1887

Chapter 4 : Incorporation of Modified Nucleotides into RNA for Studies on RNA Structure, Function and Intermolecular Interactions

MyBook is a cheap paperback edition of the original book and will be sold at uniform, low price.

Ebook: Choose a downloadable PDF or ePub file. Chapter is a downloadable PDF file. File must be downloaded within 48 hours of purchase

Buy this Chapter
Digital (?) $15.00

Preview this chapter:
Zoom in
Zoomout

Incorporation of Modified Nucleotides into RNA for Studies on RNA Structure, Function and Intermolecular Interactions, Page 1 of 2

| /docserver/preview/fulltext/10.1128/9781555818296/9781555811334_Chap04-1.gif /docserver/preview/fulltext/10.1128/9781555818296/9781555811334_Chap04-2.gif

Abstract:

This chapter focuses on techniques for intentionally incorporating both natural and unnatural modified nucleotides into RNA molecules. The incorporation of modified nucleotides can also facilitate the structural analysis of RNAs and RNA-containing complexes. The chapter provides a broad overview of the types of experiments that can be performed with chemically modified RNAs. It describes the properties of particular modified nucleotides, and discusses techniques for their incorporation into polynucleotide chains. It presents a number of examples of the ways in which synthetic approaches have been used to investigate a variety of problems. It also illustrates the methods that pertain to individual areas of expertise. Many of the modified nucleotides retain the structural properties of their unmodified counterparts and can be randomly incorporated into polynucleotide chains by enzymatic synthesis. RNA molecules with modified nucleotides at predetermined sites can also be constructed by semisynthetic methods in which the modified residue is introduced at the 5' end of the 3' RNA fragment by transcription and then ligated to the 5' RNA fragment. A novel strategy for the site-specific incorporation of modified nucleotides makes use of circularly permuted RNAs (cpRNAs). The approaches described in this chapter will prove useful in the future in the many exciting areas of research involving naturally modified and edited RNAs.

Citation: Zimmermann R, Gait M, Moore M. 1998. Incorporation of Modified Nucleotides into RNA for Studies on RNA Structure, Function and Intermolecular Interactions, p 59-84. In Grosjean H, Benne R (ed), Modification and Editing of RNA. ASM Press, Washington, DC. doi: 10.1128/9781555818296.ch4

Key Concept Ranking

Human immunodeficiency virus 1
0.47245726
0.47245726
Highlighted Text: Show | Hide
Loading full text...

Full text loading...

Figures

Image of Figure 1
Figure 1

Modified nucleotides useful in RNA cross-linking experiments.

Citation: Zimmermann R, Gait M, Moore M. 1998. Incorporation of Modified Nucleotides into RNA for Studies on RNA Structure, Function and Intermolecular Interactions, p 59-84. In Grosjean H, Benne R (ed), Modification and Editing of RNA. ASM Press, Washington, DC. doi: 10.1128/9781555818296.ch4
Permissions and Reprints Request Permissions
Download as Powerpoint
Image of Figure 2
Figure 2

Structures of disulfide cross-links used in RNA structural studies.

Citation: Zimmermann R, Gait M, Moore M. 1998. Incorporation of Modified Nucleotides into RNA for Studies on RNA Structure, Function and Intermolecular Interactions, p 59-84. In Grosjean H, Benne R (ed), Modification and Editing of RNA. ASM Press, Washington, DC. doi: 10.1128/9781555818296.ch4
Permissions and Reprints Request Permissions
Download as Powerpoint
Image of Figure 3
Figure 3

Base analogs useful in functional group analysis of RNA structures.

Citation: Zimmermann R, Gait M, Moore M. 1998. Incorporation of Modified Nucleotides into RNA for Studies on RNA Structure, Function and Intermolecular Interactions, p 59-84. In Grosjean H, Benne R (ed), Modification and Editing of RNA. ASM Press, Washington, DC. doi: 10.1128/9781555818296.ch4
Permissions and Reprints Request Permissions
Download as Powerpoint
Image of Figure 4
Figure 4

Sugar and phosphate analogs useful in analysis of RNA structures.

Citation: Zimmermann R, Gait M, Moore M. 1998. Incorporation of Modified Nucleotides into RNA for Studies on RNA Structure, Function and Intermolecular Interactions, p 59-84. In Grosjean H, Benne R (ed), Modification and Editing of RNA. ASM Press, Washington, DC. doi: 10.1128/9781555818296.ch4
Permissions and Reprints Request Permissions
Download as Powerpoint
Image of Figure 5
Figure 5

Steps involved in one cycle of solid-phase synthesis of oligoribonucleotides by the silyl-phosphoramidite method.

Citation: Zimmermann R, Gait M, Moore M. 1998. Incorporation of Modified Nucleotides into RNA for Studies on RNA Structure, Function and Intermolecular Interactions, p 59-84. In Grosjean H, Benne R (ed), Modification and Editing of RNA. ASM Press, Washington, DC. doi: 10.1128/9781555818296.ch4
Permissions and Reprints Request Permissions
Download as Powerpoint
Image of Figure 6
Figure 6

Transcription by T7 RNA polymerase of plasmid DNA (a), amplified DNA (b), and synthetic DNA (c) templates. Black rectangles denote the 17-bp T7 RNA polymerase promoter; RS signifies a restriction site.

Citation: Zimmermann R, Gait M, Moore M. 1998. Incorporation of Modified Nucleotides into RNA for Studies on RNA Structure, Function and Intermolecular Interactions, p 59-84. In Grosjean H, Benne R (ed), Modification and Editing of RNA. ASM Press, Washington, DC. doi: 10.1128/9781555818296.ch4
Permissions and Reprints Request Permissions
Download as Powerpoint
Image of Figure 7
Figure 7

Construction of recombinant RNA molecules containing modified nucleotides, (a) Replacement of A73 and A76 of yeast tRNA with 2-azidoadenosine (2NA). Whitfeld degradation entails repeated cycles of periodate oxidation, aniline cleavage and phosphatase treatment. ( ) (b) Substitution for Y37 of yeast tRNA by 2- or 8-azidoadenosine (NA). ( , and .) (c) Introduction of azidoadenosine (N,A) at position 21 of yeast tRNA by using a chimeric oligonucleotide to direct cleavage by RNase Η and the DNA ligase method to reconstruct the intact tRNA molecule. ( ) (d) Semisynthetic incorporation of 4-thioU (sU) into a long RNA molecule. Black rectangles indicate the promoter for T7 RNA polymerase. Transcripts are joined by the DNA ligase method. (Adapted from .) () Site-specific incorporation of modified nucleotides through the use of circularly permuted RNAs (cpRNAs). Black rectangle, T7 RNA polymerase promoter; GMPS, guanosine 5′-monophosphorothioate; APAB, -azidophenacyl bromide; ΑΡΑ, -azidophenacyl moiety. (Adapted from .) Asterisks indicate positions labeled with P.

Citation: Zimmermann R, Gait M, Moore M. 1998. Incorporation of Modified Nucleotides into RNA for Studies on RNA Structure, Function and Intermolecular Interactions, p 59-84. In Grosjean H, Benne R (ed), Modification and Editing of RNA. ASM Press, Washington, DC. doi: 10.1128/9781555818296.ch4
Permissions and Reprints Request Permissions
Download as Powerpoint
Image of Figure 8
Figure 8

Mechanisms of RNA joining reactions catalyzed by T4 RNA ligase (A) and T4 DNA ligase (B).

Citation: Zimmermann R, Gait M, Moore M. 1998. Incorporation of Modified Nucleotides into RNA for Studies on RNA Structure, Function and Intermolecular Interactions, p 59-84. In Grosjean H, Benne R (ed), Modification and Editing of RNA. ASM Press, Washington, DC. doi: 10.1128/9781555818296.ch4
Permissions and Reprints Request Permissions
Download as Powerpoint
Image of Figure 9
Figure 9

Template-dependent chemical ligation to form an oligoribonucleotide containing a trisubstituted pyrophosphate linkage.

