1887

Chapter 5 : Biophysical and Conformational Properties of Modified Nucleosides in RNA (Nuclear Magnetic Resonance Studies)

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

Preview this chapter:
Zoom in
Zoomout

Biophysical and Conformational Properties of Modified Nucleosides in RNA (Nuclear Magnetic Resonance Studies), Page 1 of 2

| /docserver/preview/fulltext/10.1128/9781555818296/9781555811334_Chap05-1.gif /docserver/preview/fulltext/10.1128/9781555818296/9781555811334_Chap05-2.gif

Abstract:

The location and identity of a large number of the modified nucleosides found in tRNA are highly conserved across diverse species and between tRNA isoacceptors. Conserved modification patterns in rRNAs and small nuclear RNAs also suggest that particular modified nucleosides have critical roles, although these functions are not well described compared to modifications found in tRNA. The nuclear magnetic resonance (NMR) determined biophysical properties have also provided an explanation for changes in important functions of tRNA during protein synthesis such as codon-anticodon recognition. This chapter talks about NMR determination of nucleoside conformation. The use of the percentage of 3'-endo sugar conformation as a measure of base stacking originated from NMR investigations on ribonucleotide dimers and trimers. Nucleoside modification in either the base or sugar can have significant effects on the sugar conformation, the glycosyl conformation, and base stacking. The 3'-gauche effect is mechanistically related to the anomeric effect in that it arises due to a geometrically dependent overlap between σ* and n lone pair molecular orbitals. Nucleoside bases that are in a stacked geometry generally have aromatic NMR proton shifts that are upfield of the positions seen in the absence of significant stacking. The chapter also focuses on conformational and thermodynamic effects of specific nucleoside modifications. Our knowledge of the fundamental biophysical properties of modified nucleosides will be critical to understanding how modification has been used throughout biology to optimize the function of biochemically critical processes involving RNA.

Citation: Davis D. 1998. Biophysical and Conformational Properties of Modified Nucleosides in RNA (Nuclear Magnetic Resonance Studies), p 85-102. In Grosjean H, Benne R (ed), Modification and Editing of RNA. ASM Press, Washington, DC. doi: 10.1128/9781555818296.ch5

Key Concept Ranking

Small Nuclear RNA
0.46378785
Nucleic Acids
0.40319785
0.46378785
Highlighted Text: Show | Hide
Loading full text...

Full text loading...

Figures

Image of Figure 1
Figure 1

The two limiting conformations for ribonucleosides. (A) 2′-endo sugar with the base in the pseudoequatorial conformation; (B) 3′-endo sugar with the base pseudoaxial.

Citation: Davis D. 1998. Biophysical and Conformational Properties of Modified Nucleosides in RNA (Nuclear Magnetic Resonance Studies), p 85-102. In Grosjean H, Benne R (ed), Modification and Editing of RNA. ASM Press, Washington, DC. doi: 10.1128/9781555818296.ch5
Permissions and Reprints Request Permissions
Download as Powerpoint
Image of Figure 2
Figure 2

NMR NOE experiments are used to define the glycosyl conformation for nucleosides. The interproton distances between the base H6 (pyrimidines) or H8 (purines) and the sugar protons change as a function of glycosyl angle. The figure shows the key distances involving Η1′, H2′, and H3′ protons for adenosine and how they differ for either the or conformations.

Citation: Davis D. 1998. Biophysical and Conformational Properties of Modified Nucleosides in RNA (Nuclear Magnetic Resonance Studies), p 85-102. In Grosjean H, Benne R (ed), Modification and Editing of RNA. ASM Press, Washington, DC. doi: 10.1128/9781555818296.ch5
Permissions and Reprints Request Permissions
Download as Powerpoint
Image of Figure 3
Figure 3

Molecular orbital interactions in pyrimidines that affect the thermodynamically preferred glycosyl conformation and change upon modification. Both the anomeric interaction and an interaction involving the H5-H6 bond are affected by modification. For the anomeric effect, the lone pair electrons at O4′ are in an np orbital which overlaps with the * orbital at C1′. In the 3′-endo conformation (shown) the C1′-N bond is axial and the * orbital oriented along the glycosyl bond can bond in a -like fashion with the np orbital. The same O4′ lone pair orbitals can interact with * antibonding orbitals from the pyrimidine H5-H6 double bond. An electron withdrawing group (EWG) at the 5 position increases the size of the * orbital on H6 as shown which would increase the intetaction and favor a 3′-endo conformation with a low angle.

Citation: Davis D. 1998. Biophysical and Conformational Properties of Modified Nucleosides in RNA (Nuclear Magnetic Resonance Studies), p 85-102. In Grosjean H, Benne R (ed), Modification and Editing of RNA. ASM Press, Washington, DC. doi: 10.1128/9781555818296.ch5
Permissions and Reprints Request Permissions
Download as Powerpoint
Image of Figure 4
Figure 4

Watson-Crick sU-A base pair and reversed Hoogsteen sU-A base pair. The s modification in a non-hydrogen bonding position has a direct effect on base stacking and strongly promotes the 3′-endo sugar conformation.

Citation: Davis D. 1998. Biophysical and Conformational Properties of Modified Nucleosides in RNA (Nuclear Magnetic Resonance Studies), p 85-102. In Grosjean H, Benne R (ed), Modification and Editing of RNA. ASM Press, Washington, DC. doi: 10.1128/9781555818296.ch5
Permissions and Reprints Request Permissions
Download as Powerpoint
Image of Figure 5
Figure 5

Three-dimensional structure of the ρΑρ dinucleotide step in a standard Α-form geometry. The coordinated water molecule stabilizes the N1-H imino proton against facile exchange with bulk solvent and coordination to the phosphate backbone restricts the base conformation and the backbone 5′ to the modification site.

