-
1
-
-
38849103659
-
Purine sensing by riboswitches
-
Kim J.N., Breaker R.R. Purine sensing by riboswitches. Biol. Cell 2008, 100:1-11.
-
(2008)
Biol. Cell
, vol.100
, pp. 1-11
-
-
Kim, J.N.1
Breaker, R.R.2
-
2
-
-
84865231710
-
Structure and mechanism of purine-binding riboswitches
-
Batey R.T. Structure and mechanism of purine-binding riboswitches. Q. Rev. Biophys. 2012, 45:345-381.
-
(2012)
Q. Rev. Biophys.
, vol.45
, pp. 345-381
-
-
Batey, R.T.1
-
3
-
-
0025897378
-
Posttranscriptional modification of tRNA in thermophilic archaea (Archaebacteria)
-
Edmonds C.G., Crain P.F., Gupta R., Hashizume T., Hocart C.H., Kowalak J.A., Pomerantz S.C., Stetter K.O., McCloskey J.A. Posttranscriptional modification of tRNA in thermophilic archaea (Archaebacteria). J. Bacteriol. 1991, 173:3138-3148.
-
(1991)
J. Bacteriol.
, vol.173
, pp. 3138-3148
-
-
Edmonds, C.G.1
Crain, P.F.2
Gupta, R.3
Hashizume, T.4
Hocart, C.H.5
Kowalak, J.A.6
Pomerantz, S.C.7
Stetter, K.O.8
McCloskey, J.A.9
-
4
-
-
0015514384
-
Possible anticodon sequences of tRNA His, tRNA Asm, and tRNA Asp from Escherichia coli B. Universal presence of nucleoside Q in the first position of the anticodons of these transfer ribonucleic acids
-
Harada F., Nishimura S. Possible anticodon sequences of tRNA His, tRNA Asm, and tRNA Asp from Escherichia coli B. Universal presence of nucleoside Q in the first position of the anticodons of these transfer ribonucleic acids. Biochemistry 1972, 11:301-308.
-
(1972)
Biochemistry
, vol.11
, pp. 301-308
-
-
Harada, F.1
Nishimura, S.2
-
5
-
-
0034788470
-
Queuosine modification of tRNA: a case for convergent evolution
-
Morris R.C., Elliott M.S. Queuosine modification of tRNA: a case for convergent evolution. Mol. Genet. Metab. 2001, 74:147-159.
-
(2001)
Mol. Genet. Metab.
, vol.74
, pp. 147-159
-
-
Morris, R.C.1
Elliott, M.S.2
-
6
-
-
43049099252
-
An embarrassment of riches: the enzymology of RNA modification
-
Iwata-Reuyl D. An embarrassment of riches: the enzymology of RNA modification. Curr. Opin. Chem. Biol. 2008, 12:126-133.
-
(2008)
Curr. Opin. Chem. Biol.
, vol.12
, pp. 126-133
-
-
Iwata-Reuyl, D.1
-
7
-
-
18844429219
-
Transglycosylation: a mechanism for RNA modification (and editing?)
-
Garcia G.A., Kittendorf J.D. Transglycosylation: a mechanism for RNA modification (and editing?). Bioorg. Chem. 2005, 33:229-251.
-
(2005)
Bioorg. Chem.
, vol.33
, pp. 229-251
-
-
Garcia, G.A.1
Kittendorf, J.D.2
-
8
-
-
85075274229
-
-
Landes Bioscience, Austin, Tex.
-
Grosjean H. DNA and RNA Modification Enzymes: Structure, Mechanism, Function, and Evolution 2009, Landes Bioscience, Austin, Tex.
-
(2009)
DNA and RNA Modification Enzymes: Structure, Mechanism, Function, and Evolution
-
-
Grosjean, H.1
-
9
-
-
84871436566
-
Transfer RNA modifications: nature's combinatorial chemistry playground, Wiley interdisciplinary reviews
-
Jackman J.E., Alfonzo J.D. Transfer RNA modifications: nature's combinatorial chemistry playground, Wiley interdisciplinary reviews. RNA 2013, 4:35-48.
-
(2013)
RNA
, vol.4
, pp. 35-48
-
-
Jackman, J.E.1
Alfonzo, J.D.2
-
10
-
-
20144367825
-
Structural effects of hypermodified nucleosides in the Escherichia coli and human tRNALys anticodon loop: the effect of nucleosides s2U, mcm5U, mcm5s2U, mnm5s2U, t6A, and ms2t6A
-
Durant P.C., Bajji A.C., Sundaram M., Kumar R.K., Davis D.R. Structural effects of hypermodified nucleosides in the Escherichia coli and human tRNALys anticodon loop: the effect of nucleosides s2U, mcm5U, mcm5s2U, mnm5s2U, t6A, and ms2t6A. Biochemistry 2005, 44:8078-8089.
-
(2005)
Biochemistry
, vol.44
, pp. 8078-8089
-
-
Durant, P.C.1
Bajji, A.C.2
Sundaram, M.3
Kumar, R.K.4
Davis, D.R.5
-
11
-
-
0035863196
-
A primordial tRNA modification required for the evolution of life?
-
Bjork G.R., Jacobsson K., Nilsson K., Johansson M.J., Bystrom A.S., Persson O.P. A primordial tRNA modification required for the evolution of life?. EMBO J. 2001, 20:231-239.
-
(2001)
EMBO J.
, vol.20
, pp. 231-239
-
-
Bjork, G.R.1
Jacobsson, K.2
Nilsson, K.3
Johansson, M.J.4
Bystrom, A.S.5
Persson, O.P.6
-
12
-
-
80053194776
-
Plasticity and diversity of tRNA anticodon determinants of substrate recognition by eukaryotic A37 isopentenyltransferases
-
Lamichhane T.N., Blewett N.H., Maraia R.J. Plasticity and diversity of tRNA anticodon determinants of substrate recognition by eukaryotic A37 isopentenyltransferases. RNA 2011, 17:1846-1857.
