Conformationally restricted carbohydrate-modified nucleic acids and antisense technology

Biochimica et Biophysica Acta - Gene Structure and Expression

Volumn 1489, Issue 1, 1999, Pages 167-179

  Herdewijn, P ^a  

^a REGA INSTITUTE FOR MEDICAL RESEARCH   (Belgium)

Author keywords

Carbohydrate modification; Conformationally restricted nucleoside; Hexitol nucleoside; Hybridization; Preorganization; Pyranose nucleoside

Indexed keywords

ANTISENSE OLIGONUCLEOTIDE; CARBOHYDRATE; NUCLEIC ACID; NUCLEOSIDE; NUCLEOSIDE ANALOG; OLIGONUCLEOTIDE;

CHEMICAL MODIFICATION; CONFORMATION; HYBRIDIZATION; NUCLEIC ACID PROBE; PHYSICAL CHEMISTRY; PRIORITY JOURNAL; REVIEW;

BASE PAIRING; CARBOHYDRATES; CELL-FREE SYSTEM; CELLS, CULTURED; DRUG DESIGN; GENES, RAS; HUMANS; INTERCELLULAR ADHESION MOLECULE-1; KERATINOCYTES; MOLECULAR CONFORMATION; NUCLEIC ACID CONFORMATION; NUCLEIC ACID HYBRIDIZATION; OLIGONUCLEOTIDES, ANTISENSE; RNA, MESSENGER; STRUCTURE-ACTIVITY RELATIONSHIP; SUGAR ALCOHOLS; TRANSCRIPTION, GENETIC; TRANSFECTION;

EID: 0032743844     PISSN: 01674781     EISSN: None     Source Type: Journal    
DOI: 10.1016/S0167-4781(99)00152-9     Document Type: Review

References (49)