Citation: Davis D. 1998. Biophysical and Conformational Properties of Modified Nucleosides in RNA (Nuclear Magnetic Resonance Studies), p 85-102. In Grosjean H, Benne R (ed), Modification and Editing of RNA. ASM Press, Washington, DC. doi: 10.1128/9781555818296.ch5
Permissions and Reprints Request Permissions
Download as Powerpoint
Image of Figure 6
Figure 6

The anticodon domains of tRNA and tRNA shown in panel A have pseudouridines at positions 39 and 35, respectively. As a model system for the codon-anticodon interaction where would either be remote from the anticodon triplet as in tRNA or within the anticodon triplet as in tRNA, the two RNA hairpins in panel were used to demonstrate stabilization for modification adjacent or within the double-stranded region. Pseudouridine results in an increase in the of 2.6 and 5.5°C for the tRNA and tRNA tetraloop hairpins, respectively.

Citation: Davis D. 1998. Biophysical and Conformational Properties of Modified Nucleosides in RNA (Nuclear Magnetic Resonance Studies), p 85-102. In Grosjean H, Benne R (ed), Modification and Editing of RNA. ASM Press, Washington, DC. doi: 10.1128/9781555818296.ch5
Permissions and Reprints Request Permissions
Download as Powerpoint

References

/content/book/10.1128/9781555818296.chap5
1. Agris, P. F. 1991. Wobble position modified nucleosides evolved to select transfer RNA codon recognition: a modified-wobble hypothesis. Biochimie 73: 1345 1349.
2. Agris, P. F., 1996. The importance of being modified: roles of modified nucleosides and Mg 2+ in RNA structure and function, p. 74 129. In W. Cohn, and K. Moldave (ed.), Progress in Nucleic Acid Research and Molecular Biology, vol. 53. Academic Press, San Diego, Calif..
3. Agris, P. F.,, R. Guenther,, P. C. Ingram,, M. M. Basti,, J. W. Stuart,, E. Sochacka,, and A. Malkiewicz. 1997. Unconventional structure of tRNA LysSUU anticodon explains tRNA's role in bacterial and mammalian ribosomal frameshifting and primer selection by HIV-1. RNA 3: 420 428.
4. Agris, P. F.,, H. Koh,, and D. Soli. 1973. The effect of growth temperatures on the in vivo ribose methylation of Bacillus stearothermophilus transfer RNA. Arch. Biochem. Biophys. 154: 277 282.
5. Agris, P. F.,, H. Sierzputowska-Gracz,, W. Smith,, A. Malkiewicz,, E. Sochacka,, and B. Nawrot. 1992. Thiolation of uridine carbon-2 restricts the motional dynamics of the transfer RNA wobble position nucleoside. J. Am. Chem. Soc. 114: 2652 2656.
6. Agris, P. F.,, D. Söll,, and T. Seno. 1973. Biological function of 2-thiouridine in Escherichia coli glutamic acid transfer ribonucleic acid. Biochemistry 12: 4331 4337.
7. Altona, C.,, and M. Sundaralingam. 1973. Conformational analysis of the sugar ring in nucleosides and nucleotides. Improved method for the interpretation of proton magnetic resonance coupling constants. J. Am. Chem. Soc. 95: 2333 2344.
8. Aphasizhev, R.,, A. Theobald-Dietrich,, K. D. Kostyuk,, S. N. Kochetkov,, L. Kisselev,, R. Giege,, and F. Fasiolo. 1997. Structure and aminoacylation capacities of tRNA transcripts containing deoxyribonucleotides. RNA 3: 893 904.
9. Auffinger, P.,, S. Louise-May,, and E. Westhof. 1996. Hydration of C-H groups in tRNA. Faraday Discuss. 103: 151 173.
10. Auffinger, P.,, and E. Westhof. 1997. RNA hydration: 3 ns of multiple molecular dynamics simulations of the solvated tRNA Asp anticodon hairpin. J. Mol. Biol. 269: 326 341.
11. Basti, M. M.,, J. W. Stuart,, A. T. Lam,, R. Guenther,, and P. F. Agris. 1996. Design, biological activity and NMR-solution structure of a DNA analogue of yeast tRNA Phe anticodon domain. Nat. Struct. Biol. 3: 38 44.
12. Bax, A.,, and D. G. Davis. 1985. Practical aspects of two-dimensional transverse NOE spectroscopy. J. Magn. Reson. 63: 207 213.
13. Biou, V.,, A. Yaremchuk,, M. Tukalo,, and S. Cusack. 1994. The 2.9 A crystal structure of T. thermophilus seryl-tRNA synthetase complexed with tRNA ser. Science 263: 1404 1410.
14. Björk, G. R., 1983. Modified nucleosides in RNA—their formation and function, p. 291 330. In D. Apirion (ed.), Processing of RNA. CRC Press Inc., Boca Raton, Fla..
15. Björk, G. R., 1992. The role of modified nucleosides in tRNA interactions, p. 23 85. In D. L. Hatfield,, B. J. Lee,, and R. M. Pirtle (ed.), Transfer RNA in Protein Synthesis. CRC Press, Ann Arbor, Mich..
