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Chemistry of locked nucleic acids (LNA): Design, synthesis, and bio-physical properties

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Abstract

Preparation of LNA nucleosides requires a number of synthetic steps but very efficient procedures have been developed, as have protocols for synthesis of LNA oligonucleotides on automated DNA synthesizers. In all cases, LNA oligonucleotides have exhibited good aqueous solubility as would be expected from their close structural resemblance to the natural nucleic acids. The universality of LNA mediated high-affinity and specific hybridization has been demonstrated extensively with a large number of duplex forming LNA-oligonucleotides. Most importantly, most of the members of the LNA molecular family have been shown to exert their substantial affinity increase (i) in combination with standard DNA, RNA and contemporary analogues and (ii) whether inserted as single nucleosides in an oligonucleotide or as blocks of contiguous nucleotides, an important point. The works on TFO's is expanding the usefulness of LNA to double strand recognition and it has been demonstrated that LNA it is a promising structure for further base modifications in the pursuit of global sequence specific recognition of DNA.

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References

  1. De Mesmaeker, A., Häner, R. and Moser, H.E., Acc. Chem. Res., 28 (1995) 366.

    Article  CAS  Google Scholar 

  2. Beaucage, S.L. and Iver, R.P., Tetrahedron, 49 (1993) 6123.

    CAS  Google Scholar 

  3. Herdewijn, P., Liebigs Ann., (1996) 1337.

  4. Freier, S.M. and Altmann, K.-H., Nucl. Acid Res., 25 (1997) 4429.

    CAS  Google Scholar 

  5. Ullmann, E., Opin. Drug. Discovery Dev., 3 (2000) 203.

    Google Scholar 

  6. Meldgaard, M. and Wengel, J., Bicyclic nucleosides and conformational restriction of oligonucleotides. J. Chem. Soc., Perkin Trans. 1, 1 (2000) 3539.

    Google Scholar 

  7. Wengel, J., Synthesis of 3-C-and 4-C-branched oligodeoxy-nucleotides and the development of Locked Nucleic Acid (LNA). Accounts Chem. Res., 32 (1999) 301.

    CAS  Google Scholar 

  8. Koshkin, A., Singh, S.K., Nielsen, P., Rajwanshi, V.K., Ku-mar, R., Meldgaard, M. et al.,lNA (Locked Nucleic Acids): Synthesis of the adenine, cytosine, guanine, 5-methylcytosine, thymine and uracil bicyclonucleoside monomers, oligomerisa-tion, and unprecedented nucleic acid recognition. Tetrahedron, 54 (1998) 3607.

    Article  CAS  Google Scholar 

  9. Singh, S.K., Nielsen, P., Koshkin, A. and Wengel, J., LNA (locked nucleic acids): Synthesis and high-affinity nucleic acid recognition. Chem. Commun. (1998) 455.

  10. Obika, S., Hari, Y., Sugimoto, T., Sekiguchi, M. and Iman-ishi, T., Triplex-forming enhancement with high sequence selectivity by single 2-0,4-C-methylene bridged nucleic acid (2,4-BNA) modification. Tetrahedron Lett., 41 (2000) 8923.

    CAS  Google Scholar 

  11. Koshkin, A.A., Fensholdt, J., Pfundheller, H.M. and Lomholt, C., A simplified and efficient route to 2-O,4-C-methylene-linked bicyclic ribonucleosides (locked nucleic acid). J. Org. Chem., 66(25) (2001) 8504.

    Article  CAS  PubMed  Google Scholar 

  12. Koshkin, A., Rajwanshi, V.K. and Wengel, J., Novel conveni-ent syntheses of LNA [2.2.1] bicyclo nucleosides. Tetrahedron Lett, 39 (1998) 4381.

    Article  CAS  Google Scholar 

  13. Obika, S., Nanbu, D., Hari, Y. and Morio, J.A.K., In, Y., Ishida, T. et al.,Synthesis of 2-0,4-C-methyleneuridine and-cytidine. Novel bicyclic nucleosides having a fixed C3-endosugar puckering. Tetrahedron Lett., 38(50) (1997) 8735.

    Article  CAS  Google Scholar 

  14. Brown, Tom and Brown, Dorcas J.S., Modern machine-aided methods of oligodeoxyribonucleotide synthesis. In: F. Eck-stein (Ed.) Oligonucleotides and Analogues-A Practical Approach. IRL Press, Oxford, 1991, pp. 13-14.