1. Lescrinier T., Hendrix C., Kerremans L., Rozenski J., Link A., Samyn B., Van Aerschot A., Lescrinier E., Eritja R., Van Beeumen J., Herdewijn P. DNA-binding ligands from peptide libraries containing unnatural amino acids. Chem. Eur. J. 4:1998;425-433.
2. P. Herdewijn, H. De Winter, B. Doboszewski, I. Verheggen, K. Augustyns, C. Hendrix, T. Saison-Behmoaras, C. De Ranter, A. Van Aerschot, Hexopyranosyl-like oligonucleotides, in: Y.S. Sanghvi, P.D. Cook (Eds.), Carbohydrate Modifications in Antisense Research, American Chemical Society, Washington, DC, 1994, pp. 80-99.
3. P. Herdewijn, Anhydrohexitols as conformationally constrained furanose mimics, design of an RNA-receptor, in: Y. Chapleur (Ed.), Carbohydrate Mimics, Wiley-VCH, New York, 1998, pp. 553-579.
4. P. Herdewijn, Targeting RNA with conformationally restricted oligonucleotides, Liebigs Ann. (1996) 1337-1348.
5. Altona C., Sundaralingam M. Conformational analysis of the sugar ring in nucleosides and nucleotides. A new description using the concept of pseudorotation. J. Am. Chem. Soc. 94:1972;8205-8212.
6. Dickerson R.E. DNA structure from A to Z. Methods Enzymol. 211:1992;67-111.
7. Nielsen P., Pfundheller H.M., Olsen C.E., Wengel J. Synthesis of 2′-O,3′-C-linked bicyclic nucleosides and bicyclic oligonucleotides. J. Chem. Soc. Perkin Trans. 1:1997;3423-3433.
8. Christensen N.K., Petersen M., Nielsen P., Jacobsen J.P., Olsen C.E., Wengel J. a novel class of oligonucleotide analogues containing 2′-O,3′-C-linked [3.2.0]bicycloarabinonucleoside monomers: synthesis, thermal affinity studies, and molecular modeling. J. Am. Chem. Soc. 120:1998;5458-8463.
9. S.K. Singh, J. Wengel, Universality of LNA-mediated high-affinity nucleic acid recognition, Chem. Commun. (1998) 1247-1248.
10. Tarköy M., Leumann C. Synthese und Paarungseigenschaften von Decanucleotiden aus (3′S,5′R)-2′-Desoxy-3′,5′-ethano-β-D- ribofuranosyladenin und -thymin. Angew. Chem. 105:1993;1516-1518.
11. Tarköy M., Bolli M., Schweizer B., Leumann C. Nucleic-acid analogues with constraint conformational flexibility in the sugar-phosphate backbone ('bicyclo-DNA'). Part 1. Preparation of (3′S,5′R)-2′-deoxy-3′,5′-ethano-αβ-D- ribonucleosides ('bicyclonucleosides'). Helv. Chim. Acta. 76:1993;481-510.
12. Steffens R., Leumann C. Nucleic-acid analogues with constraint conformational flexibility in the sugar-phosphate backbone ('tricyclo-DNA'). Part 1. Preparation of [(5′R,6′R)-2′-deoxy-3′,5′-ethano-5′, 6′-methano-β-D-ribofuranosyl]thymine and -adenine, and the corresponding phosphoramidites for oligonucleotide synthesis. Helv. Chim. Acta. 80:1997;2426-2439.
13. Egli M., Lubini P., Bolli M., Dobler M., Leumann C. Crystal structure of a parallel-stranded duplex of a deoxycytidylyl-(3′-5′)-deoxycytidine analogue containing intranucleosidyl C(3′)-C(5′) ethylene bridges. J. Am. Chem. Soc. 115:1993;5855-5856.
14. Bolli M., Trafelet H.U., Leumann C. Watson-Crick base-pairing properties of bicyclo-DNA. Nucleic Acids Res. 24:1996;4660-4667.
15. Eschenmoser A., Dobler M. Warum Pentose- und nicht Hexose-Nucleinsäuren? Teil 1. Einleitung und Problemstellung, Konformationsanalyse für Oligonucleotid-Ketten aus 2′,3′-Dideoxyglucopyranosyl-Bausteinen ('Homo-DNS') sowie Betrachtungen zur Konformation von A- und B-DNS. Helv. Chim. Acta. 75:1992;218-259.
16. Marquez V.E., Siddiqui M.A., Ezzitouni A., Russ P., Wang J., Wagner R.W., Matteucci M.D. Nucleosides with a twist. Can fixed forms of sugar ring pucker influence biological activity in nucleosides and oligonucleotides? J. Med. Chem. 39:1996;3739-3747.
