Erratum: An atlas of RNA base pairs involving modified nucleobases with optimal geometries and accurate energies (Nucl. Acids Res. 43:14 (6714–6729) DOI: 10.1093/nar/gkv606);An atlas of RNA base pairs involving modified nucleobases with optimal geometries and accurate energies

Nucleic Acids Research

Volumn 43, Issue 14, 2015, Pages 6714-6729

  Chawla, Mohit ^a   Oliva, Romina ^b   Bujnicki, Janusz M ^c,d   Cavallo, Luigi ^a  

^a KING ABDULLAH UNIVERSITY OF SCIENCE AND TECHNOLOGY   (Saudi Arabia)

^b UNIVERSITY OF NAPLES PARTHENOPE   (Italy)

^c INTERNATIONAL INSTITUTE OF MOLECULAR AND CELL BIOLOGY   (Poland)

^d ADAM MICKIEWICZ UNIVERSITY   (Poland)

Author keywords

[No Author keywords available]

Indexed keywords

NUCLEIC ACID BASE; ADENINE; CYTOSINE; GUANINE; RNA; URACIL;

ACCURACY; ARTICLE; ENERGY TRANSFER; GEOMETRY; HYDROGEN BOND; ISOMERIZATION; PRIORITY JOURNAL; QUANTUM MECHANICS; RNA ANALYSIS; RNA METHYLATION; RNA SEQUENCE; STRUCTURE ANALYSIS; ANALOGS AND DERIVATIVES; BASE PAIRING; CHEMICAL STRUCTURE; CHEMISTRY; ERRATUM; ERROR;

ADENINE; BASE PAIRING; CYTOSINE; GUANINE; MOLECULAR STRUCTURE; RNA; URACIL;

EID: 84959346008     PISSN: 03051048     EISSN: 13624962     Source Type: Journal    
DOI: 10.1093/nar/gkv925     Document Type: Erratum

References (84)