Citation: Zimmermann R, Gait M, Moore M. 1998. Incorporation of Modified Nucleotides into RNA for Studies on RNA Structure, Function and Intermolecular Interactions, p 59-84. In Grosjean H, Benne R (ed), Modification and Editing of RNA. ASM Press, Washington, DC. doi: 10.1128/9781555818296.ch4
Permissions and Reprints Request Permissions
Download as Powerpoint
Image of Figure 10
Figure 10

The apex region of the TAR RNA stem-loop, showing sites where chemical substitution or interference has been used to determine functionalities important in recognition by HIV-1 Tat.

Citation: Zimmermann R, Gait M, Moore M. 1998. Incorporation of Modified Nucleotides into RNA for Studies on RNA Structure, Function and Intermolecular Interactions, p 59-84. In Grosjean H, Benne R (ed), Modification and Editing of RNA. ASM Press, Washington, DC. doi: 10.1128/9781555818296.ch4
Permissions and Reprints Request Permissions
Download as Powerpoint
Image of Figure 11
Figure 11

Summary of cross-links formed between mRNA analogs and three regions of the 16S rRNA in 30S ribosomal subunits. (Data from ; and .)

Citation: Zimmermann R, Gait M, Moore M. 1998. Incorporation of Modified Nucleotides into RNA for Studies on RNA Structure, Function and Intermolecular Interactions, p 59-84. In Grosjean H, Benne R (ed), Modification and Editing of RNA. ASM Press, Washington, DC. doi: 10.1128/9781555818296.ch4
Permissions and Reprints Request Permissions
Download as Powerpoint
Image of Figure 12
Figure 12

Short-range cross-links formed between tRNA and the A, Ρ and Ε sites of the ribosome. SX, 30S subunit proteins; LX, 50S subunit proteins; arabic numerals, nucleotides in 23S rRNA; italic numerals, nucleotides in 16S rRNA. (Data from , and ; and and unpublished data.)

Citation: Zimmermann R, Gait M, Moore M. 1998. Incorporation of Modified Nucleotides into RNA for Studies on RNA Structure, Function and Intermolecular Interactions, p 59-84. In Grosjean H, Benne R (ed), Modification and Editing of RNA. ASM Press, Washington, DC. doi: 10.1128/9781555818296.ch4
Permissions and Reprints Request Permissions
Download as Powerpoint