16. Björk, G. R., 1995. Biosynthesis and function of modified nucleosides, p. 165 206. In D. Söll,, and U. L. RajBhandary (ed.), tRNA: Structure, Biosynthesis, and Function. ASM Press, Washington, D.C..
17. Choi, B. S.,, and A. G. Redfield. 1986. NMR study of isoleucine transfer RNA from Thermus thermophilus. Biochemistry 25: 1529 1534.
18. Cramer, F.,, E. M. Gottschalk,, H. Matzura,, K.-H. Scheit,, and H. Sternbach. 1971. The synthesis of the alternating copolymer poly[r(A-s 4U)] by RNA polymerase of Escherichia coli. Eur. J. Biochem. 19: 379 385.
19. Dalluge, J. J.,, T. Hamamoto,, K. Horikoshi,, R. Y. Morita,, K. O. Stetter,, and J. A. McCloskey. 1997. Posttranscriptional modification of transfer RNA in psychrophilic bacteria. J. Bacteriol. 179: 1918 1923.
20. Dalluge, J. J.,, T. Hashizume,, A. E. Sopchik,, J. A. McCloskey,, and D. R. Davis. 1996. Conformational flexibility in RNA: the role of dihydrouridine. Nucleic Acids Res. 24: 1073 1079.
21. Davanloo, P.,, M. Sprinzl,, K. Watanabe,, M. Albani,, and H. Kersten. 1979. Role of ribothymidine in the thermal stability of transfer RNA as monitored by proton magnetic resonance. Nucleic Acids Res. 6: 1571 1581.
22. Davis, D. R. 1995. Stabilization of RNA stacking by pseudouridine. Nucleic Acids Res. 23: 5020 5026.
23. Davis, D. R. Unpublished data.
24. Davis, D. R.,, R. H. Griffey,, Z. Yamaizumi,, S. Nishimura,, and C. D. Poulter. 1986. 15N-labeled tRNA: identification of dihydrouridine in £. coli tRNA fMet, tRNA Lys, and tRNA Phe by 1H- 15N two-dimensional NMR. J. Biol. Chem. 261: 3584 3587.
25. Davis, D. R.,, and C. D. Poulter. 1991. 1H- 15N NMR studies of E. coli tRNAPhe from hisT mutants: a structural role for pseudouridine. Biochemistry 30: 4223 4231.
26. Davis, D. R.,, C. A. Veltri,, and L. Nielsen. An RNA model system for investigation of pseudouridine stabilization of the codon-anticodon interaction in tRNA Lys, tRNA His and tRNA Tyr. Submitted for publication.
27. de Leeuw, F. A. A. M.,, and C. Altona. 1983. Computer-assisted pseudorotation analysis of five-membered rings by means of proton spin-spin coupling constants: program PSEUROT. J. Comp. Chem. 4: 428 437.
28. Diaz, I.,, and M. Ehrenberg. 1991. ms 2i6A deficiency enhances proofreading in translation. J. Mol. Biol. 222: 1161 1171.
29. Durant, P. C.,, and D. R. Davis. 1997. The effect of pseudouridine and pH on the structure and dynamics of the anticodon stem-loop of tRNALys,3. Nucleic Acids Symp. Ser. 36: 56 57.
30. Durant, P. C.,, and D. R. Davis. Structure and dynamics of the anticodon stem-loop of tRNA Lys. Structural stabilization of the HIV reverse transcriptase primer by an A +-C base pair and by pseudouridine. Submitted for publication.
31. Edmonds, C. G.,, P. F. Crain,, R. Gupta,, T. Hashizume,, C. H. Hocart,, J. A. Kowalak,, S. A. Pomerantz,, K. O. Stetter,, and J. A. McCloskey. 1991. Posttranscriptional modification of tRNA in thermophilic archaea (Archaebacteria). J. Bacterial. 173: 3138 3148.
32. Egert, E.,, H. J. Lindner,, W. Hillen,, and M. C. Bohm. 1980. Influence of substituents at the 5-position on the structure of uridine. J. Am. Chem. Soc. 102: 3707 3713.
33. Ernst, R. R.,, G. Bodenhausen,, and A. Wokaun. 1987. Principles of Nuclear Magnetic Resonance in One and Two Dimensions. Oxford University Press, Oxford, United Kingdom.
34. Esberg, B.,, and G. R. Björk. 1995. The methylthio group (ms 2) of N 6-(4-hydroxyisopentenyl)-2-methylthioadenosine (ms 2io6A) present next to the anticodon contributes to the decoding efficiency of the tRNA. J. Bacteriol. 177: 1967 1975.
35. Griffey, R. H.,, D. R. Davis,, Z. Yamaizumi,, S. Nishimura,, A. Bax,, B. Hawkins,, and C. D. Poulter. 1985. 15N-labeled E. coli tRNAMet, tRNA Glu, tRNA Tyr, and tRNA Phe: double resonance and two-dimensional NMR of Nl-labeled pseudouridine. J. Biol. Chem. 260: 9734 9741.
36. Griffey, R. H.,, D. R. Davis,, Z. Yamaizumi,, S. Nishimura,, B. L. Hawkins,, and C. D. Poulter. 1986. l5N-labeled tRNA: identification of 4-thiouridine in Escherichia coli tRNA Ser and tRNA Tyr by 1H -15N two-dimensional NMR spectroscopy. J. Biol. Chem. 261: 12074 12078.
37. Grosjean, H.,, and C. Houssier,. 1990. Codon recognition: evaluation of the effects of modified bases in the anticodon loop of tRNA using the temperature jump relaxation method, p. A255 A297. In C. W. Gehrke, and K. C. T. Kuo (ed.), Chromatography and Modification of Nucleosides, Part A. Elsevier Science Publishers, Amsterdam, The Netherlands.
