Extensive sugar modification improves triple helix forming oligonucleotide activity in vitro but reduces activity in vivo

Biochemistry

Volumn 46, Issue 35, 2007, Pages 10222-10233

  Alam, Md Rowshon ^a   Majumdar, Alokes ^a   Thazhathveetil, Arun Kalliat ^a   Liu, Su Ting ^a   Liu, Ji Lan ^a   Puri, Nitin ^a   Cuenoud, Bernard ^b   Sasaki, Shigeki ^c   Miller, Paul S ^d   Seidman, Michael M ^a  

^a NATIONAL INSTITUTE ON AGING   (United States)

^b NOVARTIS PHARMA AG   (Switzerland)

^c KYUSHU UNIVERSITY   (Japan)

^d JOHNS HOPKINS BLOOMBERG SCHOOL OF PUBLIC HEALTH   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

BIOPHYSICAL ASSAYS; OLIGONUCLEOTIDE ACTIVITY; TRIPLE HELIX FORMING OLIGONUCLEOTIDES (TFO);

ASSOCIATION REACTIONS; BIOACTIVITY; BIOASSAY; CHEMICAL MODIFICATION; GENETIC ENGINEERING; REACTION KINETICS; SUGARS; THERMODYNAMIC STABILITY;

OLIGONUCLEOTIDES;

2 O METHYL RIBOSE; 2' O AMINOETHYLRIBOSE; ETHYLENE DERIVATIVE; OLIGONUCLEOTIDE; PSORALEN; RIBOSE; SUGAR; UNCLASSIFIED DRUG;

ANIMAL CELL; ARTICLE; BINDING KINETICS; CHEMICAL MODIFICATION; CONCENTRATION (PARAMETERS); DRUG ACTIVITY; DRUG STRUCTURE; GENE TARGETING; IN VITRO STUDY; IN VIVO STUDY; MOLECULAR INTERACTION; NONHUMAN; PRIORITY JOURNAL; THERMOSTABILITY; TRIPLE HELIX;

ANIMALS; BASE PAIRING; BINDING SITES; BIOLOGICAL ASSAY; BRIDGED COMPOUNDS; CARBOHYDRATES; CRICETINAE; DNA; ELECTROPORATION; FICUSIN; GENE TARGETING; HYPOXANTHINE PHOSPHORIBOSYLTRANSFERASE; MODELS, CHEMICAL; NUCLEIC ACID CONFORMATION; NUCLEIC ACID DENATURATION; NUCLEIC ACID HETERODUPLEXES; OLIGONUCLEOTIDES; RIBOSE; SENSITIVITY AND SPECIFICITY; TEMPERATURE;

EID: 34548482958     PISSN: 00062960     EISSN: None     Source Type: Journal    
DOI: 10.1021/bi7003153     Document Type: Article

References (42)

