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Volumn 17, Issue 7, 2011, Pages 1393-1400

Fluorescent labeling of tRNA dihydrouridine residues: Mechanism and distribution

Author keywords

Cy3 Cy5 proflavin; Dihydrouridine; MALDI; Tetrahyhydrocytidine; tRNA

Indexed keywords

DIHYDROURIDINE; DYE; N4 BENZOAMIDO TETRAHYDROCYTIDINE; OLIGONUCLEOTIDE; PROFLAVINE; RIBONUCLEASE; TETRAHYDROURIDINE; TRANSFER RNA; UNCLASSIFIED DRUG; URIDINE DERIVATIVE;

EID: 79955506552     PISSN: 13558382     EISSN: 14699001     Source Type: Journal    
DOI: 10.1261/rna.2670811     Document Type: Article
Times cited : (31)

References (37)
  • 1
    • 0038372379 scopus 로고    scopus 로고
    • Functional microfabricated sample targets for matrix-assisted laser desorption/ionization mass spectrometry analysis of ribonucleic acids
    • DOI 10.1021/ac020710i
    • Berhane BT, Limbach PA. 2003a. Functional microfabricated sample targets for matrix-assisted laser desorption/ionization mass spectrometry analysis of ribonucleic acids. Anal Chem 75: 1997-2003. (Pubitemid 36542336)
    • (2003) Analytical Chemistry , vol.75 , Issue.9 , pp. 1997-2003
    • Berhane, B.T.1    Limbach, P.A.2
  • 2
    • 0042355182 scopus 로고    scopus 로고
    • Stable isotope labeling for matrix-assisted laser desorption/ionization mass spectrometry and post-source decay analysis of ribonucleic acids
    • DOI 10.1002/jms.504
    • Berhane BT, Limbach PA. 2003b. Stable isotope labeling for matrix-assisted laser desorption/ionization mass spectrometry and post-source decay analysis of ribonucleic acids. J Mass Spectrom 38: 872-878. (Pubitemid 37062954)
    • (2003) Journal of Mass Spectrometry , vol.38 , Issue.8 , pp. 872-878
    • Berhane, B.T.1    Limbach, P.A.2
  • 3
    • 34548341807 scopus 로고    scopus 로고
    • Fluorescent labeling of tRNAs for dynamics experiments
    • DOI 10.1261/rna.475407
    • Betteridge T, Liu H, Gamper H, Kirillov S, Cooperman BS, Hou YM. 2007. Fluorescent labeling of tRNAs for dynamics experiments. RNA 13: 1594-1601. (Pubitemid 47347429)
    • (2007) RNA , vol.13 , Issue.9 , pp. 1594-1601
    • Betteridge, T.1    Liu, H.2    Gamper, H.3    Kirillov, S.4    Cooperman, B.S.5    Hou, Y.-M.6
  • 5
    • 33745071762 scopus 로고    scopus 로고
    • Peptide bond formation does not involve acid-base catalysis by ribosomal residues
    • DOI 10.1038/nsmb1091, PII N1091
    • Bieling P, Beringer M, Adio S, Rodnina MV. 2006. Peptide bond formation does not involve acid-base catalysis by ribosomal residues. Nat Struct Mol Biol 13: 423-428. (Pubitemid 43881582)
    • (2006) Nature Structural and Molecular Biology , vol.13 , Issue.5 , pp. 423-428
    • Bieling, P.1    Beringer, M.2    Adio, S.3    Rodnina, M.V.4
  • 8
    • 0014219460 scopus 로고
    • Selective reduction of yeast transfer ribonucleic acid with sodium borohydride
    • Cerutti P, Miller N. 1967. Selective reduction of yeast transfer ribonucleic acid with sodium borohydride. J Mol Biol 26: 55-66.
    • (1967) J Mol Biol , vol.26 , pp. 55-66
    • Cerutti, P.1    Miller, N.2
  • 9
    • 0014435899 scopus 로고
    • Photoreduction of uridine and reduction of dihydrouridine with sodium borohydride
    • Cerutti P, Kondo Y, Landis WR, Witkop B. 1968. Photoreduction of uridine and reduction of dihydrouridine with sodium borohydride. J Am Chem Soc 90: 771-775.
    • (1968) J Am Chem Soc , vol.90 , pp. 771-775
    • Cerutti, P.1    Kondo, Y.2    Landis, W.R.3    Witkop, B.4
  • 11
    • 42949126723 scopus 로고    scopus 로고
    • Coupling of Ribosomal L1 Stalk and tRNA Dynamics during Translation Elongation
    • DOI 10.1016/j.molcel.2008.03.012, PII S1097276508002128
    • Fei J, Kosuri P, MacDougall DD, Gonzalez RL Jr. 2008. Coupling of ribosomal L1 stalk and tRNA dynamics during translation elongation. Mol Cell 30: 348-359. (Pubitemid 351615315)
    • (2008) Molecular Cell , vol.30 , Issue.3 , pp. 348-359