38. Grosjean, H.,, D. G. Söll,, and D. M. Crothers. 1976. Studies of the complex between transfer RNAs with complementary anti-codons. I. Origins of enhanced affinity between complementary triplets. J. Mol. Biol. 103: 499 519.
39. Grosjean, H. J.,, S. de Henau,, and D. M. Crothers. 1978. On the physical basis for ambiguity in genetic coding interactions. Proc. Natl. Acad. Sci. USA 75: 610 614.
40. Gu, J.,, and R. Reddy. 1997. Small RNA database. Nucleic Acids Res. 25: 98 102.
41. Haasnoot, C. A. G.,, F. A. A. M. De Leeuw,, and C. Altona. 1980. The relationship between proton-proton NMR coupling constants and substituent electronegativities. I. An empirical generalization of the Karplus equation. Tetrahedron 36: 2783 2792.
42. Hall, K. B.,, and L. W. McLaughlin. 1991. Properties of a Ul/ mRNA 5' splice site duplex containing pseudouridine as measured by thermodynamic and NMR methods. Biochemistry 30: 1795 1801.
43. Hall, K. B.,, and L. W. McLaughlin. 1992. Properties of pseudouridine N1 imino protons located in the major groove of an A-form RNA duplex. Nucleic Acids Res. 20: 1883 1889.
44. Hanna, M. M. 1989. Photoaffinity cross-linking methods for studying RNA-protein interactions. Methods Enzymol. 180: 383 409.
45. Hare, D. R.,, S. Ribeiro,, D. E. Wemmer,, and B. R. Reid. 1985. Complete assignment of the imino protons of Escherichia coli valine transfer RNA: two-dimensional NMR studies in water. Biochemistry 24: 4300 4306.
46. Horie, N.,, M. Hara-Yokoyama,, S. Yokoyama,, K. Watanabe,, Y. Kuchino,, S. Nishimura,, and T. Miyazawa. 1985. Two tRNA Ile species from an extreme thermophile, Thermus thermophilus HB8: effect of 2-thiolation of ribothymidine on the thermostability of tRNA. Biochemistry 24: 5711 5715.
47. Houssier, C.,, P. Degee,, K. Nicoghosian,, and H. Grosjean. 1988. Effect of uridine dethiolation in the anticodon triplet of tRNA(Glu) on its association with tRNA(Phe). J. Biomol. Struct. Dyn. 5: 1259 1266.
48. Houssier, C.,, and H. Grosjean. 1985. Temperature jump relaxation studies on the interactions between transfer RNAs wih complementary anticodons. The effect of modified bases adjacent to the anticodon triplet. J. Biomol. Struct. Dyn. 3: 387 399.
49. Inoue, H.,, Y. Hayase,, A. Imura,, S. Iwai,, K. Miura,, and E. Ohtsuka. 1987. Synthesis and hybridization studies on two complementary nona(2'-0-methyl)ribonucleotides. Nucleic Acids Res. 15: 6131 6148.
50. Isel, C.,, R. Marquet,, G. Keith,, C. Ehresmann,, and B. Ehresmann. 1993. Modified nucleotides of tRNA Lys,3 modulate primer/template loop-loop interaction in the initiation complex of HIV-1 reverse transcription. J. Biol. Chem. 34: 25269 25272.
51. Ishikura, H.,, Y. Yamada,, and S. Nishimura. 1971. Structure of serine tRNA from Escherichia coli. 1. Purification of serine tRNAs with different codon responses. Biochim. Biophys. Acta 228: 471 481.
52. Jack, A.,, J. E. Ladner,, and A. Klug. 1976. Crystallographic refinement of yeast Phenylalanine transfer RNA at 2.5 A resolution. J. Mol. Biol. 108: 619 649.
53. Juaristi, E.,, and G. Cuevas. 1995. The Anomeric Effect. CRC Press, Boca Raton, Fla..
54. Kawai, G.,, H. Ue,, M. Yasuda,, K. Sakamoto,, T. Hashizume,, J. A. McCloskey,, T. Miyazawa,, and S. Yokoyama. 1991. Relation between functions and conformational characteristics of modified nucleosides found in tRNAs. Nucleic Acids Res. Symp. Ser. 25: 49 50.
55. Kawai, G.,, T. Hashizume,, M. Yasuda,, T. Miyazawa,, J. A. McCloskey,, and S. Yokoyama. 1992a. Conformational rigidity of N 4-acetyl-2'-O-methylcytidine found in tRNA of extremely thermophylic archaebacteria (archaea). Nucleosides Nucleotides 11: 759 771.
56. Kawai, G.,, Y. Yamamoto,, T. Kamimura,, T. Masegi,, M. Sekine,, T. Hata,, T. Iimori,, T. Watanabe,, T. Miyazawa,, and S. Yokoyama. 1992b. Conformational rigidity of specific pyrimidine residues in tRNA arises from posttranscriptional modifications that enhance steric interaction between the base and the 2'-hydroxyl group. Biochemistry 31: 1040 1046.
57. Kawai, G.,, T. Yokogawa,, K. Nishikawa,, T. Ueda,, T. Hashizume,, J. A. McCloskey,, S. Yokoyama,, and K. Watanabe. 1994. Conformational properties of a novel modified nucleoside, 5-formylcytidine, found at the first position of the anticodon of bovine mitochondrial tRNAMet. Nucleosides Nucleotides 13: 1189 1199.