1. Felsenfeld, G., Davies, D. R., and Rich, A. (1957) Formation of a three stranded polynucleotide molecule, J. Am. Chem. Soc. 79, 2023-2024.
2. Frank-Kamenetskii, M. D., and Mirkin, S. M. (1995) Triplex DNA structures, Annu. Rev. Biochem. 64, 65-95.
3. Fossella, J. A., Kim, Y. J., Shih, H., Richards, E. G., and Fresco, J. R. (1993) Relative specificities in binding of Watson-Crick base pairs by third strand residues in a DNA pyrimidine triplex motif, Nucleic Acids Res. 21, 4511-4515.
4. Thuong, N. T., and Helene, C. (1993) Sequence specific recognition and modification of double helical DNA by oligonucleotides, Angew. Chem., Intl. Ed. Engl. 32, 666-690.
5. Plum, G. E., Park, Y. W., Singleton, S. F., Dervan, P. B., and Breslauer, K. J. (1990) Thermodynamic characterization of the stability and the melting behavior of a DNA triplex: a spectroscopic and calorimetric study, Proc. Natl. Acad. Sci. U.S.A. 87, 9436-9440.
6. Helene, C. (1991) The anti-gene strategy: control of gene expression by triplex-forming-oligonucleotides, Anticancer Drug Des. 6, 569-584.
7. Chubb, J. M., and Hogan, M. E. (1992) Human therapeutics based on triple helix technology, Trends Biotechnol. 10, 132-136.
8. Vasquez, K. M., and Wilson, J. H. (1998) Triplex-directed modification of genes and gene activity, Trends Biochem. Sci. 23, 4-9.
9. Maher, L. J., III (1996) Prospects for the therapeutic use of antigene oligonucleotides, Cancer Invest. 14, 66-82.
10. Lee, J. S., Woodsworth, M. L., Latimer, L. J., and Morgan, A. R. (1984) Poly(pyrimidine)-poly(purine) synthetic DNAs containing 5-methylcytosine form stable triplexes at neutral pH, Nucleic Acids Res. 12, 6603-6614.
11. Roberts, R. W., and Crothers, D. M. (1992) Stability and properties of double and triple helices: dramatic effects of RNA or DNA backbone composition, Science 258, 1463-1466.
12. Escude, C., Sun, J. S., Rougee, M., Garestier, T., and Helene, C. (1992) Stable triple helices are formed upon binding of RNA oligonucleotides and their 2′-O-methyl derivatives to double-helical DNA, C.R. Acad. Sci. III 315, 521-525.
13. Shimizu, M., Konishi, A., Shimada, Y., Inoue, H., and Ohtsuka, E. (1992) Oligo(2′-O-methyl)ribonucleotides. Effective probes for duplex DNA, FEBS Lett. 302, 155-158.
14. Asensio, J. L., Carr, R., Brown, T., and Lane, A. N. (1999) Conformational and thermodynamic properties of parallel intramolecular triple helixes containing a DNA, RNA, or 2′-OMeDNA third strand, J. Am. Chem. Soc. 121, 11063-11070.
15. Cuenoud, B., Casset, F., Husken, D., Natt, F., Wolf, R. M., Altmann, K. H., Martin, P., and Moser, H. E. (1998) Dual recognition of double stranded DNA by 2′-aminoethoxy-modified oligonucleotides, Angew. Chem., Intl. Ed. Engl. 37, 1288-1291.
16. Carlomagno, T., Blommers, M. J., Meiler, J., Cuenoud, B., and Griesinger, C. (2001) 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, 7364-7370.
17. Osborne, S. D., Powers, V. E., Rusling, D. A., Lack, O., Fox, K. R., and Brown, T. (2004) Selectivity and affinity of triplex-forming oligonucleotides containing 2′-aminoethoxy-5-(3-aminoprop-1-ynyl)uridine for recognizing AT base pairs in duplex DNA, Nucleic Acids Res. 32, 4439-4447.
18. 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.
19. Torigoe, H., Hari, Y., Sekiguchi, M., Obika, S., and Imanishi, T. (2001) 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, 2354-2360.
20. Brunet, E., Alberti, P., Perrouault, L., Babu, R., Wengel, J., and Giovannangeli, C. (2005) Exploring cellular activity of locked nucleic acid-modified triplex-forming oligonucleotides and defining its molecular basis, J. Biol. Chem. 280, 20076-20085.
21. Koizumi, M., Morita, K., Daigo, M., Tsutsumi, S., Abe, K., Obika, S., and Imanishi, T. (2003) Triplex formation with 2′-O,4′-C-ethylene- bridged nucleic acids (ENA) having C3′-endo conformation at physiological pH, Nucleic Acids Res. 31, 3267-3273.
22. Majumdar, A., Khorlin, A., Dyatkina, N., Lin, F. L., Powell, J., Liu, J., Fei, Z., Khripine, Y., Watanabe, K. A., George, J., Glazer, P. M., and Seidman, M. M. (1998) Targeted gene knockout mediated by triple helix forming oligonucleotides, Nat. Genet. 20, 212-214.
23. Puri, N., Majumdar, A., Cuenoud, B., Miller, P. S., and Seidman, M. M. (2004) Importance of clustered 2′-O-(2-aminoethyl) residues for the gene targeting activity of triple helix-forming oligonucleotides, Biochemistry 43, 1343-1351.
