Recent improvements in antigene technology

Current Opinion in Chemical Biology

Volumn 7, Issue 6, 2003, Pages 717-726

  Buchini, Sabrina ^a   Leumann, Christian J ^a  

^a UNIVERSITY OF BERN   (Switzerland)

Author keywords

[No Author keywords available]

Indexed keywords

DNA; GENOMIC DNA; NUCLEIC ACID; OLIGONUCLEOTIDE; PURINE; PYRIMIDINE;

AMINO ACID SEQUENCE; BASE PAIRING; BIOTECHNOLOGY; CELL FUNCTION; CHEMICAL STRUCTURE; CHROMOSOME INVERSION; GENE EXPRESSION REGULATION; GENE TECHNOLOGY; HUMAN; PROTEIN MOTIF; PROTEIN STABILITY; RESTRICTION MAPPING; REVIEW; SITE DIRECTED MUTAGENESIS; TRANSCRIPTION INITIATION; TRIPLE HELIX; UPREGULATION;

EID: 0344033606     PISSN: 13675931     EISSN: None     Source Type: Journal    
DOI: 10.1016/j.cbpa.2003.10.007     Document Type: Review

References (47)

1. Zain R., Sun J.-S. Do natural DNA triple-helical structures occur and function in vivo? Cell Mol. Life Sci. 60:2003;862-863.
2. Guntaka R.V., Varma B.R., Weber K.T. Triplex-forming oligonucleotides as modulators of gene expression. Int. J. Biochem. Cell Biol. 35:2003;22-31.
3. Seidman M.M., Glazer P.M. The potential for gene repair via triple helix formation. J. Clin. Invest. 112:2003;487-494.
4. Robles J., Grandas A., Pedroso E., Luque F.J., Eritja R., Orozco M. Nucleic acid triple helices: stability effects of nucleobase modifications. Curr. Org. Chem. 6:2002;1333-1368 This is a comprehensive review with 462 references, covering all relevant nucleobase modifications and their effect on triplex stability up to the end of 2001.
5. Cuenoud B., Casset F., Hüsken D., Natt F., Wolf R.M., Altmann K.-H., Martin P., Moser H.E. Dual recognition of double-stranded DNA by 2-aminoethoxy-modified oligonucleotides. Angew. Chem. Int. Ed. Engl. 37:1998;1288-1291.
6. Blommers M.J.J., Natt F., Jahnke W., Cuenoud B. Dual recognition of double-stranded DNA by 2′-aminoethoxy-modified oligonucleotides: the solution structure of an intramolecular triplex obtained by NMR spectroscopy. Biochemistry. 37:1998;17714-17725.
7. Carlomagno T., Blommers M.J.J., Meiler J., Cuenoud B., Griesinger C. Determination of aliphatic side-chain conformation using cross-correlated relaxation: application to an extraordinarily stable 2′-aminoethoxy- modified oligonucleotide triplex. J. Am. Chem. Soc. 123:2001;7364-7370.
8. Atsumi N., Ueno Y., Kanazaki M., Shuto S., Matsuda A. Nucleosides and nucleotides. Part 214: thermal stability of triplexes containing 4′-α-C-aminoalkyl-2′-deoxynucleosides. Bioorg. Med. Chem. 10:2002;2933-2939.
9. Häberli A., Leumann C.J. Synthesis of pyrrolidino C-nucleosides via Heck reaction. Org. Lett. 3:2001;489-492.
10. Häberli A., Leumann C.J. DNA binding properties of oligodeoxynucleotides containing pyrrolidino C-nucleosides. Org. Lett. 4:2002;3275-3278.
11. Häberli A., Mayer A., Leumann C.J. Pyrrolidino-DNA. Nucleosides Nucleotides Nucleic Acids. 22:2003;1187-1189.
12. Tarköy M., Phipps A.K., Schultze P., Feigon J. Solution structure of an intramolecular DNA triplex linked by hexakis(ethylene glycol) units: d(AGAGAGAA-(EG)6-TTCTCTCT-(EG)6-TCTCTCTT). Biochemistry. 37:1998;5810-5819.
13. Cassidy R.A., Puri N., Miller P.S. Effect of DNA target sequence on triplex formation by oligo-2′-deoxy- and 2′-O-methylribonucleotides. Nucleic Acids Res. 31:2003;4099-4108.
14. Bernal-Méndez E., Leumann C.J. Conformational diversity versus nucleic acid triplex stability, a combinatorial study. J. Biol. Chem. 276:2001;35320-35327 We find this to be a potentially very useful combinatorial method to rapidly screen sequence effects on triplex (or duplex) binding. The advantage over selex and related methods is that there is no enzymatic amplification step necessary, thus allowing also the screening of sugar-modified nucleotide units.
