Synthesis, characterization, and biological properties of small branched RNA fragments containing chiral (Rp and Sp) 2′,5′-phosphorothioate linkages

Nucleosides, Nucleotides and Nucleic Acids

Volumn 25, Issue 2, 2006, Pages 203-229

  Mourani, Rawan ^a   Damha, Masad J ^a  

^a MCGILL UNIVERSITY   (Canada)

Author keywords

Branched RNA; Debranching enzyme

Indexed keywords

1,4 ALPHA GLUCAN BRANCHING ENZYME; 2',5' PHOSPHODIESTER; 2',5' PHOSPHOROTHIOATE; ESTER DERIVATIVE; NUCLEOSIDE TRIPHOSPHATE; OXYGEN; PHOSPHOROTHIOIC ACID DERIVATIVE; PYROPHOSPHORIC ACID DERIVATIVE; RNA; TETRAMER; TETRANUCLEOSIDE TRIPHOSPHATE; UNCLASSIFIED DRUG;

ARTICLE; CHEMICAL BOND; CHEMICAL COMPOSITION; CHIRALITY; CRYSTALLIZATION; ENZYME DEGRADATION; ENZYME SUBSTRATE; EXAMINATION; GENETIC LINKAGE; HYDROLYSIS; RNA SYNTHESIS; STEREOCHEMISTRY; X RAY ANALYSIS; YEAST;

RNA; RNA NUCLEOTIDYLTRANSFERASES; RNA SPLICING; STEREOISOMERISM; THIOPHOSPHORIC ACID ESTERS;

EID: 31644437387     PISSN: 15257770     EISSN: 15322335     Source Type: Journal    
DOI: 10.1080/15257770500447004     Document Type: Article

References (45)

