17. Wahlestedt, C., Salmi, P., Good, L., Kela, J., Johnsson, T., Hökfelt, T., Broberger, C., Porreca, F., Lai, J., Ren, K., Ossipov, M., Koshkin, A., Jakobsen, N., Skouv, J., Oerum, H., Jacobsen, M. H., and Wengel, J. (2000) Potent and nontoxic antisense oligonucleotides containing locked nucleic acids, Proc. Natl. Acad. Sci. U.S.A. 97, 5633-5638.
18. 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.
19. Frieden, M., Christensen, S. M., Mikkelsen, N. D., Rosenbohm, C., Thrue, C. A., Westergaard, M., Hansen, H. F., Orum, H., and Koch, T. (2003) Expanding the design horizon of antisense oligonucleotides with α-L-LNA, Nucleic Acids Res. 31, 6365-6372.
20. Frieden, M., Hansen, H. F., and Koch, T. (2003) Nuclease stability of LNA oligonucleotides and LNA-DNA chimeras, Nucleosides, Nucleotides Nucleic Acids 22, 1041-1043.
21. Morita, K., Hasegawa, C., Kaneko, M., Tsutsumi, S., Sone, J., Ishikawa, T., Imanishi, T., and Koizumia, M. (2002) 2′-O,4′-C-Ethylene-Bridged Nucleic Acids (ENA): Highly Nuclease-Resistant and Thermodynamically Stable Oligonucleotides for Antisense Drug, Bioorg. Med. Chem. Lett. 12, 73-76.
22. Lauritsen, A., Dahl, B. M., Dahl, O., Vester, B., and Wengel, J. (2003) Methylphosphonate LNA: a locked nucleic acid with a methylphosphonate linkage, Bioorg. Med. Chem. Lett. 13, 253-256.
23. 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.
24. Di Giusto, D. A., and King, G. C. (2004) Strong positional preference in the interaction of LNA oligonucleotides with DNA polymerase and proofreading exonuclease activities: implications for genotyping assays, Nucleic Acids Res. 32, e32.
25. Santoro, S. W., and Joyce, G. F. (1997) A general purpose RNA-cleaving DNA enzyme, Proc. Natl. Acad. Sci. U.S.A. 94, 4262-4266.
26. 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.
27. Schubert, S., Gul, D. C., Grunert, H. P., Zeichhardt, H., Erdmann, V. A., and Kurreck, J. (2003) RNA cleaving "10-23" DNAzymes with enhanced stability and activity, Nucleic Acids Res. 31, 5982-5992.
28. Schubert, S., Fürste, J. P., Werk, D., Grunert, H.-P., Zeichhardt, H., Erdmann, V. A., and Kurreck, J. (2004) Gaining target access for deoxyribozymes, J. Mol. Biol. 339, 355-363.
29. Fahmy, R. G., and Khachigian, L. M. (2004) Locked nucleic acid modified DNA enzymes targeting early growth response-1 inhibit human vascular smooth muscle cell growth, Nucleic Acids Res. 52, 2281-2285.
30. Khachigian, L. M., Fahmy, R. G., Zhang, G., Bobryshev, Y. V., and Kaniaros, A. (2002) c-Jun regulates vascular smooth muscle cell growth and neointima formation after arterial injury. Inhibition by a novel DNA enzyme targeting c-Jun, J. Biol. Chem. 277, 22985-22991.
31. Fluiter, K., ten Asbroek, L. M. A., de Wissel, M. B., Jakobs, M. E., Wissenbach, M., Olsson, H., Olsen, O., Ørum, H., and Baas, F. (2003) In vivo tumor growth inhibition and biodistribution studies of locked nucleic acid (LNA) antisense oligonucleotides, Nucleic Acids Res. 31, 953-962.
32. Obika, S., Hemamayi, R., Masuda, T., Sugimoto, T., Nakagawa, S., Mayumi, T., and Imanishi, T. (2001) Inhibition of ICAM-1 gene expression by antisense 2′,4′-BNA oligonucleotides, Nucleic Acids Res. Suppl., 145-146.
33. Hansen, J. B., Westergaard, M., Thrue, C. A., Giwercman, B., and Oerum, H. (2003) Antisense knockdown of PKC-α using LNA-oligos, Nucleosides, Nucleotides Nucleic Acids 22, 1607-1609.
34. Elayadi, A. N., Braasch, D. A., and Corey, D. R. (2002) Implications of high-affinity hybridization by locked nucleic acid oligomers for inhibition of human telomerase, Biochemistry 41, 9973-9981.
35. Childs, J. L., Disney, M. D., and Turner, D. H. (2002) Oligonucleotide directed misfolding of RNA inhibits Candida albicans group I intron splicing, Proc. Natl. Acad. Sci. U.S.A. 99, 11091-11096.
36. Ittig, D., Liu, S., Renneberg, D., Schumperli, D., and Leumann, C. J. (2004) Nuclear antisense effects in cyclophilin A pre-mRNA splicing by oligonucleotides: a comparison of tricyclo-DNA with LNA, Nucleic Acids Res. 32, 346-353.
37. Grünweller, A., Wyszko, E., Bieber, B., Jahnel, R., Erdmann, V. A., and Kurreck, J. (2003) Comparison of different antisense strategies in mammalian cells using locked nucleic acids, 2′-O-methyl RNA, phosphorothioates and small interfering RNA, Nucleic Acids Res. 31, 3185-3193.