    • Fei, J.1    Kosuri, P.2    MacDougall, D.D.3    Gonzalez Jr., R.L.4
  • 12
    • 34748843156 scopus 로고    scopus 로고
    • A Quantitative Kinetic Scheme for 70 S Translation Initiation Complex Formation
    • DOI 10.1016/j.jmb.2007.07.032, PII S002228360700959X
    • Grigoriadou C, Marzi S, Kirillov S, Gualerzi CO, Cooperman BS. 2007a. A quantitative kinetic scheme for 70 S translation initiation complex formation. J Mol Biol 373: 562-572. (Pubitemid 47488388)
    • (2007) Journal of Molecular Biology , vol.373 , Issue.3 , pp. 562-572
    • Grigoriadou, C.1    Marzi, S.2    Kirillov, S.3    Gualerzi, C.O.4    Cooperman, B.S.5
  • 13
    • 34748909381 scopus 로고    scopus 로고
    • The Translational Fidelity Function of IF3 during Transition from the 30 S Initiation Complex to the 70 S Initiation Complex
    • DOI 10.1016/j.jmb.2007.07.031, PII S0022283607009588
    • Grigoriadou C, Marzi S, Pan D, Gualerzi CO, Cooperman BS. 2007b. The translational fidelity function of IF3 during transition from the 30 S initiation complex to the 70 S initiation complex. J Mol Biol 373: 551-561. (Pubitemid 47488387)
    • (2007) Journal of Molecular Biology , vol.373 , Issue.3 , pp. 551-561
    • Grigoriadou, C.1    Marzi, S.2    Pan, D.3    Gualerzi, C.O.4    Cooperman, B.S.5
  • 14
    • 0014194626 scopus 로고
    • Nucleic acids. IV. The catalytic reduction of pyrimidine nucleosides (human liver deaminase inhibitors)
    • Hanze AR. 1967. Nucleic acids. IV. The catalytic reduction of pyrimidine nucleosides (human liver deaminase inhibitors). J Am Chem Soc 89: 6720-6725.
    • (1967) J Am Chem Soc , vol.89 , pp. 6720-6725
    • Hanze, A.R.1
  • 15
    • 0038750904 scopus 로고    scopus 로고
    • RNase T1 mediated base-specific cleavage and MALDI-TOF MS for high-throughput comparative sequence analysis
    • doi: 10.1093/nar/gng047
    • Hartmer R, Strom N, Boecker S, Rodi CP, Hillenkamp F, Jurinke C, Boom DV. 2003. RNase T1 mediated base-specific cleavage and MALDI-TOF MS for high-throughput comparative sequence analysis. Nucleic Acids Res 31: e47. doi: 10.1093/nar/gng047.
    • (2003) Nucleic Acids Res , vol.31
    • Hartmer, R.1    Strom, N.2    Boecker, S.3    Rodi, C.P.4    Hillenkamp, F.5    Jurinke, C.6    Boom, D.V.7
  • 16
    • 38049039329 scopus 로고    scopus 로고
    • Use of DNAzymes for site-specific analysis of ribonucleotide modifications
    • Hengesbach M, Meusburger M, Lyko F, Helm M. 2008. Use of DNAzymes for site-specific analysis of ribonucleotide modifications. RNA 14: 180-187.
    • (2008) RNA , vol.14 , pp. 180-187
    • Hengesbach, M.1    Meusburger, M.2    Lyko, F.3    Helm, M.4
  • 17
    • 33846414324 scopus 로고    scopus 로고
    • Mass spectrometry-based detection of transfer RNAs by their signature endonuclease digestion products
    • DOI 10.1261/rna.272507
    • Hossain M, Limbach PA. 2007. Mass spectrometry-based detection of transfer RNAs by their signature endonuclease digestion products. RNA 13: 295-303. (Pubitemid 46147904)
    • (2007) RNA , vol.13 , Issue.2 , pp. 295-303
    • Hossain, M.1    Limbach, P.A.2
  • 18
    • 67349099918 scopus 로고    scopus 로고
    • Multiple endonucleases improve MALDI-MS signature digestion product detection of bacterial transfer RNAs
    • Hossain M, Limbach PA. 2009. Multiple endonucleases improve MALDI-MS signature digestion product detection of bacterial transfer RNAs. Anal Bioanal Chem 394: 1125-1135.
    • (2009) Anal Bioanal Chem , vol.394 , pp. 1125-1135
    • Hossain, M.1    Limbach, P.A.2
  • 19
    • 0033950924 scopus 로고    scopus 로고
    • Mapping posttranscriptional modifications in 5S ribosomal RNA by MALDI mass spectrometry
    • DOI 10.1017/S1355838200992148
    • Kirpekar F, Douthwaite S, Rosepstorff P. 2000. Mapping posttranscriptional modifications in 5S ribosomal RNA by MALDI mass spectrometry. RNA 6: 296-306. (Pubitemid 30091599)