1. Padgett, R.A.; Konarska, M.M.; Grabowski, P.J.; Hardy, S.F.; Sharp, P.A. Lariat RNAs as intermediates and products in the splicing of messenger RNA precursors. Science 1984, 225, 898-903.
2. Grabowski, P.J.; Seiler, S.R.; Sharp, P.A. A multicomponent complex is involved in the splicing of messenger RNA precursors. Cell 1985, 42, 345-353.
3. Brody E., Abelson J. The "spliceosome": yeast pre-messenger RNA associates with a 40S complex in a splicing-dependent reaction. Science 1985, 228, 963-967.
4. Frendewey, D.; Keller, W. Stepwise assembly of a pre-mRNA splicing complex requires U-snRNPs and specific intron sequences. Cell 1985, 42, 355-367.
5. Wallace, J.C., Edmonds, M. Polyadenylated nuclear RNA contains branches. Proc. Natl. Acad. Sci. USA. 1983, 80, 950-954.
6. Ruskin, B.; Green, M.R. An RNA processing activity that debranches RNA lariats. Science 1985, 229, 135-140.
7. Chapman, K.B.; Boeke, J.D. Isolation and characterization of the gene encoding yeast debranching enzyme. Cell 1991, 65, 483-491.
8. Ooi, S.L.; Samarsky, D.A.; Fournier, M.J.; Boeke, J.D. Intronic snoRNA Biosynthesis in S. cerevisiae depends on the Lariat debranching enzyme: Intron length effects and activity of a precursor snoRNA. RNA. 1998, 4, 1096-1110.
9. (a) Leader, D.J.; Clark, G.P.; Watters, J.; Beven, A.F.; Shaw, P.J.; Brown, J. W.S. Clusters of multiple different small nucleolar RNA genes in plants are expressed as and processed from polycistronic pre-snoRNAs. EMBO J. 1997, 16, 5742-5751.
10. (b) Leader, D.J.; Sanders, J.F.; Waugh, R.; Shaw, P.; Brown, J.W.S. Molecular characterization of plant U14 small nucleolar RNA genes closely linked genes are transcribed as polycistronic U14 transcripts. Nucleic Acids Res. 1994, 22, 5196-5203.
11. (c) Maxwell, E.S.; Fournier, M.J. The small nucleolar RNAs. Annu. Rev. Biochem. 1995, 64, 897-934.
12. Nam, K.; Lee, G.; Trambley, J.; Devine, S.E.; Boeke, J.D. Severe growth defect in a Schizosaccharomyces pombe mutant defective in intron lariat degradation. Mol. Cell. Biol. 1997, 17, 809-818.
13. Nam, K.; Hudson, R.H.E.; Ganeshan, K.; Chapman, K.B.; Damha, M.J.; Boeke, J.D. Yeast lariat debranching enzyme: substrate and sequence specificity. J. Biol. Chem. 1994, 269, 20613-20621.
14. Ooi, S.L.; Dann, C., III; Nam, K.; Leahy, D.; Damha, M.J.; Boeke, J.D. The yeast lariat debranching enzyme. Methods Enzymol. 2001, 342, 233-250.
15. Hudson, R.H.E. Synthesis and studies of branched oligonucleotides. Ph.D. Dissertation, University of Toronto, 1995.
16. Ganeshan, K.; Tadey, T.; Nam, K.; Braich, R.; Purdy, W.C.; Boeke, J.D.; Damha, M.J. Novel approaches to the synthesis and analysis of branched RNA. Nucleos. Nucleot. 1995, 14, 1009-1013.
17. Maschhoff, K.L.; Padgett, R.A. The stereochemical course of the first step of pre-mRNA splicing. Nucleic Acids Res. 1993, 21, 5456-5462.
18. Damha, M.J.; Ogilvie, K.K. Oligoribonucleotide synthesis. In Methods in Molecular Biology; Protocols for Oligonucleotides and Analogs; Agrawal, S., Ed.; Humana Press Inc., Totowa, NJ., 1993, 20, 81-114.
19. Wasner, M.; Arion, D.; Borkow, G.; Noronha, A.; Uddin, A.H.; Parniak, M.A.; Damha, M.J. Physicochemical and biochemical properties of 2′,5′-linked RNA and 2′,5′-RNA:3′,5′-RNA "hybrid" duplexes. Biochem. 1998, 37, 7478-7486.
20. Lecchi, P.; Le, H.M.T.; Pannell, L.K. 6-Aza-2-thiothymine: A matrix for MALDI spectra of oligonucleotides. Nucleic Acids Res. 1995, 23, 1276-1277.
21. Damha, M.J.; Ganeshan, K.; Hudson, R.H.E.; Zabarylo, S.V. Solid-phase synthesis of branched oligoribonucleotides related to messenger RNA splicing intermediates. Nucleic Acids Res. 1992, 20, 6565-6573.
22. Sambrook, J.; Fritsch, E.F.; Maniatis, T. Molecular Cloning: A Laboratory Manual; Cold Spring Harbor Laboratory Press, Plainview, NY, 1989.
23. Uhlenbeck, O.C.; Gumport, R.I. T4 RNA ligase. In The Enzymes; Boyer, P.D., Ed.; Academic Press, Inc.; New York, 1982; 15B, 31-60.
24. Nelson, P.S.; Bach, C.T.; Verheyden, J.P.H. Synthesis of P-thioadenylyl- (2′-5′)-adenosine and P-thioadenylyl-(2′-5′)-P- thioadenylyl-(2′-5′)-adenosine. J. Org. Chem. 1984, 49, 2314-2317.