24. Blommers, M. J., Natt, F., Jahnke, W., and Cuenoud, B. (1998) Dual recognition of double-stranded DNA by 2′-aminoethoxy-modified oligonucleotides: the solution structure of an intramolecular triplex obtained by NMR spectroscopy, Biochemistry 37, 17714-17725.
25. Morita, K., Yamate, K., Kurakata, S., Watanabe, K., Imanishi, T., and Koizumi, M. (2003) 2′-O,4′-C-ethylene-bridged nucleic acid (ENA) for effective antisense formation, Nucleosides, Nucleotides, Nucleic Acids 22, 1619-1621.
26. Puri, N., Majumdar, A., Cuenoud, B., Natt, F., Martin, P., Boyd, A., Miller, P. S., and Seidman, M. M. (2001) Targeted gene knockout by 2′-O-aminoethyl modified triplex forming oligonucleotides, J. Biol. Chem. 276, 28991-28998.
27. Xodo, L. E. (1995) Kinetic analysis of triple-helix formation by pyrimidine oligodeoxynucleotides and duplex DNA, Eur. J. Biochem. 228, 918-926.
28. Arya, D. P., Coffee, R. L., Jr., and Charles, I. (2001) Neomycin-induced hybrid triplex formation, J. Am. Chem Soc. 123, 11093-11094.
29. Orren, D. K., Petersen, L. N., and Bohr, V. A. (1997) Persistent DNA damage inhibits S-phase and G2 progression, and results in apoptosis, Mol. Biol. Cell 8, 1129-1142.
30. Majumdar, A., Puri, N., Cuenoud, B., Natt, F., Martin, P., Khorlin, A., Dyatkina, N., George, A. J., Miller, P. S., and Seidman, M. M. (2003) Cell cycle modulation of gene targeting by a triple helix-forming oligonucleotide, J. Biol. Chem. 278, 11072-11077.
31. Puri, N., Majumdar, A., Cuenoud, B., Natt, F., Martin, P., Boyd, A., Miller, P. S., and Seidman, M. M. (2002) Minimum number of 2′-O-(2- aminoethyl) residues required for gene knockout activity by triple helix forming oligonucleotides, Biochemistry 41, 7716-7724.
32. Richards, S., Liu, S. T., Majumdar, A., Liu, J. L., Nairn, R. S., Bernier, M., Maher, V., and Seidman, M. M. (2005) Triplex targeted genomic crosslinks enter separable deletion and base substitution pathways, Nucleic Acids Res. 33, 5382-5393.
33. Vester, B., and Wengel, J. (2004) LNA (locked nucleic acid): high-affinity targeting of complementary RNA and DNA, Biochemistry 43, 13233-13241.
34. Sun, B. W., Babu, B. R., Sorensen, 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.
35. Brunet, E., Corgnali, M., Cannata, F., Perrouault, L., and Giovannangeli, C. (2006) Targeting chromosomal sites with locked nucleic acid-modified triplex-forming oligonucleotides: study of efficiency dependence on DNA nuclear environment, Nucleic Acids Res. 34, 4546-4553.
36. Shahid, K. A., Majumdar, A., Alam, R., Liu, S. T., Kuan, J. Y., Sui, X., Cuenoud, B., Glazer, P. M., Miller, P. S., and Seidman, M. M. (2006) Targeted cross-linking of the human beta-globin gene in living cells mediated by a triple helix forming oligonucleotide, Biochemistry 45, 1970-1978.
37. Morita, K., Takagi, M., Hasegawa, C., Kaneko, M., Tsutsumi, S., Sone, J., Ishikawa, T., Imanishi, T., and Koizumi, M. (2003) Synthesis and properties of 2′-O,4′-C-ethylene-bridged nucleic acids (ENA) as effective antisense oligonucleotides, Bioorg. Med. Chem. 11, 2211-2226.
38. Lin, F. L., Majumdar, A., Klotz, L. C., Reszka, A. P., Neidle, S., and Seidman, M. M. (2000) Stability of DNA triplexes on shuttle vector plasmids in the replication pool in mammalian cells, J. Biol. Chem. 275, 39117-39124.
39. Sollogoub, M., Darby, R. A., Cuenoud, B., Brown, T., and Fox, K. R. (2002) Stable DNA triple helix formation using oligonucleotides containing 2′-aminoethoxy-5-propargylarnino-U, Biochemistry 41, 7224-7231.
40. Johnson, M. D., III, and Fresco, J. R. (1999) Third-strand in situ hybridization (TISH) to non-denatured metaphase spreads and interphase nuclei, Chromosoma 108, 181-189.
41. Nadai, A., Coll, A., Avino, A., Esteve, T., Eritja, R., and Pla, M. (2006) Efficient sequence-specific purification of Listeria innocua mRNA species by triplex affinity capture with parallel tail-clamps, ChemBioChem 7, 1039-1047.
42. Kundu, M., Nagatsugi, F., Majumdar, A., Miller, P. S., and Seidman, M. M. (2003) Enhancement and inhibition by 2′-O-hydroxyethyl residues of gene targeting mediated by triple helix forming oligonucleotides, Nucleosides, Nucleotides, Nucleic Acids 22, 1927-1938.