58. Keith, G.,, U. Englisch,, F. Cramer,, and F. Fasiolo. 1994. Does a �� syn conformation of the wobble base determine the codon and amino acid specificity of a yeast isoleucine transfer RNA?, p. 9 2. In Proceedings of the EMBO-CNRS Workshop on Nucleotide Modification and Base Conversion of RNA, Assois, France.
59. Kessler, H.,, U. Anders,, G. Gemmecker,, and S. Steuernagel. 1989. Improvement of NMR experiments by employing semiselective half-gaussian-shaped pulses. J. Magn. Reson. 85: 1 14.
60. Kowalak, J. A.,, E. Bruenger,, and J. A. McCloskey. 1995. Post-trancriptional modification of the central loop of domain V in Escherichia coli 23S ribosomal RNA. J. Biol. Chem. 270: 17758 17764.
61. Kowalak, J. A.,, J. J. Dalluge,, J. A. McCloskey,, and K. O. Stetter. 1994. The role of posttranscriptional modification in stabiliza- tion of transfer RNA from hyperthermophiles. Biochemistry 33: 7869 7876.
62. Kumar, R. K.,, and D. R. Davis. 1997a. The effects of 2-thiouridine and 4-thiouridine on sugar conformation and base stacking in RNA oligonucleotides. Nucleic Acids Res. 25: 1272 1280.
63. Kumar, R. K.,, and D. R. Davis. 1997b. Structural studies of 2-thiouridine in RNA. Nucleosides Nucleotides 16: 1469 1472.
64. Laing, L. G.,, and D. E. Draper. 1994. Thermodynamics of RNA folding in a conserved ribosomal RNA domain. J. Mol. Biol. 237: 560 576.
65. Lane, B. G.,, J. Ofengand,, and M. W. Gray. 1995. Pseudouridine and 02'-methylated nucleosides. Significance of their selective occurrence in rRNA domains that function in ribosome-catalyzed synthesis of the peptide bonds in proteins. Biochimie 77: 7 15.
66. Lee, C.-H.,, F. S. Ezra,, N. S. Kondo,, R. H. Sarma,, and S. S. Danyluk. 1976. Conformation properties of dinucleoside monophosphates: dipurines and dipyrimidines. Biochemistry 15: 3627 3638.
67. Lee, C. H.,, and I. Tinoco. 1980. Conformation studies of 13 trinucleoside phosphates by 360 MHz PMR spectroscopy. A bulged base conformation. I. Base protons and h1' protons. Biophys. Chem. 11: 283 294.
68. Lee, C. H.,, and I. Tinoco. 1977. Studies of the conformation of modified dinucleoside phosphates containing 1,N 6-ethenoadenosine and 2'-O-methylcytidine by 360 MHz 1H nuclear magnetic resonance spectroscopy. Investigation of the solution conformations of dinucleoside phosphates. Biochemistry 16: 5403 5414.
69. Limbach, P. A.,, P. F. Crain,, and J. A. McCloskey. 1994. Summary: the modified nucleosides of RNA. Nucleic Acids Res. 22: 2183 2196.
70. Litvak, S.,, L. Sarih-Cottin,, M. Fournier,, M. Andreola,, and L. Tarrago-Litvak. 1994. Priming of HIV replication by tRNA Lys,3: role of reverse transcriptase. Trends Biochem. Sci. 19: 114 118.
71. Lodmell, J. S.,, and A. E. Dahlberg. 1997. A conformational switch in Escherichia coli 16S ribosomal RNA during decoding of messenger RNA. Science 277: 1262 1267.
72. Lustig, F.,, P. Elias,, T. Axberg,, T. Samuelsson,, I. Titawella,, and U. Lagerkvist. 1981. Codon reading and translational error. Reading of the glutamine and lysine codons during protein synthesis in vitro. J. Biol. Chem. 256: 2635 2643.
73. Maden, B. E. H. 1990. The numerous modified nucleotides in eukaryotic ribosomal RNA. Prog. Nucleic Acids Res. Mol. Biol. 39: 241 303.
74. Mazumdar, S. K.,, W. Saenger,, and K. H. Scheit. 1974. Molecular structure of poly-2-thiouridylic acid, a double helix with non-equivalent polynucleotide chains. J. Mol. Biol. 85: 213 229.
75. Miller, J. P.,, Z. Hussain,, and M. P. Schweizer. 1976. The involvement of the anticodon adjacent modified nucleoside N-[9-( β-d-ribofuranosyl)purine-6-ylcarbamoyl]threonine in the biological function of E. coli tRNA Ile. Nucleic Acids Res. 3: 1185 1201.
76. Mitra, S. K.,, F. Lustig,, B. Akesson,, T. Axberg,, P. Elias,, and U. Lagerkvist. 1979. Relative efficiency of anticodons in reading the valine codons during protein synthesis in vitro. J. Biol. Chem. 254: 6397 6401.
77. Moriya, J.,, T. Yokogawa,, K. Wakita,, T. Ueda,, K. Nishikawa,, P. F. Crain,, T. Hashizume,, S. C. Pomerantz,, J. A. McCloskey,, G. Kawai,, N. Hayashi,, S. Yokoyama,, and K. Watanabe. 1994. A novel modified nucleoside found at the first position of the anticodon of methionine tRNA from bovine liver mitochondria. Biochemistry 33: 2234 2239.
78. Muramatsu, T.,, T. Miyazawa,, and S. Yokoyama. 1992. Recognition of the nucleoside in the first position of the anticodon of isoleucine tRNA by isoleucyl-tRNA synthetase from Escherichia coli. Nucleosides Nucleotides 11: 719 730.