References

/content/book/10.1128/9781555818296.chap4
1. Aboul-ela, F.,, J. Karn,, and G. Varani. 1995. The structure of the human immunodeficiency virus type-1 TAR RNA reveals principles of recognition by tat protein. J. Mol. Biol. 253:313332.
2. Aboul-ela, F.,, J. Karn,, and G. Varani. 1996. Structure of HIV-1 TAR RNA in the absence of ligands reveals a novel conformation of the trinucleotide bulge. Nucleic Acids Res. 24:39743982.
3. Abramovitz, D. L.,, R. A. Freidmen,, and A. M. Pyle. 1996. Catalytic role of 2'-hydroxyl groups within a group II intron active site. Science 271:14101413.
4. Adams, C. J.,, J. B. Murray,, J. R. P. Arnold,, and P. G. Stockley. 1994. Incorporation of a fluorescent nucleotide into oligoribO-nucleotides. Tetrahedron Lett. 35:15971600.
5. Baidya, N.,, and O. C. Uhlenbeck. 1995. The role of 2'-hydroxyl groups in an RNA-protein interaction. Biochemistry 34: 1236312368.
6. Bare, L. A. , and O. C. Uhlenbeck. 1986. Specific substitution into the anticodon loop of yeast tyrosine transfer RNA. Biochemistry 25:58255830.
7. Bare, L.,, A. G. Bruce,, R. Gesteland,, and O. C. Uhlenbeck. 1983. Uridine-33 in yeast tRNA not essential for amber suppression. Nature 305:554556.
8. Barrio, J. R.,, M. C. G. Barrio,, N. J. Leonard,, T. E. England,, and O. C. Uhlenbeck. 1978. Synthesis of modified nucleoside 3',5'-bisphosphates and their incorporation into oligoribonucleotides with T4 RNA ligase. Biochemistry 17:20772081.
9. Bayer, P.,, M. Kraft,, A. Ejchart,, M. Westendorp,, R. Frank,, and P. Rosch. 1995. Structural studies of HIV-1 tat protein. J. Mol. Biol. 247:529535.
10. Beauchemin, N.,, H. Grosjean,, and R. Cedergren. 1986. Construction, aminoacylation and 80S ribosomal complex formation with yeast initiator tRNA having an arginine CCU anticodon. FEBS Lett. 202:812.
11. Beigelman, L.,, A. Karpeisky,, and N. Usman. 1994. Synthesis of 1-deoxy-D-ribofuranose phosphoramidite and the incorporation of abasic nucleotides in stem-loop II of a hammerhead ribozyme. Bioorg. Med. Chem. Lett. 4:17151720.
12. Bevilacqua, P. C.,, and T. R. Cech. 1996. Minor-groove recognition of double-stranded RNA by the double-stranded RNA-binding domain from the RNA-activated protein kinase PKR. Biochemistry 35:99839994.
13. Bochkariov, D. E.,, and A. A. Kogon. 1992. Application of 3-[3-(3-trifluoromethyl-diazirin-3-yl)Phenyl]-2,3-dihydroxypropionic acid, carbene generating, cleavable crosslinking reagent for photoaffinity labeling. Anal. Biochem. 204:9095.
14. Breitschopf, K.,, and H. J. Gross. 1996. The discriminator bases G73 in human tRNASer and A73 in tRNALeu have significantly different roles in the recognition of aminoacyl-tRNA synthetases. Nucleic Acids Res. 24:405410.
15. Bruce, A. G.,, and O. C. Uhlenbeck. 1982. Enzymatic replacement of the anticodon of yeast Phenylalanine transfer ribonucleic acid. Biochemistry 21:855861.
16. Burgin, A. B.,, and N. R. Pace. 1990. Mapping the active site of ribonuclease P RNA using a substrate containing a photoaffinity reagent. EMBO J. 9:41114118.
17. Calnan, B. J.,, B. Tidor,, S. Biancalana,, D. Hudson,, and A. D. Frankel. 1991. Arginine-mediated RNA recognition: the arginine fork. Science 252:11671171.
18. Cech, T. R. 1986. The generality of self-splicing RNA: relationship to nuclear mRNA splicing. Cell 44:207210.
19. Cedergren, R.,, and H. Grosjean. 1987. RNA design by in vitro RNA recombination and synthesis. Biochem. Cell Biol. 65: 677692.
20. Chaix, C.,, A. M. Duplaa,, D. Molko,, and R. Teoule. 1989. Solid phase synthesis of the 5'-half of the initiator tRNA from B. subtilis. Nucleic Acids Res. 17:73817393.
21. Chamberlin, M.,, and T. Ryan,. 1982. Bacteriophage DNA-dependent RNA polymerase, p. 87105. In P. D. Boyer (ed.), The Enzymes, vol. 15, part B. Academic Press, New York, N.Y..
22. Chanfreau, G.,, and A. Jacquier. 1994. Catalytic site components common to both splicing steps of a group II intron. Science 266: 13831387.
23. Chen, C. H.,, and D. S. Sigman. 1986. Nuclease activity of 1,10-Phenanthroline-copper: sequence-specific targeting. Proc. Natl. Acad. Sci. USA 83:71477151.
24. Chiara, M. D.,, O. Gozani,, M. Bennett,, P. Champion-Arnaud,, L. Palandjian,, and R. Reed. 1996. Identification of proteins that interact with exon sequences, splice sites, and the branchpoint sequence during each stage of spliceosome assembly. Mol. Cell. Biol. 16:33173326.
25. Chiara, M. D.,, L. Palandjian,, R. Feld-Kramer,, and R. Reed. 1997. Evidence that U5 snRNP recognizes the 3' splice site for catalytic step II in mammals. EMBO J. 16:47464759.
26. Chowrira, B. M.,, A. Berzal-Herranz,, C. F. Keller,, and J. M. Burke. 1993. Four ribose 2'-hydroxyl groups essential for catalytic function of the hairpin ribozyme. J. Biol. Chem. 268:1945819462.
27. Churcher, M. J.,, C. Lamont,, F. Hamy,, C. Dingwall,, S. M. Green,, A. D. Lowe,, P. J. G. Butler,, M. J. Gait,, and J. Karn. 1993. High affinity binding of TAR RNA by the human immunodeficiency virus type-1 tat protein requires base-pairs in the RNA stem and amino acid residues flanking the basic region. J. Mol. Biol. 230: 90110.
28. Cohen, S. B.,, and T. R. Cech. 1997. Dynamics of thermal motions within a large catalytic RNA investigated by cross-linking with thiol-disulfide interchange. J. Am. Chem. Soc. 119:62596268.
29. Conrad, F.,, A. Hanne,, R. K. Gaur,, and G. Krupp. 1995. Enzymatic synthesis of 2'-modified nucleic acids: identification of important phosphate and ribose moieties in RNase P substrates. Nucleic Acids Res. 23:18451853.
30. Cooperman, B. L. 1988. Affinity labeling of ribosomes. Methods Enzymol. 164:341361.
31. Cunningham, P. R.,, and J. Ofengand. 1990. Use of inorganic pyrophosphatase to improve the yield of in vitro transcription reactions catalyzed by T7 RNA polymerase. BioTechniques 9: 713714.
32. Damha, M. J.,, and K. K. Ogilvie,. 1993. Oligoribonucleotide synthesis, p. 81114. In S. Agrawal (ed.), Methods in Molecular Biology. Humana Press, Totowa, N. J..
33. Davis, R. H. 1995. Large-scale oligoribonucleotide production. Curr. Opin. Biotechnol. 6:213217.
34. Delling, U.,, L. S. Reid,, R. W. Barnett,, M. X. Y. Ma,, S. Climie,, M. Sumner-Smith,, and N. Sonenberg. 1992. Conserved nucleotides in the TAR RNA stem of human immunodeficiency virus type 1 are critical for tat binding and trans activation: model for TAR RNA tertiary structure. J. Virol. 66:30183025.
35. Dietz, T. M.,, and T. H. Koch. 1987. Photochemical coupling of 5-bromouracil to tryptophan, tyrosine and histidine, peptide-like derivatives in aqueous fluid solution. Photochem. Photobiol. 46: 971978.
36. Donis-Keller, H. 1979. Site-specific enzymatic cleavage of RNA. Nucleic Acids Res. 7:179192.
37. Dontsova, O.,, A. Kopylov,, and R. Brimacombe. 1991. The location of mRNA in the ribosomal 30S initiation complex: site-directed cross-linking of mRNA analogues carrying several photO-reactive labels simultaneously on either side of the AUG start codon. EMBO J. 10:26132620.