1. Mercer, T.R., Gerhardt, D.J., Dinger, M.E., Crawford, J., Trapnell, C., Jeddeloh, J.A., Mattick, J.S. and Rinn, J.L. (2012) Targeted RNA sequencing reveals the deep complexity of the human transcriptome. Nat. Biotechnol., 30, 99-104.
2. Cantara, W.A., Crain, P.F., Rozenski, J., McCloskey, J.A., Harris, K.A., Zhang, X., Vendeix, F.A., Fabris, D. and Agris, P.F. (2011) The RNA Modification Database, RNAMDB: 2011 update. Nucleic Acids Res., 39, D195-D201.
3. Machnicka, M.A., Milanowska, K., Osman Oglou, O., Purta, E., Kurkowska, M., Olchowik, A., Januszewski, W., Kalinowski, S., Dunin-Horkawicz, S., Rother, K.M. et al. (2013) MODOMICS: A database of RNA modification pathways-2013 update. Nucleic Acids Res., 41, D262-D267.
4. Maden, E.H. and Wakeman, J.A. (1988) Pseudouridine distribution in mammalian 18 S ribosomal RNA. A major cluster in the central region of the molecule. Biochem. J., 249, 459-464.
5. Maden, B.E. (2001) Mapping 2'-O-methyl groups in ribosomal RNA. Methods, 25, 374-382.
6. Lane, B.G., Ofengand, J. and Gray, M.W. (1992) Pseudouridine in the large-subunit (23 S-like) ribosomal RNA. The site of peptidyl transfer in the ribosome? FEBS Lett., 302, 1-4.
7. Del Campo, M., Recinos, C., Yanez, G., Pomerantz, S.C., Guymon, R., Crain, P.F., McCloskey, J.A. and Ofengand, J. (2005) Number, position, and significance of the pseudouridines in the large subunit ribosomal RNA of Haloarcula marismortui and Deinococcus radiodurans. RNA, 11, 210-219.
8. Agris, P.F. (1996) The importance of being modified: roles of modified nucleosides and Mg2+ in RNA structure and function. Prog. Nucleic Acid Res. Mol. Biol., 53, 79-129.
9. Dunkle, J.A., Vinal, K., Desai, P.M., Zelinskaya, N., Savic, M., West, D.M., Conn, G.L. and Dunham, C.M. (2014) Molecular recognition and modification of the 30S ribosome by the aminoglycoside-resistance methyltransferase NpmA. Proc. Natl. Acad. Sci. USA, 111, 6275-6280.
10. Hoerter, J.A. and Walter, N.G. (2007) Chemical modification resolves the asymmetry of siRNA strand degradation in human blood serum. RNA, 13, 1887-1893.
11. Engelke, D.R. and Hopper, A.K. (2006) Modified view of tRNA: stability amid sequence diversity. Mol. Cell, 21, 144-145.
12. Motorin, Y. and Helm, M. (2010) tRNA stabilization by modified nucleotides. Biochem., 49, 4934-4944.
13. Yi, C. and Pan, T. (2011) Cellular dynamics of RNA modification. Acc. Chem. Res., 44, 1380-1388.
14. Carell, T., Brandmayr, C., Hienzsch, A., Muller, M., Pearson, D., Reiter, V., Thoma, I., Thumbs, P. and Wagner, M. (2012) Structure and function of noncanonical nucleobases. Angew. Chem., 51, 7110-7131.
15. Helm, M. (2006) Post-Transcriptional nucleotide modification and alternative folding of RNA. Nucleic Acids Res., 34, 721-733.
16. Karijolich, J., Kantartzis, A. and Yu, Y.T. (2010) RNA modifications: A mechanism that modulates gene expression. Methods Mol. Biol., 629, 1-19.
17. Hori, H. (2014) Methylated nucleosides in tRNA and tRNA methyltransferases. Front. Genet., 5, 1-26.
18. Torres, A.G., Batlle, E. and Ribas de Pouplana, L. (2014) Role of tRNA modifications in human diseases. Trends Mol. Med., 20, 306-314.
19. Berman, H., Henrick, K., Nakamura, H. and Markley, J.L. (2007) The worldwide Protein Data Bank (wwPDB): ensuring a single, uniform archive of PDB data. Nucleic Acids Res., 35, D301-D303.
20. Ennifar, E., Bernacchi, S., Wolff, P. and Dumas, P. (2007) Influence of C-5 halogenation of uridines on hairpin versus duplex RNA folding. RNA, 13, 1445-1452.
21. Sponer, J.E., Spackova, N., Leszczynski, J. and Sponer, J. (2005) Principles of RNA base pairing: structures and energies of the trans Watson-Crick/sugar edge base pairs. J. Phys. Chem. B, 109, 11399-11410.
22. Sponer, J.E., Spackova, N., Kulhanek, P., Leszczynski, J. and Sponer, J. (2005) Non-Watson-Crick base pairing in RNA. quantum chemical analysis of the cis Watson-Crick/sugar edge base pair family. J. Phys. Chem. A, 109, 2292-2301.
23. Sponer, J.E., Leszczynski, J., Sychrovsky, V. and Sponer, J. (2005) Sugar edge/sugar edge base pairs in RNA: stabilities and structures from quantum chemical calculations. J. Phys. Chem. B, 109, 18680-18689.