79. Muramatsu, T.,, K. Nishikawa,, F. Nemoto,, Y. Kuchino,, S. Nishimura,, T. Miyazawa,, and S. Yokoyama. 1988. Codon and amino-acid specificities of a transfer RNA are both converted by a single post-transcriptional modification. Nature 336: 179 181.
80. Murao, K.,, T. Hasegawa,, and H. Ishikura. 1982. Nucleotide sequence of valine tRNAmo 5UAC from Bacillus subtilis. Nucleic Acids Res. 10: 715 718.
81. Nanda, R. K.,, R. Tewari,, G. Govil,, and I. C. P. Smith. 1974. The conformation of β-pseudouridine about the glycosidic bond as studied by 1H homonuclear overhauser measurements and molecular orbital calculations. Can. J. Chem. 52: 371 375.
82. Neuhaus, D.,, and M. Williamson. 1989. The Nuclear Overhauser Effect in Structural and Conformational Analysis. VCH Publishers, New York, N.Y..
83. Neumann, J. M.,, J. M. Bernassau,, M. Gueron,, and S. Tran-Dinh. 1980. Comparative conformations of uridine and pseudouridine and their derivatives. Eur. J. Biochem. 108: 457 463.
84. Noggle, J. H.,, and R. E. Shirmer. 1971. The Nuclear Overhauser Effect: Chemical Applications. Academic Press, New York, N.Y..
85. Noller, H. F., 1993. On the origin of the ribosome: coevolution of subdomains of tRNA and rRNA, p. 137 156. In R. F. Gesteland, and J. F. Atkins (ed.), The RNA World. Cold Spring Harbor Laboratory Press, Cold Spring Harbor, N.Y..
86. Pais de Barros, J.-P.,, G. Keith,, C. El Adlouni,, A.-L. Glasser,, G. Mack,, G. Dirheimer,, and J. Desgres. 1996. 2'-0-methyl-5-formylcytidine (f 5Cm), a new modified nucleotide at the "wobble" position of two cytoplasmic tRNAs Leu(NAA) from bovine liver. Nucleic Acids Res. 24: 1489 1496.
87. Pallanck, L.,, and L. H. Schulman. 1991. Anticodon-dependent aminoacylation of a noncognate tRNA with isoleucine, valine, and Phenylalanine in vivo. Proc. Natl. Acad. Sci. USA 88: 3872 3876.
88. Pieles, U. B.,, K. Bohmann,, S. Weston,, S. O'Loughlin,, V. Adam,, and B. S. Sproat. 1994. New and convenient protection system for pseudouridine, highly suitable for solid-phase oligoribonucleotide synthesis. J. Chem. Soc. Perkin Trans. 1: 3423 3429.
89. Plavec, J.,, C. Thibaudeau,, and J. Chattopadhyaya. 1994a. How does the 2'-hydroxy group drive the pseudorotational equilibrium in nucleoside and nucleotide by the tuning of the 3'-gauche effect? J. Am. Chem. Soc. 116: 6558 6560.
90. Plavec, J.,, T. Thibaudeau,, G. Viswanadham,, C. Sund,, and J. Chattopadhyaya. 1994. How does the 3'-phosphate drive the sugar conformation in DNA? J. Chem. Soc. Chem. Commun., p. 781 783.
91. Plavec, J.,, W. Tong,, and J. Chattopadhyaya. 1993. How do the gauche and anomeric effects drive the pseudorotational equilibrium of the pentofuranose moiety of nucleosides? J. Am. Chem. Soc. 115: 9734 9746.
92. Plesiewicz, E.,, E. Stepien,, K. Bolewska,, and K. L. Wierzchowski. 1976. Stacking self-association of pyrimidine nucleosides and cytosines: effects of methylation and thiolation. Nucleic Acids Res. 3: 1295 1306.
93. Quigley, G. J.,, and A. Rich. 1976. Structural domains of transfer RNA molecules. Science 194: 794 806.
94. Reddy, P. R.,, D. W. Hamill,, G. B. Chheda,, and M. P. Schweizer. 1981. On the function of N-[(9- β-d-ribo-furanosyl-purine-6-ylcarbamoyl]threonine in transfer ribonucleic acid. Metal ion binding studies. Biochemistry 20: 4979 4986.
95. Rosemeyer, H.,, G. Toth,, B. Golankiewicz,, Z. Kazimierczuk,, W. Bourgeois,, U. Kretschmer,, H.-P. Muth,, and F. Seela. 1990. Synanti conformational analysis of regular and modified nucleosides by 1D 1H NOE difference spectroscopy: a simple graphical method based on conformationally rigid molecules. J. Org. Chem. 55: 5784 5790.
96. Roy, S.,, M. Z. Papastavros,, and A. G. Redfield. 1982. Nuclear Overhauser effect study of yeast aspartate transfer ribonucleic acid. Biochemistry 21: 6081 6088.
97. Roy, S.,, M. Z. Papastavros,, V. Sanchez,, and A. G. Redfield. 1984. Nitrogen-15-labeled yeast tRNA Phe. Double and two-dimensional heteronuclear NMR of guanosine and uracil ring NH groups. Biochemistry 23: 4395 4400.
98. Saenger, W. 1984. Principles of Nucleic Acid Structure. Springer-Verlag, New York, N.Y..
99. Sakamoto, K.,, G. Kawai,, T. Niimi,, T. Satoh,, M. Sekine,, Z. Yamaizumi,, S. Nishimura,, T. Miyazawa,, and S. Yokoyama. 1993. A modified uridine in the first position of the anticodon of a minor species of arginine tRNA, the argU gene product, from Escherichia coli. Eur. J. Biochem. 216: 369 375.