    Google Scholar 

  15. Koshkin, A., Nielsen, P., Meldgaard, M., Rajwanshi, V.K., Singh, S.K. and Wengel, J., LNA (Locked Nucleic Acid): An RNA mimic forming exceedingly stable LNA: LNA duplexes. J. Am. Chem. Soc., 120(50) (1998) 13252.

    Article  CAS  Google Scholar 

  16. Obika, S., Nanbu, D., Hari, Y., Morio, J.A.K., Doi, T. and Imanishi, T., Stability and Structural Features of the De-plexes Containing Nucleoside Analogues with a Fixed N-Type Conformation, Elsevier Science Ltd., 39, 1998, pp. 5401-5404.

    CAS  Google Scholar 

  17. Pon, R.T. and Yu, S., Rapid automated derivatizatiob of solid-phase supports for oligonucleotide synthesis using uronium and phosphonium coupling reagents. Tetrahedron Lett., 38 (1997) 3331.

    CAS  Google Scholar 

  18. Babu, B.R. and Wengel, J., Universal hybridization using LNA (locked nucleic acid) containing a novel pyrene LNA nucleotide monomer. Chem. Commun., 2001; (2001-First published as an Avance Article on the web, October 2001) (2000) 2114.

  19. Håkansson, A.E. and Wengel, J., The adenine derivative of alpha-L-LNA (alpha-L-ribo configured locked nucleic acid): 2-0,4-C-Methyleneribonucleosides. Synthesis and high-affinity hybridization towards DNA, RNA, LNA and alpha-L-LNA complementary sequences. Bioorg. Med. Chem. Lett., 11(7) (2001) 935.

    Article  PubMed  Google Scholar 

  20. Kumar, R., Singh, S.K., Koshkin, A.A., Rajwanshi, V.K., Meldgaard, M. and Wengel, J., The first analogues of LNA (locked nucleic acids): Phosphorothioate-LNA and 2-thio-LNA. Bioorg. Med. Chem. Lett., 8(16) (1998) 2219.

    Article  CAS  PubMed  Google Scholar 

  21. Obika, S., Hari, Y., Morio, J.A.K. and Imanishi, T., Syn-thesis of conformationally locked C-nucleosides having a 2,5-dioxabicyclo (2.2.1) heptane ring system. Tetrahedron Lett., (2000) 215.

  22. Rajwanshi, V.K., Haakansson, A.E., Dahl, B.M. and Wengel, J., LNA stereoisomers: Xylo-LNA (beta-D-xylo configures locked nucleic acid) and alfa-L-LNA (alfa-L-ribo configures locked nucleic acid). Chem. Commun. (1999) 1395.

  23. Rajwanshi, V.K., Haakansson, A.E., Kumar, R. and Wengel, J., High-affinity nucleic acid recognition using 'LNA' (locked nucleic acid., beta-D-ribo configures LNA), 'xylo-LNA' (beta-D-xylo confirgures LNA) or 'alfa-L-LNA' (alfa-L-ribo con-figured LNA). Chem. Commun. (1999) 2073.

  24. Singh, S.K., Kumar, R. and Wengel, J., Synthesis of 2-amino-LNA: A novel conformationally restricted high-affinity oligonucleotide analogue with a handle. J. Organic Chem., 63(26) (1998) 10035.

    CAS  Google Scholar 

  25. Singh, S.K. and Wengel, J., Universality of LNA-mediated high-affinity nucleic acid recognition. Chem. Commun. (1998) 1247.

  26. Wengel, J., Petersen, M., Nielsen, K.E., Jensen, G.A., Håkans-son, A.E., Kumar, R. et al.,lNA (locked nucleic acid) and the diastereoisomeric alpha-L-LNA: Conformational tuning and high-affinity recognition of DNA/RNA targets. Nucleos. Nucleot. Nucl. Acids, 20(4-7) (2001) 389.

    Google Scholar 

  27. Braasch, D.A. and Corey, R., Locked nucleic acid (LNA): Fine-tuining the recognition of DNA and RNA. Chem. Biol., 8 (2001) 1.

    Article  CAS  PubMed  Google Scholar 

  28. Rajwanshi, V.K., Håkansson, A.E., Pitsch, S., Singh, S.K., Kumar, R., Nielsen, P. et al.,The eight stereoisomers of LNA (Locked Nucleic Acid): A remarkable family of strong RNA binding molecules. Angew. Chem. Int. Ed., 39 (2000) 1656.

    Article  CAS  Google Scholar 

  29. Sørensen, A.M., Kvarnø, L., Bryld, T., Håkansson, A.E., Ver-beure, B., Gaubert, G. et al.,J. Am. Chem. Soc. (2002) (in press).