24. Sponer, J., Mladek, A., Sponer, J.E., Svozil, D., Zgarbova, M., Banas, P., Jurecka, P. and Otyepka, M. (2012) The DNA and RNA sugar-phosphate backbone emerges as the key player. An overview of quantum-chemical, structural biology and simulation studies. Phys. Chem. Chem. Phys., 14, 15257-15277.
25. Sponer, J., Jurecka, P. and Hobza, P. (2004) Accurate interaction energies of hydrogen-bonded nucleic acid base pairs. J. Am. Chem. Soc., 126, 10142-10151.
26. Sharma, P., Sharma, S., Chawla, M. and Mitra, A. (2009) Modeling the noncovalent interactions at the metabolite binding site in purine riboswitches. J. Mol. Model., 15, 633-649.
27. Sharma, P., Chawla, M., Sharma, S. and Mitra, A. (2010) On the role of Hoogsteen:Hoogsteen interactions in RNA: Ab initio investigations of structures and energies. RNA, 16, 942-957.
28. Oliva, R., Cavallo, L. and Tramontano, A. (2006) Accurate energies of hydrogen bonded nucleic acid base pairs and triplets in tRNA tertiary interactions. Nucleic Acids Res., 34, 865-879.
29. Chawla, M., Sharma, P., Halder, S., Bhattacharyya, D. and Mitra, A. (2011) Protonation of base pairs in RNA: context analysis and quantum chemical investigations of their geometries and stabilities. J. Phys. Chem. B, 115, 1469-1484.
30. Chawla, M., Abdel-Azeim, S., Oliva, R. and Cavallo, L. (2014) Higher order structural effects stabilizing the reverse Watson-Crick Guanine-Cytosine base pair in functional RNAs. Nucleic Acids Res., 42, 714-726.
31. Oliva, R., Tramontano, A. and Cavallo, L. (2007) Mg2+ binding and archaeosine modification stabilize the G15 C48 Levitt base pair in tRNAs. RNA, 13, 1427-1436.
32. Zirbel, C.L., Sponer, J.E., Sponer, J., Stombaugh, J. and Leontis, N.B. (2009) Classification and energetics of the base-phosphate interactions in RNA. Nucleic Acids Res., 37, 4898-4918.
33. Sharma, P., Sponer, J.E., Sponer, J., Sharma, S., Bhattacharyya, D. and Mitra, A. (2010) On the role of the cis Hoogsteen:sugar-edge family of base pairs in platforms and triplets-quantum chemical insights into RNA structural biology. J. Phys. Chem. B, 114, 3307-3320.
34. Poater, J., Swart, M., Guerra, C.F. and Bickelhaupt, F.M. (2011) Selectivity in DNA replication. Interplay of steric shape, hydrogen bonds, pi-stacking and solvent effects. Chem. Commun., 47, 7326-7328.
35. Guerra, C.F., Zijlstra, H., Paragi, G. and Bickelhaupt, F.M. (2011) Telomere structure and stability: covalency in hydrogen bonds, not resonance assistance, causes cooperativity in guanine quartets. Chem. Eur. J., 17, 12612-12622.
36. van der Wijst, T., Guerra, C.F., Swart, M. and Bickelhaupt, F.M. (2006) Performance of various density functionals for the hydrogen bonds in DNA base pairs. Chem. Phys. Lett., 426, 415-421.
37. Davis, D.R. (1995) Stabilization of RNA stacking by pseudouridine. Nucleic Acids Res., 23, 5020-5026.
38. Charette, M. and Gray, M.W. (2000) Pseudouridine in RNA: what, where, how, and why. IUBMB Life, 49, 341-351.
39. Desaulniers, J.P., Chang, Y.C., Aduri, R., Abeysirigunawardena, S.C., SantaLucia, J. Jr and Chow, C.S. (2008) Pseudouridines in rRNA helix 69 play a role in loop stacking interactions. Org. Biomol. Chem., 6, 3892-3895.
40. Dalluge, J.J., Hashizume, T., Sopchik, A.E., McCloskey, J.A. and Davis, D.R. (1996) Conformational flexibility in RNA: The role of dihydrouridine. Nucleic Acids Res., 24, 1073-1079.
41. Murphy, F.V.t., Ramakrishnan, V., Malkiewicz, A. and Agris, P.F. (2004) The role of modifications in codon discrimination by tRNA(Lys)UUU. Nat. Struct. Mol. Biol., 11, 1186-1191.
42. Leontis, N.B., Stombaugh, J. and Westhof, E. (2002) The non-Watson-Crick base pairs and their associated isostericity matrices. Nucleic Acids Res., 30, 3497-3531.
43. Leontis, N.B. and Westhof, E. (2001) Geometric nomenclature and classification of RNA base pairs. RNA, 7, 499-512.
44. Lemieux, S. and Major, F. (2002) RNA canonical and non-canonical base pairing types: A recognition method and complete repertoire. Nucleic Acids Res., 30, 4250-4263.
45. Yang, H., Jossinet, F., Leontis, N., Chen, L., Westbrook, J., Berman, H. and Westhof, E. (2003) Tools for the automatic identification and classification of RNA base pairs. Nucleic Acids Res., 31, 3450-3460.