100. Sakamoto, K.,, G. Kawai,, S. Watanabe,, T. Niimi,, N. Hayashi,, Y. Muto,, K. Watanabe,, T. Satoh,, M. Sekine,, and S. Yokoyama. 1996. NMR studies of the effects of the 5'-phosphate group on conformational properties of 5-methylaminomethyluridine found in the first position of the anticodon of Escherichia coli tRNA Arg,4. Biochemistry 35: 6533 6538.
101. Samuelsson, T.,, P. Elias,, F. Lustig,, T. Axberg,, G. Folsch,, B. Akesson,, and U. Lagerkvist. 1980. Aberrations of the classic codon reading scheme during protein synthesis in vitro. J. Biol. Chem. 255: 4583 4588.
102. Scheit, K. H.,, and P. Faerber. 1975. The effects of thioketo substitution upon uracil-adenine interactions in polyribonucleotides. Eur. J. Biochem. 50: 549 555.
103. Schweizer, M. P.,, N. De,, M. PulsiPher,, M. Brown,, P. R. Reddy,, C. R. Petrie,, and G. B. Chheda. 1984. Quantitative aspects of metal ion binding to certain transfer RNA anticodon loop modified nucleosides. Biochim. Biophys. Acta 802: 352 361.
104. Sekiya, T.,, K. Takeishi,, and T. Ukita. 1969. Specificity of yeast glutamic acid transfer RNA for codon recognition. Biochim. Biophys. Acta 182: 411 426.
105. Senger, B.,, S. Auxilien,, U. Englisch,, F. Cramer,, and F. Fasiolo. 1997. The modified wobble base inosine in yeast tRNA Ile is a positive determinant for aminoacylation by isoleucyl-tRNA synthetase. Biochemistry 36: 8269 8275.
106. Seno, T.,, P. F. Agris,, and D. Söll. 1974. Involvement of the anticodon region of Escherichia coli tRNA Gln and tRNA Glu in the specific interaction with cognate aminoacyl-tRNA synthetase. Biochim. Biophys. Acta 349: 328 338.
107. Sierzputowska-Gracz, H.,, R. H. Guenther,, P. F. Agris,, W. Folkman,, and B. Golankiewicz. 1991. Structure and conformation of the hypermodified purine nucleoside wyosine and its isomers: a comparison of coupling constants and distance geometry solutions. Magn. Reson. Chem. 29: 885 892.
108. Sierzputowska-Gracz, H.,, E. Sochacka,, A. Malkiewicz,, K. Kuo,, C. W. Gehrke,, and P. F. Agris. 1987. Chemistry and structure of modified uridines in the anticodon, wobble position of transfer RNA are determined by thiolation. J. Am. Chem. Soc. 109: 7171 7177.
109. Smith, W. S.,, B. Nawrot,, A. Malkiewicz,, and P. F. Agris. 1992a. RNA modified uridines. VI. Conformations of 3-[3-(S)-amino-3-carboxypropyl]uridine (acp'U) from tRNA and l-methyl-3-[3-(S)-amino-3-carboxypropyl]pseudouridine (m 1acp 3��) from rRNA. Nucleosides Nucleotides 11: 1683 1694.
110. Smith, W. S.,, H. Sierzputowska-Gracz,, E. Sochacka,, A. Malkiewicz,, and P. F. Agris. 1992b. Chemistry and structure of modified uridine dinucleosides are determined by thiolation. J. Am. Chem. Soc. 114: 7989 7997.
111. Sowers, L. C.,, B. R. Shawk,, and W. D. Sedwick. 1987. Base stacking and molecular polarizability: effect of a methyl group in the 5-position of pyrimidines. Biochem. Biophys. Res. Commun. 148: 790 794.
112. Sprinzl, M.,, C. Horn,, M. Brown,, A. Ioudovitch,, and S. Steinberg. 1998. Compilation of tRNA sequences and sequences of tRNA genes. Nucleic Acids Res. 26: 148 153.
113. Stern, L.,, and L. H. Schulman. 1978. The role of the minor base N 4-acetylcytidine in the function of the Escherichia coli noninitiator methionine transfer RNA. J. Biol. Chem. 253: 6132 6139.
114. Stuart, J. W.,, M. M. Basti,, W. S. Smith,, B. Forrest,, R. Guenther,, H. Sierzputowska-Gracz,, B. Nawrot,, A. Malkiewicz,, and P. F. Agris. 1996. Structure of the trinucleotide D-acp3U-A with coordinated Mg 2+ demonstrates that modified nucleosides contribute to regional conformations of RNA. Nucleosides Nucleotides 15: 1009 1028.
115. Sylvers, L. K.,, K. C. Rogers,, M. Shimizu,, E. Ohtsuka,, and D. Söll. 1993. A 2-thiouridine derivative in tRNAGlu is a positive determinant for aminoacylation by E. coli glutamyl-tRNA synthetase. Biochemistry 32: 3836 3841.
116. Takemoto, C.,, T. Yokogawa,, L. Benkowski,, L. L. Spremulli,, T. A. Ueda,, K. Nishikawa,, and K. Watanabe. 1995. The ability of bovine mitochondrial transfer RNA Met to decode AUG and AUA codons. Biochimie 77: 104 108.
117. Thibaudeau, C.,, J. Plavec,, and J. Chattopadhyaya. 1994a. Quantitation of the anomeric effect in adenosine and guanosine by comparison of the thermodynamics of the pseudorotational equilibrium of the pentofuranose moiety in N- and C-nucleosides. J. Am. Chem. Soc. 116: 8033 8037.