  30. Nielsen, P. and Dalskov, J.K., Alpha-LNA, locked nucleic acid with alpha-d-configuration. Chem. Commun. (2000) 1179.

  31. Nielsen, P., Christensen, N.K. and Dalskov, J.K., Chem. Eur. J. (2002) (in press).

  32. Wang, G., Girardet, J.-L. and Gunic, E., Conformationally locked nucleosides. Synthesis and stereochemical assignments of 2-C,4-C-bridged bicyclonucleosides 1,2. Tetrahedron, 55 (1999) 7707.

    CAS  Google Scholar 

  33. Wang, G., Gunic, E., Girardet, J.-L. and Stoisavljevic, V., Conformationally locked nucleosides. Synthesis and hybrid-ization properties of oligodeoxynucleotides containing 2,4-C-bridged 2-deoxynucleosides 1. Bioorg. Med. Chem. Lett., 9 (1999) 1147.

    CAS  PubMed  Google Scholar 

  34. Morita, K., Hasegawa, C., Kaneko, M., Tsutsumi, S., Sone, J., Ishikawa, T. et al.,Bioorg. Med. Chem. Lett., 12 (2002) 73.

    Article  CAS  PubMed  Google Scholar 

  35. Christensen, U., Jacobsen, N., Rajwanshi, V.K., Wengel, J. and Koch, T., Stopped-flow kinetics of locked nucleic acid (LNA)-oligonucleotide duplex formation: Studies of LNA-DNA and DNA-DNA interactions. Biochem. J., 354(3) (2001) 481.

    Article  CAS  PubMed  Google Scholar 

  36. Brameld, K.A. and Goddard, W.A., J. Am. Chem. Soc., 121 (1999) 985.

    Article  CAS  Google Scholar 

  37. Cheatham, T.E. and Kollman, P.A., J. Am. Chem. Soc., 119 (1997) 4805.

    Article  CAS  Google Scholar 

  38. González, C., Stec, W., Raynolds, M.A. and James, T.L., Biochemistry, 34 (1995) 4969.

    PubMed  Google Scholar 

  39. Bondensgaard, K., Petersen, M., Singh, S.K., Rajwanshi, V.K., Kumar, R., Wengel, J. et al.,Structural studies of LNA:RNA duplexes by NMR: Conformations and implic-ations for RNase H activity. Chem. Eur. J., 6(15) (2000) 2687.

    Article  CAS  Google Scholar 

  40. Petersen, M., Håkansson, A.E., Wengel, J. and Jacobsen, J.P., Alpha-L-LNA (alpha-I-ribo configured locked nucleic acid) recognition of RNA. A study by NMR spectroscopy and mo-lecular dynamics simulations. J. Am. Chem. Soc., 123(30) (2001) 7431.

    Article  CAS  PubMed  Google Scholar 

  41. Wahlestedt, C., Salmi, P., Good, L., Kela, J., Johnsson, T., Hokfelt, T. et al.,Potent and nontoxic antisense oligonuc-leotides containing locked nucleic acids. Proc. Natl. Acad. Sci. USA, 97(10) (2000) 5633.

    Article  CAS  PubMed  Google Scholar 

  42. Petersen, M., Bondensgaard, K., Wengel, J. and Jacobsen, J.P., J. Am. Chem. Soc. (2002); in press.

  43. Jensen, G.A., Singh, S.K., Kumar, R., Wengel, J. and Jac-obsen, J.P., A comparison of the solution structures of an LNA:DNA duplex and the unmodified DNA:DNA duplex. J. Chem. Soc., Perkin Trans., 2 (2001) 1224.

    Google Scholar 

  44. Nielsen, C.B., Singh, S.K., Wengel, J. and Jacobsen, J.P., The solution structure of a locked nucleic acid (LNA) hybridized to DNA. J. Biomol. Struct. Dyn., 17(2) (1999) 175.

    CAS  PubMed  Google Scholar 

  45. Nielsen, K.E., Singh, S.K., Wengel, J. and Jacobsen, J.P., Solution structure of an LNA hybridized to DNA: NMR study of the d(CT(L)GCT(L)T(L)CT(L)GC):d(GCAGAAGCAG) duplex containing four locked nucleotides. Bioconjug. Chem., 11(2) (2000) 228.