-
(2011)
RNA
, vol.17
, pp. 1846-1857
-
-
Lamichhane, T.N.1
Blewett, N.H.2
Maraia, R.J.3
-
13
-
-
33846269602
-
TRNA's wobble decoding of the genome: 40years of modification
-
Agris P.F., Vendeix F.A., Graham W.D. tRNA's wobble decoding of the genome: 40years of modification. J. Mol. Biol. 2007, 366:1-13.
-
(2007)
J. Mol. Biol.
, vol.366
, pp. 1-13
-
-
Agris, P.F.1
Vendeix, F.A.2
Graham, W.D.3
-
14
-
-
58149191272
-
TRNAdb 2009: compilation of tRNA sequences and tRNA genes
-
Juhling F., Morl M., Hartmann R.K., Sprinzl M., Stadler P.F., Putz J. tRNAdb 2009: compilation of tRNA sequences and tRNA genes. Nucleic Acids Res. 2009, 37:D159-D162.
-
(2009)
Nucleic Acids Res.
, vol.37
, pp. D159-D162
-
-
Juhling, F.1
Morl, M.2
Hartmann, R.K.3
Sprinzl, M.4
Stadler, P.F.5
Putz, J.6
-
15
-
-
0025370590
-
The deazaguanine-derivative, queuine, affects cell proliferation, protein phosphorylation and the expression of the proto oncogenes c-fos and c-myc in HeLa cells
-
Langgut W., Kersten H. The deazaguanine-derivative, queuine, affects cell proliferation, protein phosphorylation and the expression of the proto oncogenes c-fos and c-myc in HeLa cells. FEBS Lett. 1990, 265:33-36.
-
(1990)
FEBS Lett.
, vol.265
, pp. 33-36
-
-
Langgut, W.1
Kersten, H.2
-
16
-
-
0027379152
-
Modulation of mammalian cell proliferation by a modified tRNA base of bacterial origin
-
Langgut W., Reisser T., Nishimura S., Kersten H. Modulation of mammalian cell proliferation by a modified tRNA base of bacterial origin. FEBS Lett. 1993, 336:137-142.
-
(1993)
FEBS Lett.
, vol.336
, pp. 137-142
-
-
Langgut, W.1
Reisser, T.2
Nishimura, S.3
Kersten, H.4
-
17
-
-
0025977143
-
Queuine, a transfer-RNA anticodon wobble base, maintains the proliferative and pluripotent potential of Hl-60 cells in the presence of the differentiating agent 6-thioguanine
-
French B.T., Patrick D.E., Grever M.R., Trewyn R.W. Queuine, a transfer-RNA anticodon wobble base, maintains the proliferative and pluripotent potential of Hl-60 cells in the presence of the differentiating agent 6-thioguanine. Proc. Natl. Acad. Sci. U. S. A. 1991, 88:370-374.
-
(1991)
Proc. Natl. Acad. Sci. U. S. A.
, vol.88
, pp. 370-374
-
-
French, B.T.1
Patrick, D.E.2
Grever, M.R.3
Trewyn, R.W.4
-
18
-
-
1642445245
-
Detection of unique tRNA species in tumor tissues by Escherichia coli guanine insertion enzyme
-
Okada N., Shindo-Okada N., Sato S., Itoh Y.H., Oda K., Nishimura S. Detection of unique tRNA species in tumor tissues by Escherichia coli guanine insertion enzyme. Proc. Natl. Acad. Sci. U. S. A. 1978, 75:4247-4251.
-
(1978)
Proc. Natl. Acad. Sci. U. S. A.
, vol.75
, pp. 4247-4251
-
-
Okada, N.1
Shindo-Okada, N.2
Sato, S.3
Itoh, Y.H.4
Oda, K.5
Nishimura, S.6
-
19
-
-
0018582874
-
Alteration of the Q family of transfer RNAs in adult Drosophila melanogaster as a function of age, nutrition, and genotype
-
Owenby R.K., Stulberg M.P., Jacobson K.B. Alteration of the Q family of transfer RNAs in adult Drosophila melanogaster as a function of age, nutrition, and genotype. Mech. Ageing Dev. 1979, 11:91-103.
-
(1979)
Mech. Ageing Dev.
, vol.11
, pp. 91-103
-
-
Owenby, R.K.1
Stulberg, M.P.2
Jacobson, K.B.3
-
20
-
-
36549029244
-
Possible involvement of queuine in regulation of cell proliferation
-
Pathak C., Jaiswal Y.K., Vinayak M. Possible involvement of queuine in regulation of cell proliferation. BioFactors 2007, 29:159-173.
-
(2007)
BioFactors
, vol.29
, pp. 159-173
-
-
Pathak, C.1
Jaiswal, Y.K.2
Vinayak, M.3
-
21
-
-
0015924554
-
Activity of a transfer RNA modifying enzyme during the development of Drosophila and its relationship to the su(s) locus
-
White B.N., Tener G.M. Activity of a transfer RNA modifying enzyme during the development of Drosophila and its relationship to the su(s) locus. J. Mol. Biol. 1973, 74:635-651.
-
(1973)
J. Mol. Biol.
, vol.74
, pp. 635-651
-
-
White, B.N.1
Tener, G.M.2
-
22
-
-
0028353466
-
The nutrient factor queuine protects HeLa cells from hypoxic stress and improves metabolic adaptation to oxygen availability
-
Reisser T., Langgut W., Kersten H. The nutrient factor queuine protects HeLa cells from hypoxic stress and improves metabolic adaptation to oxygen availability. Eur. J. Biochem./FEBS 1994, 221:979-986.
-
(1994)
Eur. J. Biochem./FEBS
, vol.221
, pp. 979-986
-
-
Reisser, T.1
Langgut, W.2
Kersten, H.3
-
23
-
-
0028068635
-
Deficiency of queuine, a highly modified purine base, in transfer RNAs from primary and metastatic ovarian malignant tumors in women
-
Baranowski W., Dirheimer G., Jakowicki J.A., Keith G. Deficiency of queuine, a highly modified purine base, in transfer RNAs from primary and metastatic ovarian malignant tumors in women. Cancer Res. 1994, 54:4468-4471.