17. Altmann K.-H., Kesselring R., Francotte E., Rihs G. 4′,6′-Methano carbocyclic thymidine: a conformationally constrained building block for oligonucleotides. Tetrahedron Lett. 35:1994;2331-2334.
18. Altmann K.-H., Imwinkelried R., Kesselring R., Rihs G. 1′,6′-Methano carbocyclic thymidine: synthesis, X-ray crystal structure, and effect on nucleic acid duplex stability. Tetrahedron Lett. 35:1994;7625-7628.
19. Buff R., Hunziker J. 2′-Deoxy-2′(S)-ethinyl oligonucleotides: a modification which selectively stabilizes oligoadenylate pairing to DNA complements. Bioorg. Med. Chem. 8:1998;521-524.
20. Tarköy M., Bolli M., Leumann C. Nucleic-acid analogues with restricted conformational flexibility in the sugar-phosphate backbone ('bicyclo-DNA'). Part 3. Synthesis, pairing properties and calorimetric determination of duplex and triplex stability of decanucleotides from [(3′S,5′R)-2-deoxy-3′,5′-ethano-β-D-ribofuranosyl] adenine and -thymine. Helv. Chim. Acta. 77:1994;716-744.
21. De Winter H., Lescrinier E., Van Aerschot A., Herdewijn P. Molecular dynamics simulation to investigate differences in minor groove hydration of HNA/RNA hybrids as compared to HNA/DNA complexes. J. Am. Chem. Soc. 120:1998;5381-5394.
22. W. Saenger, Principles of Nucleic Acid Structure, Springer Verlag, New York, 1994, p. 240.
23. A. Eschenmoser, Pyranosyl Oligonucleotides. XIII International Round Table Nucleosides, Nucleotides and their Biological Applications, Montpellier, France, 6-10 September 1998.
24. 15NMR-spektroskopische Untersuchung von ddGlc(A-A-A-A-A-T-T-T-T-T) in wässriger Lösung. Helv. Chim. Acta. 76:1993;2701-2756.
25. Hossain N., Hendrix C., Lescrinier E., Van Aerschot A., Busson R., De Clercq E., Herdewijn P. Homo-N-nucleosides: incorporation into oligonucleotides and antiviral activity. Bioorg. Med. Chem. Lett. 6:1996;1465-1468.
26. Boal J.H., Wilk A., Scremin C.L., Gray G.N., Phillips L.R., Beaucage S.L. Synthesis of (2-deoxy-α- and -β-erythro-pentofuranosyl)(tymin-1-yl)alkanes and their incorporation into oligodeoxyribonucleotides. Effect of nucleobase-sugar linker flexibility on the formation of DNA-DNA and DNA-RNA hybrids. J. Org. Chem. 61:1996;8617-8626.
27. Marangoni M., Van Aerschot A., Augustyns P., Rozenski J., Herdewijn P. Synthesis and hybridization properties of inverse oligonucleotides. Nucleic Acids Res. 25:1997;3034-3041.
28. Epple C., Leumann C. Bicyclo[3.2.1]-DNA, a new DNA analog with a rigid backbone and flexibly linked bases: pairing properties with complementary DNA. Chem. Biol. 5:1998;209-216.
29. Van Aerschot A., Verheggen I., Hendrix C., Herdewijn P. 1,5-Anhydrohexitol nucleic acids, a new promising antisense construct. Angew. Chem. 34:1995;1338-1339.
30. Hendrix C., Rosemeyer H., Verheggen I., Seela F., Van Aerschot A., Herdewijn P. 1′,5′-Anhydrohexitol oligonucleotides: synthesis, base pairing and recognition by regular oligodeoxyribonucleotides and oligoribonucleotides. Chem. Eur. J. 3:1997;110-120.
31. Hendrix C., Rosemeyer H., De Bouvere B., Van Aerschot A., Seela F., Herdewijn P. 1′,5′-Anhydrohexitol oligonucleotides: hybridization and strand displacement with oligoribonucleotides, interaction with RNase H and HIV reverse transcriptase. Chem. Eur. J. 3:1997;1513-1520.
32. M. Vandermeeren, S. Preveral, S. Janssens, J. Geysen, E. Saison-Behmoaras, A. Van Aerschot, P. Herdewijn, Biological activity of hexitol nucleic acids targeted at Ha-ras and ICAM-1 mRNA, Biochem. Pharmacol. (1999) submitted.
33. D. Atkins, personal communication.
34. Sundaralingam M. Stereochemistry of nucleic acids and their constituents. IV. Allowed and preferred conformations of nucleosides, nucleoside mono-, di-, tri-, tetraphosphates, nucleic acids and polynucleotides. Biopolymers. 7:1969;821-860.