118. Thibaudeau, C.,, J. Plavec,, K. A. Watanabe,, and J. Chattopadhyaya. 1994b. How do the aglycones drive the pseudo-rotational equilibrium of the pentofuranose moiety in C-nucleosides? J. Chem. Soc. Chem. Commun., p. 537 540.
119. Thibaudeau, C.,, J. Plavec,, N. Garg,, A. Papchikhin,, and J. Chattopadhyaya. 1994c. How does the electronegativity of the sub-stituent dictate the strength of the Gauche effect? J. Am. Chem. Soc. 116: 4038 4043.
120. Thibaudeau, C.,, J. Plavec,, and J. Chattopadhyaya. 1996. Quantitation of the pD dependent thermodynamics of the N-S pseudorotational equilibrium of the pentofuranose moiety in nucleosides gives a direct measurement of the strength of the tunable anomeric effect and the pKa of the nucleobase. J. Org. Chem. 61: 266 286.
121. Uhl, W.,, J. Reiner,, and H. G. Gassen. 1983. On the conformation of 5-substituted uridines as studied by proton magnetic resonance. Nucleic Acids Res. 11: 1167 1180.
122. Varani, G.,, and I. Tinoco. 1991. RNA structure and NMR spectroscopy. Q. Rev. Biophys. 24: 479 532.
123. Varnagy, K.,, M. Jezowska-Bojczuk,, J. Swiatek,, H. Kozlowski,, I. Sovago,, and R. W. Adamiak. 1990. Metal binding ability of hypermodified nucleosides of tRNA. Potentiometric and spectroscopic studies on the metal complexes of N-[(9- β-d-ribo-furanosylpurin-6-yl)carbamoyl]threonine. J. Inorg. Biochem. 40: 357 363.
124. Wang, S.,, and E. T. Kool. 1995. Origins of the large differences in stability of DNA and RNA helices: C-5 methyl and 2'-hydroxyl effects. Biochemistry 34: 4125 4132.
125. Westhof, E.,, P. Dumas,, and D. Moras. 1985. Crystallographic refinement of yeast aspartic acid transfer RNA. J. Mol. Biol. 184: 119.
126. Westhof, E.,, O. Roder,, I. Croneiss,, and H. D. Ludemann. 1975. Ribose conformations in the common purine (β) ribosides, in some antibiotic nucleosides, and in some isopropylidene derivatives: a comparison. Z. Naturforsch. 30: 131 140.
127. Westhof, E.,, and M. Sundaralingam. 1986. Restrained refinement of the monoclinic form of yeast Phenylalanine transfer RNA. Temperature factors and dynamics, coordinated waters, and base pair propeller twist angles. Biochemistry 25: 4868 4878.
128. Wilson, R. K.,, and B. A. Roe. 1989. Presence of the hypermodified nucleotide N6-(δ 2-isopentenyl)-2-methylthioadenosine prevents codon misreading by Escherichia coli Phenylalanyl-transfer RNA. Proc. Natl. Acad. Set. USA 86: 409 413.
129. Wuthrich, K. 1986. NMR of Proteins and Nucleic Acids. Wiley-Interscience, New York, N.Y..
130. Yamamoto, Y.,, S. Yokoyama,, T. Miyazawa,, K. Watanabe,, and S. Higuchi. 1983. NMR analyses on the molecular mechanism of the conformational rigidity of 2-thioribothymidine, a modified nucleoside in extreme thermophile tRNAs. FEBS Lett. 157: 95 99.
131. Yokoyama, S.,, and T. Muramatsu. 1990. NMR analysis of structures and functions of modified nucleosides in transfer ribonucleic acids. Nucleosides Nucleotides 9: 303 310.
132. Yokoyama, S.,, and S. Nishimura,. 1995. Modified nucleosides and codon recognition, p. 207 224. In D. Söll, and U. L. Raj Bhandary (ed.), tRNA: Structure, Biosynthesis, and Function. ASM Press, Washington, D.C..
133. Yokoyama, S.,, T. Watanabe,, K. Murao,, H. Ishikura,, Z. Yamaizumi,, S. Nishimura,, and T. Miyazawa. 1985. Molecular mechanism of codon recognition by tRNA species with modified uridine in the first position of the anticodon. Proc. Natl. Acad. Sci. USA 82: 4905 4909.
134. Yokoyama, S.,, Z. Yamaizumi,, S. Nishimura,, and T. Miyazawa. 1979. 1H NMR studies on the conformational characteristics of 2-thiopyrimidine nucleotides found in transfer RNAs. Nucleic Acids Res. 6: 2611 2627.
135. Yu, Y.-T.,, and J. A. Steitz. 1997. A new strategy for introducing photoactivatable 4-thiouridine into specific positions in a long RNA molecule. RNA 3: 807 810.

Tables

Generic image for table
Table 1

Modification effects on the 2′-endo/3′-endo sugar conformational equilibrium thermodynamics

Citation: Davis D. 1998. Biophysical and Conformational Properties of Modified Nucleosides in RNA (Nuclear Magnetic Resonance Studies), p 85-102. In Grosjean H, Benne R (ed), Modification and Editing of RNA. ASM Press, Washington, DC. doi: 10.1128/9781555818296.ch5

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