-
(1994)
Cancer Res.
, vol.54
, pp. 4468-4471
-
-
Baranowski, W.1
Dirheimer, G.2
Jakowicki, J.A.3
Keith, G.4
-
24
-
-
0022408375
-
Relationship of queuine-lacking transfer RNA to the grade of malignancy in human leukemias and lymphomas
-
Emmerich B., Zubrod E., Weber H., Maubach P.A., Kersten H., Kersten W. Relationship of queuine-lacking transfer RNA to the grade of malignancy in human leukemias and lymphomas. Cancer Res. 1985, 45:4308-4314.
-
(1985)
Cancer Res.
, vol.45
, pp. 4308-4314
-
-
Emmerich, B.1
Zubrod, E.2
Weber, H.3
Maubach, P.A.4
Kersten, H.5
Kersten, W.6
-
25
-
-
0026737277
-
Relationship of the queuine content of transfer ribonucleic acids to histopathological grading and survival in human lung cancer
-
Huang B.S., Wu R.T., Chien K.Y. Relationship of the queuine content of transfer ribonucleic acids to histopathological grading and survival in human lung cancer. Cancer Res. 1992, 52:4696-4700.
-
(1992)
Cancer Res.
, vol.52
, pp. 4696-4700
-
-
Huang, B.S.1
Wu, R.T.2
Chien, K.Y.3
-
26
-
-
0035130319
-
Increased expression of queuosine synthesizing enzyme, tRNA-guanine transglycosylase, and queuosine levels in tRNA of leukemic cells
-
Ishiwata S., Katayama J., Shindo H., Ozawa Y., Itoh K., Mizugaki M. Increased expression of queuosine synthesizing enzyme, tRNA-guanine transglycosylase, and queuosine levels in tRNA of leukemic cells. J. Biochem. 2001, 129:13-17.
-
(2001)
J. Biochem.
, vol.129
, pp. 13-17
-
-
Ishiwata, S.1
Katayama, J.2
Shindo, H.3
Ozawa, Y.4
Itoh, K.5
Mizugaki, M.6
-
27
-
-
3042815958
-
Elevated expression level of 60-kDa subunit of tRNA-guanine transglycosylase in colon cancer
-
Ishiwata S., Ozawa Y., Katayama J., Kaneko S., Shindo H., Tomioka Y., Ishiwata T., Asano G., Ikegawa S., Mizugaki M. Elevated expression level of 60-kDa subunit of tRNA-guanine transglycosylase in colon cancer. Cancer Lett. 2004, 212:113-119.
-
(2004)
Cancer Lett.
, vol.212
, pp. 113-119
-
-
Ishiwata, S.1
Ozawa, Y.2
Katayama, J.3
Kaneko, S.4
Shindo, H.5
Tomioka, Y.6
Ishiwata, T.7
Asano, G.8
Ikegawa, S.9
Mizugaki, M.10
-
28
-
-
0031566184
-
Effects of a diet deficient in tyrosine and queuine on germfree mice
-
Marks T., Farkas W.R. Effects of a diet deficient in tyrosine and queuine on germfree mice. Biochem. Biophys. Res. Commun. 1997, 230:233-237.
-
(1997)
Biochem. Biophys. Res. Commun.
, vol.230
, pp. 233-237
-
-
Marks, T.1
Farkas, W.R.2
-
29
-
-
0345624489
-
Transfer RNA modification status influences retroviral ribosomal frameshifting
-
Carlson B.A., Kwon S.Y., Chamorro M., Oroszlan S., Hatfield D.L., Lee B.J. Transfer RNA modification status influences retroviral ribosomal frameshifting. Virology 1999, 255:2-8.
-
(1999)
Virology
, vol.255
, pp. 2-8
-
-
Carlson, B.A.1
Kwon, S.Y.2
Chamorro, M.3
Oroszlan, S.4
Hatfield, D.L.5
Lee, B.J.6
-
30
-
-
0033965439
-
Transfer RNA modification, temperature and DNA superhelicity have a common target in the regulatory network of the virulence of Shigella flexneri: the expression of the virF gene
-
Durand J.M., Dagberg B., Uhlin B.E., Bjork G.R. Transfer RNA modification, temperature and DNA superhelicity have a common target in the regulatory network of the virulence of Shigella flexneri: the expression of the virF gene. Mol. Microbiol. 2000, 35:924-935.
-
(2000)
Mol. Microbiol.
, vol.35
, pp. 924-935
-
-
Durand, J.M.1
Dagberg, B.2
Uhlin, B.E.3
Bjork, G.R.4
-
31
-
-
0028041249
-
VacC, a virulence-associated chromosomal locus of Shigella flexneri, is homologous to tgt, a gene encoding tRNA-guanine transglycosylase (Tgt) of Escherichia coli K-12
-
Durand J.M., Okada N., Tobe T., Watarai M., Fukuda I., Suzuki T., Nakata N., Komatsu K., Yoshikawa M., Sasakawa C. vacC, a virulence-associated chromosomal locus of Shigella flexneri, is homologous to tgt, a gene encoding tRNA-guanine transglycosylase (Tgt) of Escherichia coli K-12. J. Bacteriol. 1994, 176:4627-4634.
-
(1994)
J. Bacteriol.
, vol.176
, pp. 4627-4634
-
-
Durand, J.M.1
Okada, N.2
Tobe, T.3
Watarai, M.4
Fukuda, I.5
Suzuki, T.6
Nakata, N.7
Komatsu, K.8
Yoshikawa, M.9
Sasakawa, C.10
-
32
-
-
34547886845
-
Site-specific modification of Shigella flexneri virF mRNA by tRNA-guanine transglycosylase in vitro
-
Hurt J.K., Olgen S., Garcia G.A. Site-specific modification of Shigella flexneri virF mRNA by tRNA-guanine transglycosylase in vitro. Nucleic Acids Res. 2007, 35:4905-4913.
-
(2007)
Nucleic Acids Res.