38. Dontsova, O.,, S. Dokudovskaya,, A. Kopylov,, A. Bogdanov,, J. Rinke-Appel,, N. Jünke,, and R. Brimacombe. 1992aa. Three widely separated positions in the 16S RNA lie in or close to the ribosomal decoding region: a site-directed cross-linking study with mRNA analogues. EMBO J. 11:31053116.
39. Dontsova, O. A.,, K. V. Rosen,, S. L. Bogdanova,, E. A. Skripkin,, A. M. Kopylov,, and A. A. Bogdanov. 1992bb. Identification of the Escherichia coli 30S ribosomal protein neighboring mRNA during initiation of translation. Biochimie 74:363371.
40. Doudna, J. A.,, and J. H. Cate. 1997. RNA structure: crystal clear? Curr. Opin. Struct. Biol. 7:310316.
41. Doudna, J. A.,, J. W. Szostak,, A. Rich,, and N. Usman. 1990. Chemical synthesis of oligoribonucleotides containing 2-aminopurine: substrates for the investigation of ribozyme function. J. Org. Chem. 55:55475549.
42. Dreyer, G. B.,, and P. B. Dervan. 1985. Sequence specific cleavage of single-stranded DNA: oligodeoxynucleotide-EDTA-Fe(II). Proc. Natl. Acad. Sci. USA 82:968972.
43. Eadie, J. S.,, L. J. McBride,, J. W. Efcavitch,, L. B. Hoff,, and R. Cathcart. 1987. High-performance liquid chromatographic analysis of oligodeoxyribonucleotide base composition. Anal. Biochem. 165:442447.
44. Earnshaw, D. J.,, B. Masquida,, S. Müller,, S. T. Sigurdsson,, F. Eckstein,, E. Westhof,, and M. J. Gait. 1997. Inter-domain cross-linking and molecular modelling of the hairpin ribozyme. J. Mol. Biol. 274:197212.
45. Eaton, B. E.,, and W. A. Pieken. 1995. Ribonucleosides and RNA. Annu. Rev. Biochem. 64:837863.
46. England, T. E.,, and O. C. Uhlenbeck. 1978. Enzymatic oligonucleotide synthesis with T4 RNA ligase. Biochemistry 17:20692076.
47. Engler, M. J.,, and C. C. Richardson,. 1982. DNA ligases, p. 329. In P. D. Boyer (ed.), The Enzymes, vol. 15, part B. Academic Press, New York, N.Y.
48. Enright, C.,, and B. Sollner-Webb,. 1994. Ribosomal RNA processing in vertebrates, p. 135172. In S. J. Higgins, and B. D. Hames (ed.), RNA Processing: a Practical Approach, vol. II. IRL Press, Oxford, United Kingdom.
49. Evans, R. K., and B. E. Haley. 1987. Synthesis and biological properties of 5-azidO-2'-deoxyuridine 5'-triphosphate, a photoactive nucleotide suitable for making light-sensitive DNA. Biochemistry 26:269276.
50. Fabrizio, P.,, and J. Abelson. 1992. Thiophosphates in yeast U6 snRNA specifically affect pre-mRNA splicing in vitro. Nucleic Acids Res. 20:36593664.
51. Favre, A.,, and J.-L. Fourrey. 1995. Structural probing of small endonucleolytic ribozymes in solution using thiO-substituted nucleobases as intrinsic photolabels. Acc. Chem. Res. 28:375382.
52. Ferre-D'Amare, A. R.,, and J. A. Doudna. 1996. Use of cis- and trans-ribozymes to remove 5' and 3' heterogeneities from milligrams of in vitro transcribed RNA. Nucleic Acids Res. 24:977978.
53. Fournier, M.,, E. Haumont,, S. de Henau,, J. Gangloff,, and H. Grosjean. 1983. Post-transcriptional modification of the wobble nucleotide in anticodon-substituted yeast tRNAArgII after microinjection into Xenopus laevis oocytes. Nucleic Acids Res. 11:707718.
54. Frugier, M.,, C. Florentz,, M. W. Hosseini,, J.-M. Lehn,, and R. Giege. 1994. Synthetic polyamines stimulate in vitro transcription by T7 RNA polymerase. Nucleic Acids Res. 22:27842790.
55. Fu, D.-J.,, and L. W. McLaughlin. 1992. Importance of specific adenosine N7-nitrogens for efficient cleavage by a hammerhead ribozyme. A model for magnesium binding. Biochemistry 31: 1094110949.
56. Fu, D.-J.,, S. B. Rajur,, and L. W. McLaughlin. 1993. Importance of specific N7-nitrogens and purine amino groups for efficient cleavage by a hammerhead ribozyme. Biochemistry 32: 1062910637.
57. Gait, M. J.,, J. Grasby,, J. Karn,, K. Mersmann,, and C. E. Pritchard. 1995. Synthetic ribonucleotide analogues for structure-function studies. Nucleosides Nucleotides 14:11331144.
58. Gait, M. J.,, and J. Karn. 1993. RNA recognition by the human immunodeficiency virus tat and rev proteins. Trends Biochem. Sci. 18:255259.
59. Gait, M. J.,, C. E. Pritchard,, and G. Slim,. 1991. Oligoribonucleotide synthesis, p. 2548. In M. J. Gait (ed.), Oligonucleotides and Analogues: a Practical Approach. IRL Press, Oxford, United Kingdom.
60. Gasparutto, D.,, T. Livache,, H. Bazin,, A.-M. Duplaa,, A. Guy,, A. Khorlin,, D. Molko,, A. Roget,, and R. Teoule. 1992. Chemical synthesis of a biologically active natural tRNA with its minor bases. Nucleic Acids Res. 19:51595166.
61. Gaur, R. K.,, J. Valcárcel,, and M. R. Green. 1995. Sequential recognition of the pre-mRNA branch point by U2AF65 and a novel spliceosome-associated 28-kDa protein. RNA 1:407417.
62. Gaur, R. K.,, L. W. McLaughlin,, and M. R. Green. 1997. Functional group substitutions of the branchpoint adenosine in a nuclear pre-mRNA and a group II intron. RNA 3:861869.
63. Goodwin, J. T.,, S. E. Osborne,, E. J. Scholle,, and G. D. Glick. 1996. Design, synthesis, and analysis of yeast tRNAPhe analogs possessing intra- and interhelical disulfide cross-links. J. Am. Chem. Soc. 118:52075215.
64. Gott, J. M.,, M. C. Willis,, T. K. Koch,, and O. C. Uhlenbeck. 1991. A specific, UV-induced RNA-protein cross-link using 5-bromouridine-substituted RNA. Biochemistry 30:62906295.
65. Grasby, J. A.,, and M. J. Gait. 1994. Synthetic oligoribonucleotides carrying site-specific modifications for RNA structure-function studies. Biochimie 76:12231234.
66. Grasby, J. A.,, P. J. G. Butler,, and M. J. Gait. 1993. The synthesis of oligoribonucleotides containing O6-methylguanosine: the role of conserved guanosine residues in hammerhead ribozyme cleavage. Nucleic Acids Res. 21:44444450.
67. Grasby, J. A.,, M. Singh,, J. Karn,, and M. J. Gait. 1995. Synthesis and applications of oligoribonucleotides containing N4-methylcytidine. Nucleosides Nucleotides 14:11291132.
68. Griffin, E. A. J.,, Q. Zhifeng,, W. J. J. Michels,, and A. M. Pyle. 1995. Group II intron ribozymes that cleave DNA and RNA linkages with similar efficiency, and lack contacts with substrate 2'-hydroxyl groups. Chem. Biol. 2:761770.
69. Gurevich, V. V. 1996. Use of bacteriophage RNA polymerase in RNA synthesis. Methods Enzymol. 275:382397.
70. Haley, B. E. 1983. Development and utilization of 8-azidopurine nucleotide photoaffinity probes. Fed. Proc. 42:28312836.
71. Hamm, M. L.,, and J. A. Piccirilli. 1997. Incorporation of 2'-deoxy-2'-mercaptocytidine into oligonucleotides via phosphor-amidite chemistry. J. Org. Chem. 62:34153420.
72. Hamy, F.,, U. Asseline,, J. A. Grasby,, S. Iwai,, C. E. Pritchard,, G. Slim,, P. J. G. Butler,, J. Karn,, and M. J. Gait. 1993. Hydrogen-bonding contacts in the major groove are required for human immunodeficiency virus type-1 tat protein recognition of TAR RNA. J. Mol. Biol. 230:111123.
73. Hanna, M. M. 1996. Photochemical cross-linking analysis of protein-nucleic acid interactions in Escherichia coli transcription complexes from lambda PR- promoter. Methods Enzymol. 274: 403418.
74. Haumont, E.,, M. Fournier,, S. de Henau,, and H. Grosjean. 1984. Enzymatic conversion of adenosine to inosine in the wobble position of yeast tRNAAsp: the dependence on anticodon sequence. Nucleic Acids Res. 12:27052715.