    Article  CAS  PubMed  Google Scholar 

  46. Petersen, M., Nielsen, C.B., Nielsen, K.E., Jensen, G.A., Bondensgaard, K., Singh, S.K. et al.,The conformations of locked nucleic acids (LNA). J. Mol. Recognit., 13(1) (2000) 44.

    Article  CAS  PubMed  Google Scholar 

  47. Egli, M., Minasov, G., Teplova, M., Kumar, R. and Wengel, J., X-ray crystal structure of a locked nucleic acid (LNA) duplex composed of a palindromic 10-mer DNA strand containing one LNA thymine monomer. Chem. Commun. (2001) 651.

  48. Sarafianos, S.G., Das, K., Tantillo, C., Clark, A.D., Ding, J., Whitcomb, J.M. et al.,EMBO J., 20 (2001) 1449.

    Article  CAS  PubMed  Google Scholar 

  49. Trapane, T.L. and Ts'O., P.O.P., Triplex formation at single-stranded nucleic acid target sites of unrestricted sequences by two added strands of oligonucleotides: A proposed model. J. Am. Chem. Soc., 116 (1994) 10437.

    CAS  Google Scholar 

  50. Von Nguyen, T. and Thuong, Claude Hélène, Sequenzspezi-fische Erkennung und Modifikation von Doppelhelix-DNA durch Oligonucleotide. Angw. Chem. Int. Ed. Engl., 32 (1993) 666.

    Google Scholar 

  51. Wang, Shaohui and Kool, Eric T., Recognition of single-stranded nucleic acid by triplex formation: The binding of pyrimidine-rich sequences. J. Am. Chem. Soc., 116 (1994) 8857.

    CAS  Google Scholar 

  52. Satoshi, Obika and Takeshi, Imanishi, 3-Amino-2,4-BNA: Novel bridged nucleic acids having an N3-P5 phosphoramid-ate linkage. Chem. Commun. (2001) 1992.

  53. Lee, J.S., Woodsworth, M.L., Latimer, L.J. and Morgan, A.R., Nucl. Acid Res., 12 (1984) 6603.

    CAS  Google Scholar 

  54. Satoshi, Obika, Takeshi, Uneda, Tomomi, Sugimoto, Daishu, Nanbu, Takashi, Takefumi and Takeshi, Imanishi, 2-O,4-C-methylene bridged nucleic acid (2,4-BNA): Synthesis and triplex-forming properties. Bioorg. Medic. Chem., 9 (2001) 1001.

    Google Scholar 

  55. Obika, S., Hari, Y., Sekiguchi, M. and Imanishi, T., A 2,4-bridged nucleic acid containing 2-pyridone as a nucleobase: Efficient recognition of a C-G interruption by triplex forma-tion with a pyrimidine. Motif. Angew. Chem. Int., 40 (2001) 2079.

    CAS  Google Scholar 

  56. Satoshi, Obika, Yoshiyuki, Hari, Hiroyasu, Inohara and Take-shi, Imanishi, 2,4-BNA bearing unnatural nucleobases: To-wards the expansion of the target sequence double-starnded DNA in triplex formation. Nucl. Acid Res., Suppl. No. 1 (2001) 171.

    Google Scholar 

  57. Satoshi, Obika, Yoshiyuki, Hari, Satoshi, Obika and Takeshi, Imanishi, A 2,4-bridged nucleic acid containing 2-pyridone as a nucleobase: Efficient recognition of a C-G interruption by triplex formation with a pyrimidine motif. Angw. Chem. Int. Ed. Engl., 40 (2001) 2079.

    Google Scholar 

  58. Nielsen, K.E., Rasmussen, J., Kumar, R., Wengel, J., Jacob-sen, J.P. and Petersen, M., Bioconjugate Chem., in press.

  59. Nielsen, J.T., Stein, P.C. and Petersen, M., NMR structure of an á-L-LNA:RNA hybrid: structural implications for RNase H recognition. Nucl. Acids. Res., 31 (2003) 5858.

    CAS  PubMed  Google Scholar 

  60. Nielsen, K.M., Petersen, M., Håkansson, A.E., Wengel, J. and Jacobsen, J.P., Alpha-L-LNA (alpha-L-ribo configured locked nucleic acid) recognition of DNA: An NMR spectroscopic study. Chemistry, 8(13) (2002) 3001.

    CAS  PubMed  Google Scholar 

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Wengel, J., Petersen, M., Frieden, M. et al. Chemistry of locked nucleic acids (LNA): Design, synthesis, and bio-physical properties. Int J Pept Res Ther 10, 237–253 (2003). https://doi.org/10.1007/s10989-004-4926-6

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