46. Sponer, J.E., Reblova, K., Mokdad, A., Sychrovsky, V., Leszczynski, J. and Sponer, J. (2007) Leading RNA tertiary interactions: structures, energies, and water insertion of A-minor and P-interactions. A quantum chemical view. J. Phys. Chem. B, 111, 9153-9164.
47. Chawla, M., Credendino, R., Poater, A., Oliva, R. and Cavallo, L. (2015) Structural stability, acidity, and halide selectivity of the fluoride riboswitch recognition site. J. Am. Chem. Soc., 137, 299-306.
48. Becke, A.D. (1996) Density-functional thermochemistry. Abstr. Pap. Am. Chem. Soc., 212, 112-COMP.
49. Becke, A.D. (1993) Density-Functional Thermochemistry .3. The Role of Exact Exchange. J. Chem. Phys., 98, 5648-5652.
50. Dunning, T.H. (1989) Gaussian-Basis Sets for Use in Correlated Molecular Calculations .1. The Atoms Boron through Neon and Hydrogen. J. Chem. Phys., 90, 1007-1023.
51. Moller, C. and Plesset, M.S. (1934) Note on an approximation treatment for many-electron systems. Phys. Rev., 46, 0618-0622.
52. Weigend, F. and Haser, M. (1997) RI-MP2: first derivatives and global consistency. Theor. Chem. Acc., 97, 331-340.
53. Boys, S.F. and Bernardi, F. (1970) Calculation of small molecular interactions by differences of separate total energies-some procedures with reduced errors. Mol. Phys., 19, 553-566.
54. Sponer, J., Sponer, J.E., Mladek, A., Jurecka, P., Banas, P. and Otyepka, M. (2013) Nature and magnitude of aromatic base stacking in DNA and RNA: Quantum chemistry, molecular mechanics, and experiment. Biopolymers, 99, 978-988.
55. Konevega, A.L., Soboleva, N.G., Makhno, V.I., Semenkov, Y.P., Wintermeyer, W., Rodnina, M.V. and Katunin, V.I. (2004) Purine bases at position 37 of tRNA stabilize codon-Anticodon interaction in the ribosomal A site by stacking and Mg2+-dependent interactions. RNA, 10, 90-101.
56. Miyauchi, K., Kimura, S. and Suzuki, T. (2013) A cyclic form of N6-Threonylcarbamoyladenosine as a widely distributed tRNA hypermodification. Nat. Chem. Biol., 9, 105-111.
57. Carlile, T.M., Rojas-Duran, M.F., Zinshteyn, B., Shin, H., Bartoli, K.M. and Gilbert, W.V. (2014) Pseudouridine profiling reveals regulated mRNA pseudouridylation in yeast and human cells. Nature, 515, 143-146.
58. Anderson, J., Phan, L., Cuesta, R., Carlson, B.A., Pak, M., Asano, K., Bjork, G.R., Tamame, M. and Hinnebusch, A.G. (1998) The essential Gcd10p-Gcd14p nuclear complex is required for 1-methyladenosine modification and maturation of initiator methionyl-TRNA. Genes Dev., 12, 3650-3662.
59. Anderson, J., Phan, L. and Hinnebusch, A.G. (2000) The Gcd10p/Gcd14p complex is the essential two-subunit tRNA(1-methyladenosine) methyltransferase of Saccharomyces cerevisiae. Proc. Natl. Acad. Sci. U.S.A., 97, 5173-5178.
60. Li, Z., Gillis, K.A., Hegg, L.A., Zhang, J. and Thurlow, D.L. (1996) Effects of nucleotide substitutions within the T-loop of precursor tRNAs on interaction with ATP/CTP:tRNA nucleotidyltransferases from Escherichia coli and yeast. Biochem. J., 314, 49-53.
61. Schmeing, T.M., Huang, K.S., Strobel, S.A. and Steitz, T.A. (2005) An induced-fit mechanism to promote peptide bond formation and exclude hydrolysis of peptidyl-TRNA. Nature, 438, 520-524.
62. Adams, P.L., Stahley, M.R., Kosek, A.B., Wang, J.M. and Strobel, S.A. (2004) Crystal structure of a self-splicing group I intron with both exons. Nature, 430, 45-50.
63. Gate, J.H., Gooding, A.R., Podell, E., Zhou, K.H., Golden, B.L., Szewczak, A.A., Kundrot, C.E., Cech, T.R. and Doudna, J.A. (1996) RNA tertiary structure mediation by adenosine platforms. Science, 273, 1696-1699.
64. Lu, X.J., Olson, W.K. and Bussemaker, H.J. (2010) The RNA backbone plays a crucial role in mediating the intrinsic stability of the GpU dinucleotide platform and the GpUpA/GpA miniduplex. Nucleic Acids Res., 38, 4868-4876.
65. Moulinier, L., Eiler, S., Eriani, G., Gangloff, J., Thierry, J.C., Gabriel, K., McClain, W.H. and Moras, D. (2001) The structure of an AspRS-TRNA(Asp) complex reveals a tRNA-dependent control mechanism. EMBO J., 20, 5290-5301.