, vol.35
, pp. 4905-4913
-
-
Hurt, J.K.1
Olgen, S.2
Garcia, G.A.3
-
33
-
-
34250192588
-
Crystal structures of tRNA-guanine transglycosylase (TGT) in complex with novel and potent inhibitors unravel pronounced induced-fit adaptations and suggest dimer formation upon substrate binding
-
Stengl B., Meyer E.A., Heine A., Brenk R., Diederich F., Klebe G. Crystal structures of tRNA-guanine transglycosylase (TGT) in complex with novel and potent inhibitors unravel pronounced induced-fit adaptations and suggest dimer formation upon substrate binding. J. Mol. Biol. 2007, 370:492-511.
-
(2007)
J. Mol. Biol.
, vol.370
, pp. 492-511
-
-
Stengl, B.1
Meyer, E.A.2
Heine, A.3
Brenk, R.4
Diederich, F.5
Klebe, G.6
-
34
-
-
0037310429
-
Biosynthesis of the 7-deazaguanosine hypermodified nucleosides of transfer RNA
-
Iwata-Reuyl D. Biosynthesis of the 7-deazaguanosine hypermodified nucleosides of transfer RNA. Bioorg. Chem. 2003, 31:24-43.
-
(2003)
Bioorg. Chem.
, vol.31
, pp. 24-43
-
-
Iwata-Reuyl, D.1
-
35
-
-
84864396740
-
Biosynthesis of pyrrolopyrimidines
-
McCarty R.M., Bandarian V. Biosynthesis of pyrrolopyrimidines. Bioorg. Chem. 2012, 43:15-25.
-
(2012)
Bioorg. Chem.
, vol.43
, pp. 15-25
-
-
McCarty, R.M.1
Bandarian, V.2
-
36
-
-
0017298136
-
Letter: the structure of Q* nucleoside isolated from rabbit liver transfer ribonucleic acid
-
Kasai H., Nakanishi K., Macfarlane R.D., Torgerson D.F., Ohashi Z., McCloskey J.A., Gross H.J., Nishimura S. Letter: the structure of Q* nucleoside isolated from rabbit liver transfer ribonucleic acid. J. Am. Chem. Soc. 1976, 98:5044-5046.
-
(1976)
J. Am. Chem. Soc.
, vol.98
, pp. 5044-5046
-
-
Kasai, H.1
Nakanishi, K.2
Macfarlane, R.D.3
Torgerson, D.F.4
Ohashi, Z.5
McCloskey, J.A.6
Gross, H.J.7
Nishimura, S.8
-
37
-
-
0017459030
-
Isolation of mammalian tRNAAsp and tRNATyr by lectin-Sepharose affinity column chromatography
-
Okada N., Shindo-Okada N., Nishimura S. Isolation of mammalian tRNAAsp and tRNATyr by lectin-Sepharose affinity column chromatography. Nucleic Acids Res. 1977, 4:415-423.
-
(1977)
Nucleic Acids Res.
, vol.4
, pp. 415-423
-
-
Okada, N.1
Shindo-Okada, N.2
Nishimura, S.3
-
38
-
-
2342511433
-
New RNA motifs suggest an expanded scope for riboswitches in bacterial genetic control
-
Barrick J.E., Corbino K.A., Winkler W.C., Nahvi A., Mandal M., Collins J., Lee M., Roth A., Sudarsan N., Jona I., Wickiser J.K., Breaker R.R. New RNA motifs suggest an expanded scope for riboswitches in bacterial genetic control. Proc. Natl. Acad. Sci. U. S. A. 2004, 101:6421-6426.
-
(2004)
Proc. Natl. Acad. Sci. U. S. A.
, vol.101
, pp. 6421-6426
-
-
Barrick, J.E.1
Corbino, K.A.2
Winkler, W.C.3
Nahvi, A.4
Mandal, M.5
Collins, J.6
Lee, M.7
Roth, A.8
Sudarsan, N.9
Jona, I.10
Wickiser, J.K.11
Breaker, R.R.12
-
39
-
-
34247181095
-
A riboswitch selective for the queuosine precursor preQ1 contains an unusually small aptamer domain
-
Roth A., Winkler W.C., Regulski E.E., Lee B.W., Lim J., Jona I., Barrick J.E., Ritwik A., Kim J.N., Welz R., Iwata-Reuyl D., Breaker R.R. A riboswitch selective for the queuosine precursor preQ1 contains an unusually small aptamer domain. Nat. Struct. Mol. Biol. 2007, 14:308-317.
-
(2007)
Nat. Struct. Mol. Biol.
, vol.14
, pp. 308-317
-
-
Roth, A.1
Winkler, W.C.2
Regulski, E.E.3
Lee, B.W.4
Lim, J.5
Jona, I.6
Barrick, J.E.7
Ritwik, A.8
Kim, J.N.9
Welz, R.10
Iwata-Reuyl, D.11
Breaker, R.R.12
-
40
-
-
58149191274
-
Rfam: updates to the RNA families database
-
Gardner P.P., Daub J., Tate J.G., Nawrocki E.P., Kolbe D.L., Lindgreen S., Wilkinson A.C., Finn R.D., Griffiths-Jones S., Eddy S.R., Bateman A. Rfam: updates to the RNA families database. Nucleic Acids Res. 2009, 37:D136-D140.
-
(2009)
Nucleic Acids Res.
, vol.37
, pp. D136-D140
-
-
Gardner, P.P.1
Daub, J.2
Tate, J.G.3
Nawrocki, E.P.4
Kolbe, D.L.5
Lindgreen, S.6
Wilkinson, A.C.7
Finn, R.D.8
Griffiths-Jones, S.9
Eddy, S.R.10
Bateman, A.11
-
41
-
-
34547873145
-
Identification of 22 candidate structured RNAs in bacteria using the CMfinder comparative genomics pipeline
-
Weinberg Z., Barrick J.E., Yao Z., Roth A., Kim J.N., Gore J., Wang J.X., Lee E.R., Block K.F., Sudarsan N., Neph S., Tompa M., Ruzzo W.L., Breaker R.R. Identification of 22 candidate structured RNAs in bacteria using the CMfinder comparative genomics pipeline. Nucleic Acids Res. 2007, 35:4809-4819.