75. Hayase, Y.,, H. Inoue,, and E. Ohtsuka. 1990. Secondary structure in formylmethionine tRNA influences the site-directed cleavage of ribonuclease H using chimeric 2'-O-methyl oligodeoxyribO-nucleotides. Biochemistry 29:87938797.
76. Hayase, Y.,, M. Jahn,, M. J. Rogers,, L. A. Sylvers,, M. Koizumi,, H. Inoue,, E. Ohtsuka,, and D. Soil. 1992. Recognition of bases in Escherichia coli tRNAGln by glutaminyl-tRNA synthetase: a complete identity set. EMBO J. 11:41594165.
77. He, B.,, D. L. Riggs,, and M. M. Hanna. 1995. Preparation of probe-modified RNA with 5-mercaptO-UTP for analysis of protein-RNA interactions. Nucleic Acids Res. 23:12311238.
78. He, B.,, M. Rong,, D. Lyakhov,, H. Gartenstein,, G. Diaz,, R. Castagna,, W. T. McAllister,, and R. K. Durbin. 1997. Rapid mutagenesis and purification of phage RNA polymerases. Protein Expr. Purif. 9:142151.
79. Higgins, N. P.,, and N. C. Cozzarelli. 1979. DNA-joining enzymes: a review. Methods Enzymol. 68:5071.
80. Hixson, S. H.,, and S. S. Hixson. 1975. p-AzidoPhenacyl bromide, a versatile photolabile bifunctional reagent. Reaction with glyceraldehyde-3-phosphate dehydrogenase. Biochemistry 14: 4251254.
81. Hou, Y.-M.,, and P. Schimmel. 1988. A simple structural feature is a major determinant of the identity of transfer RNA. Nature 333:140145.
82. Inoue, H.,, Y. Hayase,, A. Imura,, S. Iwai,, and E. Ohtsuka. 1987. Sequence-dependent hydrolysis of RNA using modified oligonucleotide splints and RNase H. FEBS Lett. 215:327330.
83. Iwai, S.,, C. E. Pritchard,, D. A. Mann,, J. Karn,, and M. J. Gait. 1992. Recognition of the high affinity binding site in rev-response element RNA by the human immunodeficiency virus type-1 rev protein. Nucleic Acids Res. 24:64656472.
84. Karn, J.,, M. J. Churcher,, K. Rittner,, N. Keen,, and M. J. Gait,. 1996. Control of transcriptional elongation by the human immunodeficiency virus tat protein, p. 254286. In S. Goodbourn (ed.), Eukaryotic Gene Transcription. Oxford University Press, Oxford, United Kingdom.
85. Kaufmann, G.,, and U. Z. Littauer. 1974. Covalent joining of Phenylalanine transfer ribonucleic acid half-molecules by T4 RNA ligase. Proc. Natl. Acad. Sci. USA 71:37413745.
86. Kim, C. H.,, D. E. Ryan,, T. Marciniec,, and J. Abelson. 1997. Site-specific deoxynucleotide substitutions in yeast U6 snRNA block splicing of pre-mRNA in vitro. EMBO J. 16:21192129.
87. Krug, M.,, P. L. de Haseth,, and O. C. Uhlenbeck. 1982. Enzymatic synthesis of a 21-nucleotide coat binding fragment of R17 ribonucleic acid. Biochemistry 21:47134720.
88. Kuznetsova, S. A.,, M. G. Ivanovskaya,, and Z. A. Shabarova. 1990. Chemical reactions in double-stranded nucleic acids. IX. Directed introduction of substituted pyrophosphate bonds into DNA structure. Bioorg. Khim. 16:219225.
89. Lamond, A. I.,, and B. S. Sproat,. 1994. Isolation and characterization of ribonucleoprotein complexes, p. 103140. In S. J. Higgins, and B. D. Hames (ed.), RNA Processing: a Practical Approach, vol. I. IRL Press, Oxford, United Kingdom.
90. Lin, S. Y.,, and A. D. Riggs. 1974. Photochemical attachment of lac repressor to bromodeoxyuridine-substituted lac operator by ultraviolet radiation. Proc. Natl. Acad. Sci. USA 71:947951.
91. Lin, F.-L.,, M. Boublik,, and J. Ofengand. 1984. Immunoelectron microscopic localization of the S19 site on the 30S ribosomal subunit which is crosslinked to A site bound transfer RNA. J. Mol. Biol. 172:4155.
92. Liu, Q.,, J. B. Green,, A. Khodadadi,, P. Haeberli,, L. Beigelman,, and A. M. Pyle. 1997. Branch-site selection in a group II intron mediated by active recognition of the adenine amino group and steric exclusion of non-adenine functionalities. J. Mol. Biol. 267: 163171.
93. Loria, A.,, and T. Pan. 1997. Recognition of the T stem-loop of a pre-tRNA substrate by the ribozyme from Bacillus subtilis RNase P. Biochemistry 36:63176325.
94. MacMillan, A. M.,, and G. L. Verdine. 1990. Synthesis of functionally tethered oligodeoxynucleotides by the convertible nucleoside approach. J. Org. Chem. 55:59315933.
95. MacMillan, A. M.,, C. C. Query,, C. R. Allerson,, S. Chen,, G. L. Verdine,, and P. A. Sharp. 1994. Dynamic association of proteins with the pre-mRNA branch region. Genes Dev. 8:30083020.
96. Madhani, H. D.,, and C. Guthrie. 1994. Dynamic RNA-RNA interactions in the spliceosome. Annu. Rev. Genet. 28:126.
97. Maschhoff, K. L.,, and R. A. Padgett. 1993. The stereochemical course of the first step of pre-mRNA splicing. Nucleic Acids Res. 21:54565462.
98. McKay, D. B. 1996. Structure and function of the hammerhead ribozyme: an unfinished story. RNA 2:395403.
99. McLain, W. H.,, and K. Foss. 1988. Changing the identity of a tRNA by introducing a G-U wobble pair near the 3' acceptor end. Science 240:793796.
100. Meisenheimer, K. M.,, P. L. Meisenheimer,, M. C. Willis,, and T. H. Koch. 1996. High yield photocrosslinking of a 5-iodouridine (IC) substituted RNA to its associated protein. Nucleic Acids Res. 24:981982.
101. Milligan, J. F.,, and O. C. Uhlenbeck. 1988. Synthesis of small RNAs using T7 RNA polymerase. Methods Enzymol. 180: 5162.
102. Milligan, J. F.,, and O. C. Uhlenbeck. 1989. Determination of RNA-protein contacts using thiophosphate substitutions. Biochemistry 28:28492855.
103. Moore, M. J.,, and C. C. Query,. 1998. Use of site-specifically modified RNAs constructed by RNA ligation, p. 75108. In C. Smith (ed.), RNA-Protein Interactions: a Practical Approach. IRL Press, Oxford, United Kingdom.
104. Moore, M. J.,, and P. A. Sharp. 1992. Site-specific modification of pre-mRNA: the 2' hydroxyl groups at the splice sites. Science 256:992997.
105. Moore, M. J.,, and P. A. Sharp. 1993. Evidence for two active sites in the spliceosome provided by stereochemistry of pre-mRNA splicing. Nature 365:364368.
106. Moroney, S. E.,, and J. A. Piccirilli. 1991. Abortive products as initiating nucleotides during transcription by T7 RNA polymerase. Biochemistry 30:1034310349.
107. Musier-Forsyth, K.,, and P. Schimmel. 1992. Functional contacts of a transfer RNA synthetase with 2'-hydroxyl groups in the RNA minor groove. Nature 357:513515.
108. Musier-Forsyth, K.,, and P. Schimmel. 1994. Acceptor helix interactions in a class II tRNA synthetase: photoaffinity cross-linking of an RNA miniduplex substrate. Biochemistry 33:773779.
109. Musier-Forsyth, K.,, N. Usman,, S. Scaringe,, J. Doudna,, R. Green,, and P. Schimmel. 1991. Specificity for aminoacylation of an RNA helix: an unpaired, exocyclic amino group in the minor groove. Science 253:784786.
110. Naryshkin, N. A.,, M. A. Farrow,, M. G. Ivanovskaya,, T. S. Orestkaya,, Z. A. Shabarova,, and M. J. Gait. 1997. Chemical cross-linking of the human immunodeficiency virus type 1 Tat protein to synthetic models of the RNA recognition sequence TAR containing site-specific trisubstituted pyrophosphate analogues. Biochemistry 36:34963505.
111. Naryshkin, N. A.,, M. G. Ivanovskaya,, T. S. Oretskaya,, E. M. Volkov,, M. J. Gait,, and Z.A. Shabarova. 1996. Synthesis and properties of mixed ribO- and deoxyribooligonucleotide duplexes containing an internucleotide trisubstituted pyrophosphate bond. Bioorg. Khim. 22:592598.