15. Obika S., Uneda T., Sugimoto T., Nanbu D., Minami T., Doi T., Imanishi T. 2′-O,4′-C-Methylene bridged nucleic acid (2′,4′-BNA): Synthesis and triplex forming properties. Bioorg. Med. Chem. 9:2001;1001-1011.
16. Torigoe H., Hari Y., Sekiguchi M., Obika S., Imanishi T. 2′-O,4′-C-methylene bridged nucleic acid modification promotes pyrimidine motif triplex DNA formation at physiological pH: thermodynamic and kinetic studies. J. Biol. Chem. 276:2001;2354-2360.
17. m enhancements to LNA, but does not suffer from the non-binding of fully modified oligonucleotides to their DNA target.
18. Demidov V.V., Frank-Kamenetskii M.D. Sequence-specific targeting of duplex DNA by peptide nucleic acids via triplex strand invasion. Methods. 23:2001;108-122.
19. Nielsen P.E. Targeting double stranded DNA with peptide nucleic acids (PNA). Curr. Med. Chem. 8:2001;545-550.
20. Basye J., Trent J.O., Gao D., Ebbinghaus S.W. Triplex formation by morpholino oligodeoxyribonucleotides in the HER-2/neu promoter requires the pyrimidine motif. Nucleic Acids Res. 29:2001;4873-4880.
21. Guianvarc'h D, Benhida R, Fourrey J-L, Maurisse R, Sun J-S: Incorporation of a novel nucleobase allows stable oligonucleotide-directed triple helix formation at the target sequence containing a purine.pyrimidine interruption. Chem Commun (Camb) 2001:1814-1815.
22. Guianvarc'h D., Fourrey J.-L., Maurisse R., Sun J.-S., Benhida R. Design of artificial nucleobases for the recognition of the AT inversion by triple-helix forming oligonucleotides: a structure-stability relationship study and neighbour base effect. Bioorg. Med. Chem. 11:2003;2751-2759.
23. Guianvarc'h D., Fourrey J.-L., Maurisse R., Sun J.-S., Benhida R. Synthesis, incorporation into triplex forming oligonucleotide, and binding properties of a novel 2′-deoxy-C-nucleoside featuring a 6-(thiazolyl-5)benzimidazole nucleobase. Org. Lett. 4:2003;4209-4212.
24. Mokhir A.A., Connors W.H., Richert C. Synthesis and monitored selection of nucleotide surrogates for binding T:A base pairs in homopurine- homopyrimidine DNA triple helices. Nucleic Acids Res. 29:2001;3674-3684.
25. Parel S.P., Leumann C.J. Triple-helix formation in the antiparallel binding motif of oligodeoxynucleotides containing N(9)- and N(7)-2-aminopurine deoxynucleosides. Nucleic Acids Res. 29:2001;2260-2267.
26. Obika S., Hari Y., Sekiguchi M., Imanishi T. 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. Angew. Chem. Int. Ed. Engl. 40:2001;2079-2081.
27. Prévot-Halter I., Leumann C. Selective recognition of a C-G base-pair in the parallel DNA triple-helical binding motif. Bioorg. Med. Chem. Lett. 9:1999;2657-2660.
28. Prévot I., Leumann C.J. Evaluation of novel third strand bases for the recognition of a C-G base-pair in the parallel DNA triple-helical binding motif. Helv. Chim. Acta. 85:2002;502-515.
29. Parel S.P., Marfurt J., Leumann C.J. DNA triple-helix formation at pyrimidine-purine inversion sites. Nucleosides Nucleotides Nucleic Acids. 20:2001;411-417.
30. Doronina S.O., Behr J.-P. Synthesis of 4-guanidinopyrimidine nucleosides for triple helix-mediated guanine and cytosine recognition. Tetrahedron Lett. 39:1998;547-550.
31. Li J.S., Fan Y.H., Zhang Y., Marky L.A., Gold B. Design of triple helix forming C-glycoside molecules. J. Am. Chem. Soc. 125:2003;2084-2093.
32. Obika S., Hari Y., Sekiguchi M., Imanishi T. Stable oligonucleotide- directed triplex formation at target sites with CG interruptions: strong sequence-specific recognition by 2′,4′-bridged nucleic-acid- containing 2-pyridones under physiological conditions. Chemistry. 8:2002;4796-4802 This article describes probably the best CG inversion binder known so far. The combination of conformationally restricted sugar analogues with novel bases that selectively recognize pyrimidine bases is a very promising strategy to alleviate the sequence restriction problem in DNA triplex formation.