-
(2007)
Nucleic Acids Res.
, vol.35
, pp. 4809-4819
-
-
Weinberg, Z.1
Barrick, J.E.2
Yao, Z.3
Roth, A.4
Kim, J.N.5
Gore, J.6
Wang, J.X.7
Lee, E.R.8
Block, K.F.9
Sudarsan, N.10
Neph, S.11
Tompa, M.12
Ruzzo, W.L.13
Breaker, R.R.14
-
42
-
-
41649108068
-
Confirmation of a second natural preQ1 aptamer class in Streptococcaceae bacteria
-
Meyer M.M., Roth A., Chervin S.M., Garcia G.A., Breaker R.R. Confirmation of a second natural preQ1 aptamer class in Streptococcaceae bacteria. RNA 2008, 14:685-695.
-
(2008)
RNA
, vol.14
, pp. 685-695
-
-
Meyer, M.M.1
Roth, A.2
Chervin, S.M.3
Garcia, G.A.4
Breaker, R.R.5
-
43
-
-
84879103214
-
Structure of a class II preQ1 riboswitch reveals ligand recognition by a new fold
-
Liberman J.A., Salim M., Krucinska J., Wedekind J.E. Structure of a class II preQ1 riboswitch reveals ligand recognition by a new fold. Nat. Chem. Biol. 2013, 9:353-355.
-
(2013)
Nat. Chem. Biol.
, vol.9
, pp. 353-355
-
-
Liberman, J.A.1
Salim, M.2
Krucinska, J.3
Wedekind, J.E.4
-
44
-
-
84893843560
-
Structural determinants for ligand capture by a class II preQ1 riboswitch
-
Kang M., Eichhorn C.D., Feigon J. Structural determinants for ligand capture by a class II preQ1 riboswitch. Proc. Natl. Acad. Sci. U. S. A. 2014, 116:E663-E671.
-
(2014)
Proc. Natl. Acad. Sci. U. S. A.
, vol.116
, pp. E663-E671
-
-
Kang, M.1
Eichhorn, C.D.2
Feigon, J.3
-
45
-
-
62549154008
-
Structural Insights into riboswitch control of the biosynthesis of queuosine, a modified nucleotide found in the anticodon of tRNA
-
(Erratum in: 2010, 2039, 2653-2655)
-
Kang M., Peterson R., Feigon J. Structural Insights into riboswitch control of the biosynthesis of queuosine, a modified nucleotide found in the anticodon of tRNA. Mol. Cell 2009, 33:784-790. (Erratum in: 2010, 2039, 2653-2655).
-
(2009)
Mol. Cell
, vol.33
, pp. 784-790
-
-
Kang, M.1
Peterson, R.2
Feigon, J.3
-
46
-
-
62049086072
-
Cocrystal structure of a class I preQ1 riboswitch reveals a pseudoknot recognizing an essential hypermodified nucleobase
-
Klein D.J., Edwards T.E., Ferre-D'Amare A.R. Cocrystal structure of a class I preQ1 riboswitch reveals a pseudoknot recognizing an essential hypermodified nucleobase. Nat. Struct. Mol. Biol. 2009, 16:343-344.
-
(2009)
Nat. Struct. Mol. Biol.
, vol.16
, pp. 343-344
-
-
Klein, D.J.1
Edwards, T.E.2
Ferre-D'Amare, A.R.3
-
47
-
-
66449089224
-
The structural basis for recognition of the PreQ0 metabolite by an unusually small riboswitch aptamer domain
-
Spitale R.C., Torelli A.T., Krucinska J., Bandarian V., Wedekind J.E. The structural basis for recognition of the PreQ0 metabolite by an unusually small riboswitch aptamer domain. J. Biol. Chem. 2009, 284:11012-11016.
-
(2009)
J. Biol. Chem.
, vol.284
, pp. 11012-11016
-
-
Spitale, R.C.1
Torelli, A.T.2
Krucinska, J.3
Bandarian, V.4
Wedekind, J.E.5
-
48
-
-
79960114180
-
Comparison of a preQ1 riboswitch aptamer in metabolite-bound and free states with implications for gene regulation
-
Jenkins J.L., Krucinska J., McCarty R.M., Bandarian V., Wedekind J.E. Comparison of a preQ1 riboswitch aptamer in metabolite-bound and free states with implications for gene regulation. J. Biol. Chem. 2011, 286:24626-24637.
-
(2011)
J. Biol. Chem.
, vol.286
, pp. 24626-24637
-
-
Jenkins, J.L.1
Krucinska, J.2
McCarty, R.M.3
Bandarian, V.4
Wedekind, J.E.5
-
49
-
-
67650445952
-
Evidence for pseudoknot formation of class I preQ1 riboswitch aptamers
-
Rieder U., Lang K., Kreutz C., Polacek N., Micura R. Evidence for pseudoknot formation of class I preQ1 riboswitch aptamers. Chembiochem 2009, 10:1141-1144.
-
(2009)
Chembiochem
, vol.10
, pp. 1141-1144
-
-
Rieder, U.1
Lang, K.2
Kreutz, C.3
Polacek, N.4
Micura, R.5
-
50
-
-
79953716261
-
Comparison of solution and crystal structures of preQ1 riboswitch reveals calcium-induced changes in conformation and dynamics
-
Zhang Q., Kang M., Peterson R.D., Feigon J. Comparison of solution and crystal structures of preQ1 riboswitch reveals calcium-induced changes in conformation and dynamics. J. Am. Chem. Soc. 2011, 133:5190-5193.
-
(2011)
J. Am. Chem. Soc.
, vol.133
, pp. 5190-5193
-
-
Zhang, Q.1
Kang, M.2
Peterson, R.D.3
Feigon, J.4
-
51
-
-
65649096161
-
Crystallization of the glmS ribozyme-riboswitch
-
Klein D.J., Ferre-D'Amare A.R. Crystallization of the glmS ribozyme-riboswitch. Methods Mol. Biol. 2009, 540:129-139.