38. Braasch, D. A., Jensen, S., Liu, Y., Kaur, K., Arar, K., White, M. A., and Corey, D. R. (2003) RNA interference in mammalian cells by chemically-modified RNA, Biochemistry 42, 7967-7975.
39. Schwarz, D. S., Hutvágner, G., Du, T., Xu, Z., Aronin, N., and Zamore, P. D. (2003) Asymmetry in the Assembly of the RNAi Enzyme Complex, Cell 115, 199-208.
40. Arzumanov, A., Stetsenko, D. A., Malakhov, A. D., Reichelt, S., Sorensen, M. D., Babu, B. R., Wengel, J., and Gait, M. J. (2003) A structure-activity study of the inhibition of HIV-1 Tatdependent trans-activation by mixmer 2′-O-methyl oligoribonucleotides containing locked nucleic acid (LNA), α-L-LNA, or 2′-thio-LNA residues, Oligonucleotides 13, 435-453.
41. Buchini, S., and Leumann, C. J. (2003) Recent improvements in antigene technology, Curr. Opin. Chem. Biol. 7, 717-726.
42. Obika, S., Hari, Y., Sugimoto, T., Sekiguchi, M., and Imanishi, T. (2000) Triplex-forming enhancement with high sequence selectivity by single 2′-O,4′-C-methylene bridged nucleic acid (2′,4′-BNA) modification, Tetrahedron Lett. 41, 8923-8927.
43. Obika, S., Uneda, T., Sugimoto, T., Nanbu, D., Minami, T., Doi, T., and Imanishi, T. (2001) 2′-O,4′-C-Methylene bridged nucleic acid (2′,4′-BNA): synthesis and triplex-forming properties, Bioorg. Med. Chem. 9, 1001-1011.
44. Sun, B. W., Babu, B. R., Sørensen, M. D., Zakrzewska, K., Wengel, J., and Sun, J. S. (2004) Sequence and pH effects of LNA-containing triple helix-forming oligonucleotides: physical chemistry, biochemistry, and modeling studies, Biochemistry 43, 4160-4169.
45. Goni, J. R., de la Cruz, X., and Orozco, M. (2004) Triplex-forming oligonucleotide target sequences in the human genome, Nucleic Acids Res. 32, 354-360.
46. Hertoghs, K. M., Ellis, J. H., and Catchpole, I. R. (2003) Use of locked nucleic acid oligonucleotides to add functionality to plasmid DNA, Nucleic Acids Res. 31, 5817-5830.
47. Mouritzen, P., Nielsen, A. T., Pfundheller, H. M., Choleva, Y., Kongsbak, L., and Møller, S. (2003) Single nucleotide polymorphism genotyping using locked nucleic acid (LNA), Expert Rev. Mol. Diagn. 3, 27-38.
48. Jacobsen, N., Bentzen, J., Meldgaard, M., Jakobsen, M. H., Fenger, M., Kauppinen, S., and Skouv, J. (2002) LNA-enhanced detection of single nucleotide polymorphisms in the apolipoprotein E, Nucleic Acids Res. 30, e100.
49. Jacobsen, N., Fenger, M., Bentzen, J., Rasmussen, S. L., Jakobsen, M. H., Fenstholt, J., and Skouv, J. (2002) Genotyping of the apolipoprotein B R3500Q mutation using immobilized locked nucleic acid capture probes, Clin. Chem. 48, 657-660.
50. OØrum, H., Jakobsen, M. H., Koch, T., Vuust, J., and Borre, M. B. (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.
51. Ugozzoli, L. A., Latorra, D., Pucket, R., Arar, K., and Hamby, K. (2004) Real-time genotyping with oligonucleotide probes containing locked nucleic acids, Anal. Biochem. 324, 143-152.
52. Letertre, C., Perelle, S., Dilasser, F., Arar, K., and Fach, P. (2003) Evaluation of the performance of LNA and MGB probes in 5′-nuclease PCR assays, Mol. Cell Probes 17, 307-311.
53. + RNA from 4 M guanidine thiocyanate-lysed cell extracts using locked nucleic acid-oligo(T) capture, Nucleic Acids Res. 32, e64.
54. Tolstrup, N., Nielsen, P. S., Kolberg, J. G., Frankel, A. M., Vissing, H., and Kauppinen, S. (2003) OligoDesign: Optimal design of LNA (locked nucleic acid) oligonucleotide capture probes for gene expression profiling, Nucleic Acids Res. 31, 3758-3762.
55. Silahtaroglu, A. N., Tommerup, N., and Vissing, H. (2003) FISHing with locked nucleic acids (LNA): evaluation of different LNA/DNA mixmers, Mol. Cell Probes 17, 165-169.
56. Sørensen, M. D., Petersen, M., and Wengel, J. (2003) Functionalized LNA (locked nucleic acid): high-affinity hybridization of oligonucleotides containing N-acylated and N-alkylated 2′-amino-LNA monomers, Chem. Commun. 17, 2130-2131.
57. Dominick, P. K., and Jarstfer, M. B. (2004) A Conformationally Constrained Nucleotide Analogue Controls the Folding Topology of a DNA G-Quadruplex, J. Am. Chem. Soc. 126, 5050-5051.
58. Benenson, Y., Gil, B., Ben-Dor, U., Adar, R., and Shapiro, E. (2004) An autonomous molecular computer for logical control of gene expression, Nature 429, 423-429.