35. Hunziker J., Roth H.-J., Böhringer M., Giger A., Diederichsen U., Göbel M., Krishnan R., Jaun B., Leumann C., Eschenmoser A. Warum Pentose- und nicht Hexose-nucleinsäuren? Teil III. Oligo(2′,3′-dideoxy-β-D-glucopyranosyl)nucleotide ('Homo-DNS'): Paarungs-Eigenschaften. Helv. Chim. Acta. 76:1993;259-353.
36. E. Lescrinier, R. Busson, H. Heus, C. Hilbers, P. Herdewijn, Structure determination of a RNH/HNA hybrid by NMR spectroscopy, Nat. Struct. Biol., submitted.
37. Verheggen I., Van Aerschot A., Toppet S., Snoeck R., Janssen G., Balzarini J., De Clercq E., Herdewijn P. Synthesis and antiherpes virus activity of 1,5-anhydrohexitol nucleosides. J. Med. Chem. 36:1993;2033-2040.
38. Verheggen I., Van Aerschot A., Van Meervelt L., Rozenski J., Wiebe L., Snoeck R., Andrei G., Balzarini J., Claes P., De Clercq E., Herdewijn P. Synthesis, biological evaluation, and structure analysis of a series of new 1,5-anhydrohexitol nucleosides. J. Med. Chem. 38:1995;826-835.
39. Ostrowski T., Wroblowski B., Busson R., Rozenski J., De Clercq E., Bennett M.S., Champness J.N., Summers W.C., Sanderson M.R., Herdewijn P. 5-Substituted pyrimidines with an 1,5-anhydro-2,3-dideoxy-D-arabino-hexitol moiety at N-1: synthesis, antiviral activity, conformational analysis, and interaction with viral thymidine kinase. J. Med. Chem. 41:1998;4343-4353.
40. Maurinsh Y., Rosemeyer H., Esnouf R., Wang J., Ceulemans G., Lescrinier E., Hendrix C., Busson R., Seela F., VanAerschot A., Herdewijn P. Synthesis and pairing properties of oligonucleotides containing 3-hydroxy-4-hydroxymethyl-1-cyclohexanyl nucleosides. Chem. Eur. J. 5:1999;2139-2150.
41. Johannesson H., Halle B. Minor groove hydration of DNA in solution: dependence on base composition and sequence. J. Am. Chem. Soc. 120:1998;6859-6870.
42. Hossain N., Wroblowski B., Van Aerschot A., Rozenski J., De Bruyn A., Herdewijn P. Oligonucleotides composed of 2′-deoxy-1′,5′-anhydro-D-mannitol nucleosides with a purine base moiety. J. Org. Chem. 63:1998;1574-1582.
43. Allart B., Khan K., Rosemeyer H., Schepers G., Hendrix C., Rothenbacher K., Seela F., VanAerschot A., Herdewijn P. D-Altritol nucleic acids (ANA) hybridization properties stability and initial structural analysis. Chem. Eur. J. 5:1999;2424-2431.
44. Sponer J., Leszczynski J., Hobza P. Nature of nucleic acid-base stacking: nonempirical ab initio and empirical potential characterization of 10 stacked base dimers. Comparison of stacked and H-bonded base pairs. J. Phys. Chem. 100:1996;5590-5596.
45. Doboszewski B., Blaton N., Herdewijn P. Easy synthesis and different conformational behavior of purine and pyrimidine β-D-glycero-pent-2′-enopyranosyl nucleosides. J. Org. Chem. 60:1995;7909-7919.
46. 1H NMR spectroscopy. Impact of π→σ* interactions on the axial preference of the purine versus pyrimidine nucleobase. J. Am. Chem. Soc. 119:1997;9782-9792.
47. Maurinsh Y., Schraml J., De Winter H., Blaton N., Peeters O., Lescrinier E., Rozenski J., Van Aerschot A., De Clercq E., Busson R., Herdewijn P. Synthesis and conformational study of 3-hydroxy-4-(hydroxymethyl)-1-cyclohexanyl purines and pyrimidines. J. Org. Chem. 62:1997;2861-2871.
48. Doboszewski B., De Winter H., Van Aerschot A., Herdewijn P. Synthesis of 3′-deoxy-3′-C-hydroxymethyl-aldopentopyranosyl nucleosides and their incorporation in oligonucleotides. Part II. Tetrahedron. 51:1995;12319-12336.
49. Doboszewski B., Blaton N., Rozenski J., De Bruyn A., Herdewijn P. 3′-Deoxy-3′-hydroxymethyl-aldopentopyranosyl nucleoside synthesis. Part I. Tetrahedron. 51:1995;5381-5396.