-
(2009)
Methods Mol. Biol.
, vol.540
, pp. 129-139
-
-
Klein, D.J.1
Ferre-D'Amare, A.R.2
-
53
-
-
26444620938
-
The kinetics of ligand binding by an adenine-sensing riboswitch
-
Wickiser J.K., Cheah M.T., Breaker R.R., Crothers D.M. The kinetics of ligand binding by an adenine-sensing riboswitch. Biochemistry 2005, 44:13404-13414.
-
(2005)
Biochemistry
, vol.44
, pp. 13404-13414
-
-
Wickiser, J.K.1
Cheah, M.T.2
Breaker, R.R.3
Crothers, D.M.4
-
54
-
-
15944382675
-
The speed of RNA transcription and metabolite binding kinetics operate an FMN riboswitch
-
Wickiser J.K., Winkler W.C., Breaker R.R., Crothers D.M. The speed of RNA transcription and metabolite binding kinetics operate an FMN riboswitch. Mol. Cell 2005, 18:49-60.
-
(2005)
Mol. Cell
, vol.18
, pp. 49-60
-
-
Wickiser, J.K.1
Winkler, W.C.2
Breaker, R.R.3
Crothers, D.M.4
-
55
-
-
84865243362
-
Riboswitch structure in the ligand-free state, Wiley interdisciplinary reviews
-
Liberman J.A., Wedekind J.E. Riboswitch structure in the ligand-free state, Wiley interdisciplinary reviews. RNA 2012, 3:369-384.
-
(2012)
RNA
, vol.3
, pp. 369-384
-
-
Liberman, J.A.1
Wedekind, J.E.2
-
56
-
-
18144365521
-
Roles of Mg2+ in TPP-dependent riboswitch
-
Yamauchi T., Miyoshi D., Kubodera T., Nishimura A., Nakai S., Sugimoto N. Roles of Mg2+ in TPP-dependent riboswitch. FEBS Lett. 2005, 579:2583-2588.
-
(2005)
FEBS Lett.
, vol.579
, pp. 2583-2588
-
-
Yamauchi, T.1
Miyoshi, D.2
Kubodera, T.3
Nishimura, A.4
Nakai, S.5
Sugimoto, N.6
-
57
-
-
33646007627
-
An RNA sensor for intracellular Mg(2+)
-
Cromie M.J., Shi Y., Latifi T., Groisman E.A. An RNA sensor for intracellular Mg(2+). Cell 2006, 125:71-84.
-
(2006)
Cell
, vol.125
, pp. 71-84
-
-
Cromie, M.J.1
Shi, Y.2
Latifi, T.3
Groisman, E.A.4
-
58
-
-
33745635350
-
Structural basis for gene regulation by a thiamine pyrophosphate-sensing riboswitch
-
Serganov A., Polonskaia A., Phan A.T., Breaker R.R., Patel D.J. Structural basis for gene regulation by a thiamine pyrophosphate-sensing riboswitch. Nature 2006, 441:1167-1171.
-
(2006)
Nature
, vol.441
, pp. 1167-1171
-
-
Serganov, A.1
Polonskaia, A.2
Phan, A.T.3
Breaker, R.R.4
Patel, D.J.5
-
59
-
-
33744469562
-
Structure of the eukaryotic thiamine pyrophosphate riboswitch with its regulatory ligand
-
Thore S., Leibundgut M., Ban N. Structure of the eukaryotic thiamine pyrophosphate riboswitch with its regulatory ligand. Science 2006, 312:1208-1211.
-
(2006)
Science
, vol.312
, pp. 1208-1211
-
-
Thore, S.1
Leibundgut, M.2
Ban, N.3
-
60
-
-
77950292093
-
Dissecting electrostatic screening, specific ion binding, and ligand binding in an energetic model for glycine riboswitch folding
-
Lipfert J., Sim A.Y., Herschlag D., Doniach S. Dissecting electrostatic screening, specific ion binding, and ligand binding in an energetic model for glycine riboswitch folding. RNA 2010, 16:708-719.
-
(2010)
RNA
, vol.16
, pp. 708-719
-
-
Lipfert, J.1
Sim, A.Y.2
Herschlag, D.3
Doniach, S.4
-
61
-
-
34548253368
-
Structure and mechanism of a metal-sensing regulatory RNA
-
Dann C.E., Wakeman C.A., Sieling C.L., Baker S.C., Irnov I., Winkler W.C. Structure and mechanism of a metal-sensing regulatory RNA. Cell 2007, 130:878-892.
-
(2007)
Cell
, vol.130
, pp. 878-892
-
-
Dann, C.E.1
Wakeman, C.A.2
Sieling, C.L.3
Baker, S.C.4
Irnov, I.5
Winkler, W.C.6
-
62
-
-
84890410887
-
Single transcriptional and translational preQ1 riboswitches adopt similar pre-folded ensembles that follow distinct folding pathways into the same ligand-bound structure
-
Suddala K.C., Rinaldi A.J., Feng J., Mustoe A.M., Eichhorn C.D., Liberman J.A., Wedekind J.E., Al-Hashimi H.M., Brooks C.L., Walter N.G. Single transcriptional and translational preQ1 riboswitches adopt similar pre-folded ensembles that follow distinct folding pathways into the same ligand-bound structure. Nucleic Acids Res. 2013, 41:10462-10475.
-
(2013)
Nucleic Acids Res.
, vol.41
, pp. 10462-10475
-
-
Suddala, K.C.1
Rinaldi, A.J.2
Feng, J.3
Mustoe, A.M.4
Eichhorn, C.D.5
Liberman, J.A.6
Wedekind, J.E.7
Al-Hashimi, H.M.8
Brooks, C.L.9
Walter, N.G.10
-
63
-
-
84867801144
-
Molecular mechanism of preQ1 riboswitch action: a molecular dynamics study
-
Banas P., Sklenovsky P., Wedekind J.E., Sponer J., Otyepka M. Molecular mechanism of preQ1 riboswitch action: a molecular dynamics study. J. Phys. Chem. B 2012, 116:12721-12734.