25. Ma, M.Y.X.; Dignam, J.C.; Fong, G.W.; Li, L.; Gray, S.H.; Jacob-Samuel, B.; George, S.T. Evaluation of 3-ethoxy-1,2,4-dithiazoline-5-one (EDITH) as a new sulfurising reagent in combination with labile exocyclic amino protecting groups for solid-phase oligonucleotide synthesis. Nucleic Acids Res. 1997, 25, 3590-3593.
26. Xu, Q.; Musier-Forsyth, K.; Hammer, R.P.; Barany, G. Use of 1,2,3- dithiazolidine-3,5-dione (DtsNH) and 3-ethoxy-1,2,4-dithiazoline-5-one for synthesis of phosphorothioate-containing oligodeoxyribonucleotides. Nucleic Acids Res. 1986, 24, 1602-1607.
27. Xu, Q.; Barany, G.; Hammer, R.P.; Musier-Forsyth, K. Efficient introduction of phosphorothioates into RNA oligonucleotides by 3-ethoxy-1,2,4-dithiazoline-5-one (EDITH). Nucleic Acids Res. 1996, 24, 3643-3644.
28. Iyer, R.P.; Egan, W.; Regan, J.B.; Beaucage, S.L. 3H-1,2-Benzodithiole-3- one 1,1-dioxide as an improved sulfurizing reagent in the solid-phase synthesis of oligodeoxyribonucleoside phosphorothioates. J. Am. Chem. Soc. 1990, 112, 1253-1254.
29. Iyer, R.P.; Phillips, L.R.; Egan, W.; Regan, J.B.; Beaucage, S.L. The automated synthesis of sulfur-containing oligodeoxyribonucleotides using 3H-1,2- benzodithiol-3-one 1,1-dioxide as a sulfur-transfer reagent J. Org. Chem. 1990, 55, 4693-4699.
30. Cantor, C.R.; Schimmel, P.R.; Biophysical Chemistry - Part II: Techniques for the Study of Biological Structure and Function; W. H. Freeman and Co., San Francisco., 1990, 349-472.
31. Bush, C.A. Basic Principles in Nucleic Acid Chemistry, Ts'o, P.O.P. Ed., Academic Press, New York, 1974, 2, 92-169.
32. Harada, N.; Nakanishi, K. In Circular Dichroic Spectroscopy; Exciton Coupling in Organic Stereochemistry; University Science Books, New York, 1983.
33. Damha, M.J. Developments in the chemical synthesis of oligonucleotides and their analogs. Ph.D. Dissertation, McGill University, 1987.
34. Warsaw, M.M.; Cantor, C.R. Oligonucleotide interactions. IV. Conformational differences between deoxy- and ribodinucleoside phosphates; Biopolymers 1970, 9, 1079-1103.
35. Brahms, J.; Maurizot, J.C.; Michelson, A.M. Conformational stability of dinucleotides in solution. J. Mol. Biol. 1967, 25, 481-495.
36. Burgers, P.M.J.; Eckstein, F. A study of the mechanism of DNA polymerase I from Escherichia coli with diastereomeric phosphorothioate analogs of deoxyadenosine triphosphate J. Biol. Chem. 1979, 254, 6889-6893.
37. Braich, R.S. Branched nucleic acids: Novel probes for studying pre-m RNA processing and triple helical DNA. Ph.D. Dissertation, McGill University, 1999.
38. Kierzek, R.; Kopp, D.W.; Edmonds, M.; Caruthers, M.H. Chemical synthesis of branched RNA. Nucleic Acids Res. 1986, 14, 4751-4764.
39. Khalid, M.F.; Damha, M.J.; Shuman, S.; Schwer, B. Structure-function analysis of yeast RNA debranching enzyme (Dbr1), a manganese-dependent phosphodiesterase, Nucleic Acids Research, 2005, 33, 6349-6360.
40. Koonin, E.V. Conserved sequence pattern in a wide variety of phosphoesterases. Protein Sci. 1994; 3, 356-358.
41. Zhuo, S.; Clemens, J.C.; Stone, R.L.; Dixon, J.E. Mutational analysis of a Ser/Thr phosphatase: identification of residues important in phosphoesterase substrate binding and catalysis. J. Biol. Chem. 1994, 269, 26234-26238.
42. Goldberg, J.; Huang, H.; Kwon, Y.; Greengard, P.; Nairn, A.C.; Kuriyan, J. Three-dimensional structure of the catalytic subunit of protein serine/threonine phosphatase-1. Natuure 1995, 376, 745-753.
43. Voegtli, W.C.; White, D.J.; Reiter, N.J.; Rusnak, F.; Rosenzweig, A.C. Structure of the bacteriophage lambda Ser/Thr protein phosphatase with sulfate ion bound in two coordination modes. Biochem. 2000, 39, 15365-15374.
44. Hopfner, K.P.; Karcher, A.; Craig, L.; Woo, T.T.; Carney, J.P.; Tainer, J.A. Structural biochemistry and interaction architecture of the DNA double-strand break repair Mre11 nuclease and Rad50-ATPase. Cell 2001, 105, 473-485.
45. Burgers, P.M.J.; Eckstein, F.; Hunneman, D.H. Stereochemistry of hydrolysis by snake venom phosphodiesterase. J. Biol. Chem. 1979, 254, 7476-7478.