112. Newman, A. J.,, S. Teigelkamp,, and J. D. Beggs. 1995. snRNA interactions at 5' and 3' splice sites monitored by photoactivated crosslinking in yeast spliceosomes. RNA 1:968980.
113. Nilsen, T. W. 1994. RNA-RNA interactions in the spliceosome: unraveling the ties that bind. Cell 78:14.
114. Nolan, J. M.,, D. H. Burke,, and N. R. Pace. 1993. Circularly permuted tRNAs as specific photoaffinity probes of ribonuclease P RNA structure. Science 261:762765.
115. Ofengand, J.,, J. Ciesiolka,, R. Denman,, and K. Nurse,. 1986. Structural and functional interactions of the tRNA-ribosome complex, p. 473494. In B. Hardesty, and G. Kramer (ed.), Structure, Function and Genetics of Ribosomes. Springer, New York, N.Y..
116. Ogilvie, K. K.,, E. A. Thompson,, M. A. Quilliam,, and J. B. Westmore. 1974. Selective protection of hydroxyl groups in deoxynucleosides using alkylsilyl reagents. Tetrahedron Lett. 1974:28652868.
117. Ohtsuka, E.,, T. Doi,, R. Fukumoto,, J. Matsugi,, and M. Ikehara. 1983. Modification of the anticodon triplet of E. coli tRNAMetf by replacement with trimers complementary to non-sense cO-dons UAG and UAA. Nucleic Acids Res. 11:38633872.
118. Owens, J. R.,, A.-Y. M. Woody,, and B. E. Haley. 1987. Characterization of the guanosine-3'-diphosphate-5'-diphosphate binding site on E. coli RNA polymerase using a photoprobe, 8-azidoguanosine-3'-5'-bisphosphate. Biochem. Biophys. Res. Commun. 142:964971.
119. Padgett, R. A.,, M. Podar,, S. C. Boulanger,, and P. S. Perlman. 1994. The stereochemical course of group II intron self-splicing. Science 266:16851688.
120. Paulsen, H.,, and W. Wintermeyer. 1984. Incorporation of 1,N6-ethanoadenosine into the 3' terminus of tRNA using T4 RNA ligase. Eur. J. Biochem. 138:117123.
121. Perreault, J.-P.,, D. Labuda,, N. Usman,, J.-H. Yang,, and R. Cedergren. 1991. Relationship between 2'-hydroxyls and magnesium binding in the hammerhead RNA domain: a model for ribozyme catalysis. Biochemistry 30:40204025.
122. Perreault, J.-P.,, T. Wu,, B. Cousineau,, K. K. Ogilvie,, and R. Cedergren. 1990. Mixed deoxyribO- and ribO-oligonucleotides with catalytic activity. Nature 344:565567.
123. Philippsen, P.,, R. Thiebe,, W. Wintermeyer,, and H. G. Zachau. 1968. Splitting of Phenylalanine specific tRNA into half molecules by chemical means. Biochem. Biophys. Res. Commun. 33: 922928.
124. Piccirilli, J. A.,, J. S. Vyle,, M. H. Caruthers,, and T. R. Cech. 1993. Metal ion catalysis in the Tetrahymena ribozyme reaction. Nature 361:8588.
125. Pieken, W. A.,, D. B. Olsen,, F. Benseler,, H. Aurup,, and F. Eckstein. 1991. Kinetic characterization of ribonuclease-resistant 2'-modified hammerhead ribozymes. Science 253:314317.
126. Podar, M.,, P. S. Perlman,, and R. A. Padgett. 1995. Stereochemical selectivity of group II intron splicing, reverse splicing, and hydrolysis reactions. Mol. Cell. Biol. 15:44664478.
127. Podkowinski, J.,, and P. Gornicki. 1991. Neighbourhood of the central fold of the tRNA molecule bound to the E. coli ribosome-affinity labeling studies with modified tRNAs carrying photoreactive probes attached to the dihydrouridine loop. Nucleic Acids Res. 19:801808.
128. Price, S. R.,, N. Ito,, C. Oubridge,, J. M. Avis,, and K. Nagai. 1995. Crystallization of RNA-protein complexes. I. Methods for the large-scale preparation of RNA suitable for crystallographic studies. J. Mol. Biol. 249:398408.
129. Prince, J. B.,, B. H. Taylor,, D. L. Thurlow,, J. Ofengand,, and R. A. Zimmermann. 1982. Covalent cross-linking of tRNAVal1 at the ribosomal P site: identification of cross-linked residues. Proc. Natl. Acad. Sci. USA 79:54505454.
130. Pritchard, C. E.,, J. A. Grasby,, F. Hamy,, A. M. Zacharek,, M. Singh,, J. Karn,, and M. J. Gait. 1994. Methylphosphonate mapping of phosphate contacts critical for recognition by the human immunodeficiency virus tat and rev proteins. Nucleic Acids Res. 22:25922600.
131. Pyle, A. M.,, and T. R. Cech. 1991. Ribozyme recognition of RNA by tertiary interactions with specific ribose 2'-OH groups. Nature 350:628631.
132. Pyle, A. M.,, F. L. Murphy,, and T. R. Cech. 1992. RNA substrate binding site in the catalytic core of the Tetrahymena ribozyme. Nature 358:123128.
133. Query, C. C.,, M. J. Moore,, and P. A. Sharp. 1994. Branch nucleophile selection in pre-mRNA splicing: evidence for the bulged duplex model. Genes Dev. 8:587597.
134. Query, C. C.,, S. A. Strobel,, and P. A. Sharp. 1996. Three recognition events at the branch-site adenine. EMBO J. 15: 13921402.
135. Reddy, M. P.,, F. Farooqui, and Hanna, N. B. 1995. Methylamine deprotection provides increased yield of oligoribonucleotides. Tetrahedron Lett. 36:89298932.
136. Reyes, J. L.,, P. Kois,, B. Konforti,, and M. M. Konarska. 1996. The canonical GU dinucleotide at the 5' splice site is recognized by p220 of the U5 snRNP within the spliceosome. RNA 2: 213225.
137. Rinke-Appel, J.,, N. Jiinke,, K. Stade,, and R. Brimacombe. 1991. The path of mRNA through the Escherichia coli ribosome: site-directed cross-linking of mRNA analogues carrying a photoreactive label at various points 3' to the decoding site. EMBO J. 10:21952202.
138. Rinke-Appel, J.,, N. Jiinke,, R. Brimacombe,, S. Dokudovskaya,, O. Dontsova,, and A. Bogdanov. 1993. Site-directed cross-linking of mRNA analogues to 16S ribosomal RNA: a complete scan of cross-links from all positions between " + 1" and " + 16" on the mRNA, downstream from the decoding site. Nucleic Acids Res. 21:28532859.
139. Rinke-Appel, J.,, N. Jünke,, R. Brimacombe,, I. Lavrik,, S. Dokudovskaya,, O. Dontsova,, and A. Bogdanov. 1994. Contacts between 16S ribosomal RNA and mRNA, within the spacer region separating the AUG initiator codon and the Shine-Dalgarno sequence: a site-directed cross-linking study. Nucleic Acids Res. 22: 30183025.
140. Rinke-Appel, J.,, N. Jünke,, M. Osswald,, and R. Brimacombe. 1995. The ribosomal environment of tRNA: crosslinks to rRNA from positions 8 and 20:1 in the central fold of tRNA located at the A, P, or E site. RNA 1:19181028.
141. Romaniuk, E.,, L. W. McLaughlin,, T. Neilson,, and P. J. Romaniuk. 1982. The effect of acceptor oligonucleotide sequence in the T4 RNA ligase reaction. Eur. J. Biochem. 125:639643.
142. Romaniuk, P. J.,, and O. C. Uhlenbeck. 1983. Joining of RNA molecules with RNA ligase. Methods Enzymol. 100:5259.
143. Rosen, K. V.,, and R. A. Zimmermann. 1997. Phototaffiniry labeling of 30S-subunit proteins S7 and S11 by 4-thiouridine-substituted tRNAPhe situated at the P site of Escherichia coli ribosomes. RNA 3:10281036.
144. Rosen, K. V.,, and R. A. Zimmermann. Unpublished data.
145. Rosen, K. V.,, R. W. Alexander,, J. Wower,, and R. A. Zimmermann. 1993. Mapping the central fold of tRNAfMet in the P site of the Escherichia coli ribosome. Biochemistry 32:1280212811.
146. Sampson, J. R.,, and O. C. Uhlenbeck. 1988. Biochemical and physical characterization of an unmodified yeast Phenylalanine transfer RNA transcribed in vitro. Proc. Natl. Acad. Sci. USA 85: 10331037.