33. Sollogoub M., Darby R.A., Cuenoud B., Brown T., Fox K.R. Stable DNA triple helix formation using oligonucleotides containing 2′-aminoethoxy-5- propargylamino-U. Biochemistry. 41:2002;7224-7231 An interesting way to improve triplex stability that may be applied also to non-standard bases. Unfortunately, only monomolecular triplexes have been investigated so far. Thus, the rigorous proof of principle has yet to come.
34. Roig V., Asseline U. Oligo-2′-deoxyribonucleotides containing uracil modified at the 5-position with linkers ending with guanidinium groups. J. Am. Chem. Soc. 125:2003;4416-4417.
35. Buchini S., Leumann C.J. Dual recognition of a pyrimidine-purine inversion site: synthesis and binding properties of triplex forming oligonucleotides containing 2′-aminoethoxy-5-methyl-1H-pyrimidin-2-one ribonucleosides. Tetrahedron Lett. 44:2003;5065-5068.
36. Nagatsugi F., Matsuyama Y., Maeda M., Sasaki S. Selective cross-linking to the adenine of the TA interrupting site within the triple-helix. Bioorg. Med. Chem. Lett. 12:2002;487-489.
37. Liang X., Asanuma H., Komiyama M. Photoregulation of DNA triplex formation by azobenzene. J. Am. Chem. Soc. 124:2002;1877-1883.
38. Besch R., Giovannangeli C., Kammerbauer C., Degitz K. Specific inhibition of ICAM-1 expression mediated by gene targeting with triplex-forming oligonucleotides. J. Biol. Chem. 277:2002;32473-32479.
39. Macris M.A., Glazer P.M. Transcription depedence of chromosomal gene targeting by triplex-forming oligonucleotides. J. Biol. Chem. 278:2003;3357-3362.
40. Stütz A.M., Hoeck J., Natt F., Cuenoud B., Woisetschläger M. Inhibition of interleukin-4- and CD40-induced IgE germline gene promoter activity by 2′-aminoethoxy-modified triplex-forming oligonucleotides. J. Biol. Chem. 276:2001;11759-11765.
41. Puri N., Majumdar A., Cuenoud B., Natt F., Martin P., Boyd A., Miller P.S., Seidman M.M. Targeted gene knockout by 2′-O-aminoethyl modified triplex forming oligonucleotides. J. Biol. Chem. 276:2001;28991-28998.
42. Puri N., Majumdar A., Cuenoud B., Natt F., Martin P., Boyd A., Miller P.S., Seidman M.M. Minimum number of 2′-O-(2-aminoethyl) residues required for gene knockout activity by triple helix forming oligonucleotides. Biochemistry. 41:2002;7716-7724 This paper contains important information as to the design of AE-TFOs related to knockout activity. It also contains a side by side comparison of the functionality of AE-TFOs with standard 2′-OM-TFOs.
43. Majumdar A., Puri N., Cuenoud B., Natt F., Martin P., Khorlin A., Dyatkina N., George A.J., Miller P.S., Seidman M.M. Cell cycle modulation of gene targeting by a triple helix-forming oligonucleotide. J. Biol. Chem. 278:2003;11072-11077.
44. Nagatsugi F., Sasaki S., Miller P.S., Seidman M.M. Site-specific mutagenesis by triple helix-forming oligonucleotides containing a reactive nucleoside analog. Nucleic Acids Res. 31:2003;e31.
45. Diviacco S., Rapozzi V., Xodo L.E., Hélène C., Quadrifoglio F., Giovannangeli C. Site-directed inhibition of DNA replication by triple helix formation. FASEB J. 15:2001;2660-2668.
46. Rogers F.A., Vasquez K.M., Egholm M., Glazer P.M. Site-directed recombination via bifunctional PNA-DNA conjugates. Proc. Natl. Acad. Sci. U.S.A. 99:2002;16695-16700 Achieving correction of defective genes via triplex induced site directed recombination with donor DNA is a very appealing goal as it is complementary to gene therapy. There is still a long way to go though.
47. Sorensen MD, Petersen M, Wengel J: Functionalized LNA (locked nucleic acid): high-affinity hybridization of oligonucleotides containing N-acylated and N-alkylated, 2′-amino-LNA monomers. Chem Commun 2003:2130-2132.