-
(2012)
J. Phys. Chem. B
, vol.116
, pp. 12721-12734
-
-
Banas, P.1
Sklenovsky, P.2
Wedekind, J.E.3
Sponer, J.4
Otyepka, M.5
-
64
-
-
84864185753
-
Pseudoknot preorganization of the preQ1 class I riboswitch
-
Santner T., Rieder U., Kreutz C., Micura R. Pseudoknot preorganization of the preQ1 class I riboswitch. J. Am. Chem. Soc. 2012, 134:11928-11931.
-
(2012)
J. Am. Chem. Soc.
, vol.134
, pp. 11928-11931
-
-
Santner, T.1
Rieder, U.2
Kreutz, C.3
Micura, R.4
-
65
-
-
84863405959
-
Unraveling the structural complexity in a single-stranded RNA tail: implications for efficient ligand binding in the prequeuosine riboswitch
-
Eichhorn C.D., Feng J., Suddala K.C., Walter N.G., Brooks C.L., Al-Hashimi H.M. Unraveling the structural complexity in a single-stranded RNA tail: implications for efficient ligand binding in the prequeuosine riboswitch. Nucleic Acids Res. 2012, 40:1345-1355.
-
(2012)
Nucleic Acids Res.
, vol.40
, pp. 1345-1355
-
-
Eichhorn, C.D.1
Feng, J.2
Suddala, K.C.3
Walter, N.G.4
Brooks, C.L.5
Al-Hashimi, H.M.6
-
66
-
-
79953060592
-
Cooperative and directional folding of the preQ1 riboswitch aptamer domain
-
Feng J., Walter N.G., Brooks C.L. Cooperative and directional folding of the preQ1 riboswitch aptamer domain. J. Am. Chem. Soc. 2011, 133:4196-4199.
-
(2011)
J. Am. Chem. Soc.
, vol.133
, pp. 4196-4199
-
-
Feng, J.1
Walter, N.G.2
Brooks, C.L.3
-
67
-
-
84866463347
-
Computational study of unfolding and regulation mechanism of preQ1 riboswitches
-
Gong Z., Zhao Y., Chen C., Xiao Y. Computational study of unfolding and regulation mechanism of preQ1 riboswitches. PLoS One 2012, 7:e45239.
-
(2012)
PLoS One
, vol.7
, pp. e45239
-
-
Gong, Z.1
Zhao, Y.2
Chen, C.3
Xiao, Y.4
-
68
-
-
84883281341
-
Protonation of trimethylamine N-oxide (TMAO) is required for stabilization of RNA tertiary structure
-
Denning E.J., Thirumalai D., MacKerell A.D. Protonation of trimethylamine N-oxide (TMAO) is required for stabilization of RNA tertiary structure. Biophys. Chem. 2013, 184:8-16.
-
(2013)
Biophys. Chem.
, vol.184
, pp. 8-16
-
-
Denning, E.J.1
Thirumalai, D.2
MacKerell, A.D.3
-
69
-
-
84882246260
-
Urea-induced denaturation of preQ1-riboswitch
-
Yoon J., Thirumalai D., Hyeon C. Urea-induced denaturation of preQ1-riboswitch. J. Am. Chem. Soc. 2013, 135:12112-12121.
-
(2013)
J. Am. Chem. Soc.
, vol.135
, pp. 12112-12121
-
-
Yoon, J.1
Thirumalai, D.2
Hyeon, C.3
-
70
-
-
0041620358
-
PSEUDOVIEWER2: visualization of RNA pseudoknots of any type
-
Han K., Byun Y. PSEUDOVIEWER2: visualization of RNA pseudoknots of any type. Nucleic Acids Res. 2003, 31:3432-3440.
-
(2003)
Nucleic Acids Res.
, vol.31
, pp. 3432-3440
-
-
Han, K.1
Byun, Y.2
-
71
-
-
14644435818
-
Structure of the human telomerase RNA pseudoknot reveals conserved tertiary interactions essential for function
-
Theimer C.A., Blois C.A., Feigon J. Structure of the human telomerase RNA pseudoknot reveals conserved tertiary interactions essential for function. Mol. Cell 2005, 17:671-682.
-
(2005)
Mol. Cell
, vol.17
, pp. 671-682
-
-
Theimer, C.A.1
Blois, C.A.2
Feigon, J.3
-
72
-
-
78649422018
-
Poly(A) tail recognition by a viral RNA element through assembly of a triple helix
-
Mitton-Fry R.M., DeGregorio S.J., Wang J., Steitz T.A., Steitz J.A. Poly(A) tail recognition by a viral RNA element through assembly of a triple helix. Science 2010, 330:1244-1247.
-
(2010)
Science
, vol.330
, pp. 1244-1247
-
-
Mitton-Fry, R.M.1
DeGregorio, S.J.2
Wang, J.3
Steitz, T.A.4
Steitz, J.A.5
-
73
-
-
84883432280
-
Tuning a riboswitch response through structural extension of a pseudoknot
-
Souliere M.F., Altman R.B., Schwarz V., Haller A., Blanchard S.C., Micura R. Tuning a riboswitch response through structural extension of a pseudoknot. Proc. Natl. Acad. Sci. U. S. A. 2013, 110:E3256-E3264.
-
(2013)
Proc. Natl. Acad. Sci. U. S. A.
, vol.110
, pp. E3256-E3264
-
-
Souliere, M.F.1
Altman, R.B.2
Schwarz, V.3
Haller, A.4
Blanchard, S.C.5
Micura, R.6
-
74
-
-
71249121480
-
Aptamers and riboswitches: perspectives in biotechnology
-
Weigand J.E., Suess B. Aptamers and riboswitches: perspectives in biotechnology. Appl. Microbiol. Biotechnol. 2009, 85:229-236.
-
(2009)
Appl. Microbiol. Biotechnol.