66. Nissen, P., Kjeldgaard, M., Thirup, S., Polekhina, G., Reshetnikova, L., Clark, B.F. and Nyborg, J. (1995) Crystal structure of the ternary complex of Phe-TRNAPhe, EF-Tu, and a GTP analog. Science, 270, 1464-1472.
67. Lin, Y. and Kielkopf, C.L. (2008) X-ray structures of U2 snRNA-branchpoint duplexes containing conserved pseudouridines. Biochemistry, 47, 5503-5514.
68. Zhanpeisov, N.U., Sponer, J. and Leszczynski, J. (1998) Reverse Watson-Crick isocytosine-cytosine and guanine-cytosine base pairs stabilized by the formation of the minor tautomers of bases. An ab initio study in the gas phase and in a water cluster. J. Phys. Chem. A, 102, 10374-10379.
69. Grimme, S., Antony, J., Ehrlich, S. and Krieg, H. (2010) A consistent and accurate ab initio parametrization of density functional dispersion correction (DFT-D) for the 94 elements H-Pu. J. Chem. Phys., 132, 154104-1-154104-18.
70. Watanabe, K., Shinma, M., Oshima, T. and Nishimura, S. (1976) Heat-Induced stability of tRNA from an extreme thermophile, Thermus thermophilus. Biochem. Biophys. Res. Commun., 72, 1137-1144.
71. Kowalak, J.A., Dalluge, J.J., Mccloskey, J.A. and Stetter, K.O. (1994) The role of posttranscriptional modification in stabilization of transfer RNA from hyperthermophiles. Biochemistry, 33, 7869-7876.
72. Horie, N., Harayokoyama, M., Yokoyama, S., Watanabe, K., Kuchino, Y., Nishimura, S. and Miyazawa, T. (1985) Two tRNAIle1 species from an extreme thermophile, Thermus thermophilus HB8: effect of 2-Thiolation of ribothymidine on the thermostability of tRNA. Biochemistry, 24, 5711-5715.
73. Steinberg, S. and Cedergren, R. (1995) A correlation between N-2-dimethylguanosine presence and alternate tRNA conformers. RNA, 1, 886-891.
74. Urbonavicius, J., Armengaud, J. and Grosjean, H. (2006) Identity elements required for enzymatic formation of N-2, N-2-dimethylguanosine from N-2-monomethylated derivative and its possible role in avoiding alternative conformations in archaeal tRNA. J. Mol. Biol., 357, 387-399.
75. Helm, M., Brule, H., Degoul, F., Cepanec, C., Leroux, J.P., Giege, R. and Florentz, C. (1998) The presence of modified nucleotides is required for cloverleaf folding of a human mitochondrial tRNA. Nucleic Acids Res., 26, 1636-1643.
76. Helm, M., Giege, R. and Florentz, C. (1999) A Watson-Crick base-pair-disrupting methyl group (m1A9) is sufficient for cloverleaf folding of human mitochondrial tRNALys. Biochemistry, 38, 13338-13346.
77. Voigts-Hoffmann, F., Hengesbach, M., Kobitski, A.Y., van Aerschot, A., Herdewijn, P., Nienhaus, G.U. and Helm, M. (2007) A methyl group controls conformational equilibrium in human mitochondrial tRNA(Lys). J. Am. Chem. Soc., 129, 13382-13383.
78. Sumita, M., Desaulniers, J.P., Chang, Y.C., Chui, H.M., Clos, L. 2nd and Chow, C.S. (2005) Effects of nucleotide substitution and modification on the stability and structure of helix 69 from 28S rRNA. RNA, 11, 1420-1429.
79. Meroueh, M., Grohar, P.J., Qiu, J., SantaLucia, J. Jr, Scaringe, S.A. and Chow, C.S. (2000) Unique structural and stabilizing roles for the individual pseudouridine residues in the 1920 region of Escherichia coli 23S rRNA. Nucleic Acids Res., 28, 2075-2083.
80. Ofengand, J., Bakin, A., Wrzesinski, J., Nurse, K. and Lane, B.G. (1995) The pseudouridine residues of ribosomal RNA. Biochem. Cell Biol., 73, 915-924.
81. Jiang, J., Aduri, R., Chow, C.S. and SantaLucia, J. Jr (2014) Structure modulation of helix 69 from Escherichia coli 23S ribosomal RNA by pseudouridylations. Nucleic Acids Res., 42, 3971-3981.
82. Arnez, J.G. and Steitz, T.A. (1994) Crystal structure of unmodified tRNA(Gln) complexed with glutaminyl-TRNA synthetase and ATP suggests a possible role for pseudo-uridines in stabilization of RNA structure. Biochemistry, 33, 7560-7567.
83. Newby, M.I. and Greenbaum, N.L. (2002) Investigation of Overhauser effects between pseudouridine and water protons in RNA helices. Proc. Natl. Acad. Sci. U.S.A., 99, 12697-12702.
84. Neumann, J.M., Bernassau, J.M., Gueron, M. and Tran-Dinh, S. (1980) Comparative conformations of uridine and pseudouridine and their derivatives. Eur. J. Biochem., 108, 457-463.