147. SantaLucia, J., Jr.,, R. Kierzek,, and D. H. Turner. 1991. Functional group substitutions as probes of hydrogen bonding between GA mismatches in RNA internal loops. J. Am. Chem. Soc. 113: 43134322.
148. Santoro, S. W.,, and G. F. Joyce. 1997. A general purpose RNA-cleaving DNA enzyme. Proc. Natl. Acad. Sci. USA 94: 42624266.
149. Scaringe, S. A. , C. Francklyn, and N. Usman. 1990. Chemical synthesis of biologically active oligoribonucleotides using β-cyanoethyl protected ribonucleoside phosphoramidites. Nucleic Acids Res. 18:54335441.
150. Schatz, D.,, R. Leberman,, and F. Eckstein. 1991. Interaction of Escherichia coli tRNASer with its cognate aminoacyl-tRNA synthetase as determined by footprinting with phosphorothioate-containing tRNA transcripts. Proc. Natl. Acad. Sci. USA 88: 61326136.
151. Schenborn, E. T.,, and R. C. Mierendorf. 1985. A novel transcription property of SP6 and T7 RNA polymerases: dependence on template structure. Nucleic Acids Res. 13: 62236236.
152. Schmidt, S.,, L. Beigelman,, A. Karpeisky,, N. Usman,, U. S. Sorenson,, and M. J. Gait. 1996. Base and sugar requirements for RNA cleavage of essential nucleoside residues in internal loop B of the hairpin ribozyme: implications for secondary structure. Nucleic Acids Res. 24:573581.
153. Schulman, L. H.,, and H. Pelka. 1983. Anticodon loop size and sequence requirements for recognition of formylmethionine tRNA by methionyl-tRNA synthetase. Proc. Natl. Acad. Sci. USA 80:67556789.
154. Scott, W. G.,, J. T. Finch,, R. Grenfell,, J. Fogg,, T. Smith,, M. J. Gait,, and A. Klug. 1995. Rapid crystallization of chemically syn-thesised hammerhead RNAs using a double screening procedure. J. Mol. Biol. 250:327332.
155. Seela, F.,, and K. Mersmann. 1992. 7-Deazaguanosine: phosphor-amidite and phosphonate building blocks for solid-phase oligoribonucleotide synthesis. Heterocycles 34:229236.
156. Seela, F.,, and K. Mersmann. 1993. 7-Deazaguanosine: synthesis of an oligoribonucleotide building block and disaggregation of the U-G-G-G-G-U-G4 structure by the modified base. Helv. Chim. Acta 76:14351449.
157. Seela, F.,, K. Mersmann,, J. A. Grasby,, and M. J. Gait. 1993. 7-Deazaadenosine: oligoribonucleotide building block synthesis and autocatalytic hydrolysis of base-modified hammerhead ribozymes. Helv. Chim. Acta 76:18091820.
158. Sergiev, P. V.,, I. N. Lavrik,, V. A. Wlassoff,, S. S. Dokudovskaya,, O. A. Dontsova,, A. A. Bogdanov,, and R. Brimacombe. 1997. The path of mRNA through the bacterial ribosome: a site-directed crosslinking study using new photoreactive derivatives of guanosine and uridine. RNA 3:464475.
159. Sharp, P. A. 1985. On the origins of RNA splicing and introns. Cell 42:397400.
160. Shibahara, S.,, S. Mukai,, T. Hishihara,, H. Inoue,, E. Ohtsuka,, and H. Morisawa. 1987. Site-directed cleavage of RNA. Nucleic Acids Res. 15:44034415.
161. Sigurdsson, S.,, T. Tuschl,, and F. Eckstein. 1995. Probing RNA tertiary structure: interhelical cross-linking of the hammerhead ribozyme. RNA 1:575583.
162. Sigurdsson, S. T.,, and F. Eckstein. 1996. Site specific labelling of sugar residues in oligoribonucleotides: reactions of aliphatic isocyanates with 2'-amino groups. Nucleic Acids Res. 24: 31293133.
163. Sinha, N. D.,, P. Davis,, N. Usman,, J. Perez,, R. Hodga,, J. Kremsky,, and R. Casale. 1993. Labile exocyclic amine protection of nucleosides in DNA, RNA and oligonucleotide analog synthesis facilitating N-deacylation, minimizing depurination and chain degradation. Biochimie 75:1323.
164. Slim, G.,, and M. J. Gait. 1991. Configurationally defined phosphorothioate-containing oligoribonucleotides in the study of the mechanism of cleavage of hammerhead ribozymes. Nucleic Acids Res. 19:11831188.
165. Slim, G.,, and M. J. Gait. 1992. The role of the exocyclic amino groups of conserved purines in hammerhead ribozyme cleavage. Biochem. Biophys. Res. Commun. 183:605609.
166. Sontheimer, E. J. 1994. Site-specific RNA crosslinking with 4-thiouridine. Mol. Biol. Rep. 20:3544.
167. Sontheimer, E. J.,, and J. A. Steitz. 1993. The U5 and U6 small nuclear RNAs as active site components of the spliceosome. Science 262:19891996.
168. Sontheimer, E. J.,, S. Sun,, and J. A. Piccirilli. 1997. Metal ion catalysis during splicing of premessenger RNA. Nature 388: 801805.
169. Sproat, B.,, F. Colonna,, B. Mullah,, D. Tsou,, A. Andrus,, A. Hampel,, and R. Vinayak. 1995. An efficient method for the isolation and purification of oligoribonucleotides. Nucleosides Nucleotides 14:255273.
170. Stade, K.,, J. Rinke-Appel,, and R. Brimacombe. 1989. Site-directed cross-linking of mRNA analogues to the ribosome: identification of 30S ribosomal components that can be cross-linked to the mRNA at various points 5' with respect to the decoding site. Nucleic Acids Res. 17:98899908.
171. Stepanova, O. B.,, V. G. Metelev,, N. V. Chichkova,, V. D. Smirnov,, N. P. Rodionova,, J. G. Atabekov,, A. A. Bogdanov,, and Z. A. Shabarova. 1979. Addressed fragmentation of RNA molecules. FEBS Lett. 103:197201.
172. Strobel, S. A.,, and T. R. Cech. 1993. Tertiary interactions with the internal guide sequence mediate docking of the P1 helix into the catalytic core of the Tetrahymena ribozyme. Biochemistry 32:1359313604.
173. Strobel, S. A.,, and T. R. Cech. 1995. Minor groove recognition of the conserved G•U pair at the Tetrahymena ribozyme reaction site. Science 267:675679.
174. Strobel, S. A.,, and T. R. Cech. 1996. Exocyclic amine of the conserved G•U pair at the cleavage site of the Tetrahymena ribozyme contributes to 5'-splice site selection and transition state stabilization. Biochemistry 35:12011211.
175. Strobel, S. A., and K. Shetty. 1997. Defining the chemical groups essential for Tetrahymena group I intron function by nucleotide analog interference mapping. Proc. Natl. Acad. Sci. USA 94: 29032908.
176. Strobel, S. A.,, T. R. Cech,, N. Usman,, and L. Beigelman. 1994. The 2,6-diaminopurine riboside 5-methylisocytidine wobble base pair: an isoenergetic substitution for the study of G•U pairs in RNA. Biochemistry 33:1382413835.
177. Sumner-Smith, M.,, S. Roy,, R. Barnett,, L. S. Reid,, R. Kuperman,, U. Delling,, and N. Sonenberg. 1991. Critical chemical features in trans-acting-responsive RNA are required for interaction with human immunodeficiency virus type 1 Tat protein. J. Virol. 65: 51965201.
178. Suntharalingam, M.,, E. Dulude,, and M. J. Moore. 1997. Unpublished data.
179. Sylvers, L. A.,, and J. Wower. 1993. Nucleic acid-incorporated azidonucleotides: probes for studying the interaction of RNA or DNA with proteins and nucleic acids. Bioconjug. Chem. 4: 411418.
180. Sylvers, L. A.,, J. Wower,, S. S. Hixson,, and R. A. Zimmermann. 1989. Preparation of 2-azidoadenosine 3',5'-[5'-32P]bisphosphate for incorporation into transfer RNA: photoaffinity labeling of Escherichia coli ribosomes. FEBS Lett. 245:913.
181. Sylvers, L. A.,, A. M. Kopylov,, J. Wower,, S. S. Hixson,, and R. A. Zimmermann. 1992. Photochemical cross-linking of the anticodon loop of yeast tRNAPhe to 30S-subunit protein S7 at the ribosomal A and P sites. Biochimie 74:381389.