, vol.85
, pp. 229-236
-
-
Weigand, J.E.1
Suess, B.2
-
75
-
-
84863617223
-
Engineered riboswitches: expanding researchers' toolbox with synthetic RNA regulators
-
Wittmann A., Suess B. Engineered riboswitches: expanding researchers' toolbox with synthetic RNA regulators. FEBS Lett. 2012, 586:2076-2083.
-
(2012)
FEBS Lett.
, vol.586
, pp. 2076-2083
-
-
Wittmann, A.1
Suess, B.2
-
76
-
-
84876532777
-
Exploiting preQ(1) riboswitches to regulate ribosomal frameshifting
-
Yu C.H., Luo J., Iwata-Reuyl D., Olsthoorn R.C. Exploiting preQ(1) riboswitches to regulate ribosomal frameshifting. ACS Chem. Biol. 2013, 8:733-740.
-
(2013)
ACS Chem. Biol.
, vol.8
, pp. 733-740
-
-
Yu, C.H.1
Luo, J.2
Iwata-Reuyl, D.3
Olsthoorn, R.C.4
-
77
-
-
33845700514
-
Riboswitches as antibacterial drug targets
-
Blount K.F., Breaker R.R. Riboswitches as antibacterial drug targets. Nat. Biotechnol. 2006, 24:1558-1564.
-
(2006)
Nat. Biotechnol.
, vol.24
, pp. 1558-1564
-
-
Blount, K.F.1
Breaker, R.R.2
-
78
-
-
80053041142
-
Riboswitches: discovery of drugs that target bacterial gene-regulatory RNAs
-
Deigan K.E., Ferre-D'Amare A.R. Riboswitches: discovery of drugs that target bacterial gene-regulatory RNAs. Acc. Chem. Res. 2011, 44:1329-1338.
-
(2011)
Acc. Chem. Res.
, vol.44
, pp. 1329-1338
-
-
Deigan, K.E.1
Ferre-D'Amare, A.R.2
-
80
-
-
33845710324
-
Antibacterial lysine analogs that target lysine riboswitches
-
Blount K.F., Wang J.X., Lim J., Sudarsan N., Breaker R.R. Antibacterial lysine analogs that target lysine riboswitches. Nat. Chem. Biol. 2007, 3:44-49.
-
(2007)
Nat. Chem. Biol.
, vol.3
, pp. 44-49
-
-
Blount, K.F.1
Wang, J.X.2
Lim, J.3
Sudarsan, N.4
Breaker, R.R.5
-
81
-
-
77954079519
-
Novel riboswitch ligand analogs as selective inhibitors of guanine-related metabolic pathways
-
Mulhbacher J., Brouillette E., Allard M., Fortier L.C., Malouin F., Lafontaine D.A. Novel riboswitch ligand analogs as selective inhibitors of guanine-related metabolic pathways. PLoS Pathog. 2010, 6:e1000865.
-
(2010)
PLoS Pathog.
, vol.6
, pp. e1000865
-
-
Mulhbacher, J.1
Brouillette, E.2
Allard, M.3
Fortier, L.C.4
Malouin, F.5
Lafontaine, D.A.6
-
82
-
-
84872678577
-
Experimental treatment of Staphylococcus aureus bovine intramammary infection using a guanine riboswitch ligand analog
-
Ster C., Allard M., Boulanger S., Lamontagne Boulet M., Mulhbacher J., Lafontaine D.A., Marsault E., Lacasse P., Malouin F. Experimental treatment of Staphylococcus aureus bovine intramammary infection using a guanine riboswitch ligand analog. J. Dairy Sci. 2013, 96:1000-1008.
-
(2013)
J. Dairy Sci.
, vol.96
, pp. 1000-1008
-
-
Ster, C.1
Allard, M.2
Boulanger, S.3
Lamontagne Boulet, M.4
Mulhbacher, J.5
Lafontaine, D.A.6
Marsault, E.7
Lacasse, P.8
Malouin, F.9
-
83
-
-
77950798696
-
Aptamer-controlled biofuel cells in logic systems and used as self-powered and intelligent logic aptasensors
-
Zhou M., Du Y., Chen C., Li B., Wen D., Dong S., Wang E. Aptamer-controlled biofuel cells in logic systems and used as self-powered and intelligent logic aptasensors. J. Am. Chem. Soc. 2010, 132:2172-2174.
-
(2010)
J. Am. Chem. Soc.
, vol.132
, pp. 2172-2174
-
-
Zhou, M.1
Du, Y.2
Chen, C.3
Li, B.4
Wen, D.5
Dong, S.6
Wang, E.7
-
85
-
-
84884227283
-
Synthetic biology of cyanobacteria: unique challenges and opportunities
-
Berla B.M., Saha R., Immethun C.M., Maranas C.D., Moon T.S., Pakrasi H.B. Synthetic biology of cyanobacteria: unique challenges and opportunities. Front. Microbiol. 2013, 4:246.
-
(2013)
Front. Microbiol.
, vol.4
, pp. 246
-
-
Berla, B.M.1
Saha, R.2
Immethun, C.M.3
Maranas, C.D.4
Moon, T.S.5
Pakrasi, H.B.6
-
86
-
-
84885929738
-
Theophylline-dependent riboswitch as a novel genetic tool for strict regulation of protein expression in cyanobacterium Synechococcus elongatus PCC 7942
-
Nakahira Y., Ogawa A., Asano H., Oyama T., Tozawa Y. Theophylline-dependent riboswitch as a novel genetic tool for strict regulation of protein expression in cyanobacterium Synechococcus elongatus PCC 7942. Plant Cell Physiol. 2013, 54:1724-1735.
-
(2013)
Plant Cell Physiol.
, vol.54
, pp. 1724-1735
-
-
Nakahira, Y.1
Ogawa, A.2
Asano, H.3
Oyama, T.4
Tozawa, Y.5
-
87
-
-
0035010211
-
Geometric nomenclature and classification of RNA base pairs
-
Leontis N.B., Westhof E. Geometric nomenclature and classification of RNA base pairs. RNA 2001, 7:499-512.
-
(2001)
RNA
, vol.7
, pp. 499-512
-
-
Leontis, N.B.1
Westhof, E.2
|