182. Sylvers, L. A.,, K. C. Rogers,, M. Shimizu,, E. Ohtsuka,, and D. Söll. 1993. A 2-thiouridine derivative in tRNAc;l" is a positive determinant for aminoacylation by Escherichia coli glutamyl-tRNA synthetase. Biochemistry 32:38363841.
183. Tanner, N. K.,, M. M. Hanna,, and J. Abelson. 1988. Binding interactions between yeast tRNA ligase and a precursor transfer ribonucleic acid containing two photoreactive uridine analogues. Biochemistry 27:88528861.
184. Teigelkamp, S.,, A. J. Newman,, and J. D. Beggs. 1995a. Extensive interactions of PRP8 protein with the 5' and 3' splice sites during splicing suggest a role in stabilization of exon alignment by U5 snRNA. EMBO J. 14:26022612.
185. Teigelkamp, S.,, E. Whittaker,, and J. D. Beggs. 1995b. Interaction of the yeast splicing factor PRP8 with substrate RNA during both steps of splicing. Nucleic Acids Res. 23:320326.
186. Tsou, D.,, A. Andrus,, and R. Vinayak. 1995a. Improvements in large scale synthesis, isolation and purification of oligoribonucleotides. Nucleic Acids Symposium, Noordwijkerhout, The Netherlands.
187. Tsou, D.,, A. Hampel,, A. Andrus,, and R. Vinayak. 1995b. Large scale synthesis of oligoribonucleotides on high-loaded polystyrene (HLP) support. Nucleosides Nucleotides 14:14811492.
188. Tuschl, T.,, M. M. P. Ng,, W. Pieken,, F. Benseler,, and F. Eckstein. 1993. Importance of exocyclic base functional groups of central core guanosines for hammerhead ribozyme activity. Biochemistry 32:1165811668.
189. Uhlenbeck, O. C.,, and R. I. Gumport,. 1982. T4 RNA ligase, p. 3158. In P. D. Boyer (ed.), The Enzymes, vol. 15, part B. Academic Press, New York, N.Y..
190. Umen, J. G.,, and C. Guthrie. 1995. Prpl6p, Slu7p, and Prp8p interact with the 3' splice site in two distinct stages during the second catalytic step of pre-mRNA splicing. RNA 1:584597.
191. Usman, N.,, and R. Cedergren. 1992. Exploiting the chemical synthesis of RNA. Trends Biochem. Sci. 17:334339.
192. Wahle, E.,, and W. Keller,. 1994. 3' end-processing of mRNA, p. 134. In S. J. Higgins, and B. D. Hames (ed.), RNA Processing: a Practical Approach, vol. II. IRL Press, Oxford, United Kingdom.
193. Wang, J.-F.,, W. D. Downs,, and T. R. Cech. 1993. Movement of the guide sequence during RNA catalysis by a group I intron. Science 260:504508.
194. Weinstein, L. B.,, B. C. Jones,, R. Cosstick,, and T. R. Cech. 1997. A second catalytic metal ion in group I ribozyme. Nature 388: 805808.
195. Weintraub, H. 1973. The assembly of newly replicated DNA into chromatin. Cold Spring Harbor Symp. Quant. Biol. 38:247256.
196. Whitfeld, P. R.,, and R. Markham. 1953. Natural configuration of purine nucleotides in ribonucleic acids. Chemical hydrolysis of the dinucleoside phosphates. Nature 171:11511152.
197. Willis, M. C.,, B. J. Hicke,, O. C. Uhlenbeck,, T. R. Cech, and T. H. Koch. 1993. Photocrosslinking of 5-iodouracil-substituted RNA and DNA to proteins. Science 262:12551257.
198. Willis, M. C.,, K. A. LeCuyer, K. M. Meisenheimer, O. C. Uhlenbeck, and ?. H. Koch. 1994. An RNA-protein contact deter-emined by 5-bromouridine substitution, photocrosslinking and sequencing. Nucleic Acids Res. 22:49474952.
199. Wincott, F.,, A. DiRenzo,, C. Shaffer,, S. Grimm,, D. Tracz,, C. Workman,, D. Sweedler,, C. Gonzalez,, S. Scaringe,, and N. Usman. 1995. Synthesis, deprotection, analysis and purification of RNA and ribozymes. Nucleic Acids Res. 23:26772684.
200. Wittenberg, W. L.,, and O. C. Uhlenbeck. 1985. Specific replacement of functional groups of uridine-33 in yeast Phenylalanine transfer ribonucleic acid. Biochemistry 24: 27052712.
201. Woody, A.-Y. M.,, R. K. Evans,, and B. E. Haley. 1988. Characterization of a photoaffinity analog of UTP, 5-azidO-UTP, for analysis of the substrate binding site on E. coli RNA polymerase. Biochem. Biophys. Res. Commun. 150:917924.
202. Wower, J.,, S. S. Hixson,, and R. A. Zimmermann. 1988. Photochemical cross-linking of yeast tRNAPhe containing 8-azidoadenosine at positions 73 and 76 to the Escherichia coli ribosome. Biochemistry 27:81148121.
203. Wower, J.,, S. S. Hixson,, and R. A. Zimmermann. 1989. Labeling the peptidyl transferase center of the Escherichia coli ribosome with photoreactive tRNAPhe derivatives containing azidoadenO-sine at the 3' end of the acceptor arm: a model of the tRNA-ribosome complex. Proc. Natl. Acad. Sci. USA 86:52325236.
204. Wower, J.,, T. A. Malloy IV,, S. S. Hixson,, and R. A. Zimmermann. 1990. Probing tRNA binding sites on the Escherichia coli 30S ribosomal subunit with photoreactive analogs of the anticodon arm. Biochim. Biophys. Acta 1050:3844.
205. Wower, J.,, P. Scheffer,, L. A. Sylvers,, W. Wintermeyer,, and R. A. Zimmermann. 1993aa. Topography of the ? site on the Escherichia coli ribosome. EMBO ]. 12:617623.
206. Wower, J.,, L. A. Sylvers,, K. V. Rosen,, S. S. Hixson,, and R. A. Zimmermann,. 1993b. A model of the tRNA binding sites on the Escherichia coli ribosome, p. 455464. In K. H. Nierhaus,, F. Franceschi,, A. R. Subramanian,, V. A. Erdmann,, and B. Wittmann-Liebold (ed.), The Translational Apparatus. Plenum Press, New York, N.Y.
207. Wower, J.,, K. V. Rosen,, S. S. Hixson,, and R. A. Zimmermann. 1994a. Recombinant photoreactive tRNA molecules as probes for cross-linking studies, Biochimie 76:12351246.
208. Wower, J.,, S. S. Hixson,, L. A. Sylvers,, Y. Xing,, and R. A. Zimmermann. 1994b. Synthesis of 2,6-diazidO-9-(/3-D-ribofuranosyl)purine 3',5' bisphosphate: incorporation into transfer RNA and photochemical labeling of Escherichia coli ribosomes. Bioconjug. Chem. 5:158161.
209. Wower, J.,, I. K. Wower,, S. V. Kirillov,, K. V. Rosen,, S. S. Hixson,, and R. A. Zimmermann. 1995. Peptidyl transferase and beyond. Biochem. Cell Biol. 73:10411047.
210. Wu, T.,, K. K. Ogilvie,, and R. T. Pon. 1989. Prevention of chain cleavage in the chemical synthesis of 2'-silylated oligoribonucleotides. Nucleic Acids Res. 17:35013517.
211. Wyatt, J. R.,, E. J. Sontheimer,, and J. A. Steitz. 1992. Site-specific crosslinking of mammalian U5 snRNP to the 5' splice site prior to the first step of pre-messenger RNA splicing. Genes Dev. 6: 25422553.
212. Wu, T.,, K. K. Ogilvie,, and R. T. Pon. 1989. Prevention of chain cleavage in the chemical synthesis of 2'-silylated oligoribonucleotides. Nucleic Acids Res. 17:35013517.
213. Xu, Q.,, G. Barany,, R. P. Hammer,, and K. Musier-Forsyth. 1996. Efficient introduction of phosphorothioates into RNA oligonucleotides by 3-ethoxy-l,2,4-dithiazoline-5-one (EDITH).Nucleic Acids Res. 24:36433644.
214. Yu, Y.-T.,, and J. A. Steitz. 1997. A new strategy for introducing photoactivatable 4-thiouridine (4SU) into specific positions in a long RNA molecule. RNA 3:807810.
215. Yu, Y.-T.,, P. A. Maroney,, E. Darzynkiewicz,, and T. W. Nilsen. 1995. U6 snRNA function in nuclear pre-mRNA splicing: a phosphorothioate interference analysis of the U6 phosphate backbone. RNA 1:4654.

This is a required field
Please enter a valid email address
Please check the format of the address you have entered.
Approval was a Success
Invalid data
An Error Occurred
Approval was partially successful, following selected items could not be processed due to error