    • (2000) RNA , vol.6 , Issue.2 , pp. 296-306
    • Kirpekar, F.1    Douthwaite, S.2    Roepstorff, P.3
  • 21
    • 0034143609 scopus 로고    scopus 로고
    • Initiation of protein synthesis with fluorophore-Met-tRNA(f) and the involvement of IF-2
    • DOI 10.1016/S0300-9084(00)00381-3
    • McIntosh B, Ramachandiran V, Kramer G, Hardesty B. 2000. Initiation of protein synthesis with fluorophore-Met-tRNA(f) and the involvement of IF-2. Biochimie 82: 167-174. (Pubitemid 30153555)
    • (2000) Biochimie , vol.82 , Issue.2 , pp. 167-174
    • McIntosh, B.1    Ramachandiran, V.2    Kramer, G.3    Hardesty, B.4
  • 23
    • 33847051154 scopus 로고    scopus 로고
    • Identification of Two Distinct Hybrid State Intermediates on the Ribosome
    • DOI 10.1016/j.molcel.2007.01.022, PII S1097276507000457
    • Munro JB, Altman RB, O'Connor N, Blanchard SC. 2007. Identification of two distinct hybrid state intermediates on the ribosome. Mol Cell 25: 505-517. (Pubitemid 46274447)
    • (2007) Molecular Cell , vol.25 , Issue.4 , pp. 505-517
    • Munro, J.B.1    Altman, R.B.2    O'Connor, N.3    Blanchard, S.C.4
  • 25
    • 33847024820 scopus 로고    scopus 로고
    • Kinetically Competent Intermediates in the Translocation Step of Protein Synthesis
    • DOI 10.1016/j.molcel.2007.01.014, PII S1097276507000366
    • Pan D, Kirillov SV, Cooperman BS. 2007. Kinetically competent intermediates in the translocation step of protein synthesis. Mol Cell 25: 519-529. (Pubitemid 46274443)
    • (2007) Molecular Cell , vol.25 , Issue.4 , pp. 519-529
    • Pan, D.1    Kirillov, S.V.2    Cooperman, B.S.3
  • 26
    • 58249096649 scopus 로고    scopus 로고
    • Synthesis and functional activity of tRNAs labeled with fluorescent hydrazides in the D-loop
    • Pan D, Qin H, Cooperman BS. 2009. Synthesis and functional activity of tRNAs labeled with fluorescent hydrazides in the D-loop. RNA 2: 346-354.
    • (2009) RNA , vol.2 , pp. 346-354
    • Pan, D.1    Qin, H.2    Cooperman, B.S.3
  • 27
    • 0032535207 scopus 로고    scopus 로고
    • Complete kinetic mechanism of elongation factor Tu-dependent binding of aminoacyl-tRNA to the A site of the E.coli ribosome
    • DOI 10.1093/emboj/17.24.7490
    • Pape T, Wintermeyer W, Rodnina MV. 1998. Complete kinetic mechanism of elongation factor Tu-dependent binding of aminoacyl- tRNA to the A site of the E. coli ribosome. EMBO J 17: 7490-7497. (Pubitemid 29002715)
    • (1998) EMBO Journal , vol.17 , Issue.24 , pp. 7490-7497
    • Pape, T.1    Wintermeyer, W.2    Rodnina, M.V.3
  • 28
    • 0035536582 scopus 로고    scopus 로고
    • The Preparation of 1-Allyluracil. N(1)- Alkylation of N(3)-Protected Uracil Derivatives
    • Paryzek Z, Tabaczka B. 2001. The Preparation of 1-Allyluracil. N(1)- Alkylation of N(3)-Protected Uracil Derivatives. Org Prep Proced Int 33: 400-404.
    • (2001) Org Prep Proced Int , vol.33 , pp. 400-404
    • Paryzek, Z.1    Tabaczka, B.2
  • 29
    • 0032412430 scopus 로고    scopus 로고
    • Matrix-assisted laser desorption/ionization time-of-flight mass spectrometry for the analysis of RNase H cleavage products
    • DOI 10.1002/(SICI)1096-9888(199812)33:12<1226::AID-JMS739>3.0.CO;2- #
    • Polo LM, Limbach PA. 1998. Matrix-assisted laser desorption/ionization time-of-flight mass spectrometry for the analysis of RNase H cleavage products. J Mass Spectrom 33: 1226-1231. (Pubitemid 29004875)
    • (1998) Journal of Mass Spectrometry , vol.33 , Issue.12 , pp. 1226-1231
    • Polo, L.M.1    Limbach, P.A.2
  • 30
    • 0038433302 scopus 로고    scopus 로고
    • An Elongation Factor G-Induced Ribosome Rearrangement Precedes tRNA-mRNA Translocation
    • DOI 10.1016/S1097-2765(03)00230-2
    • Savelsbergh A, Katunin VI, Mohr D, Peske F, Rodnina MV, Wintermeyer W. 2003. An elongation factor G-induced ribosome rearrangement precedes tRNA-mRNA translocation. Mol Cell 11: 1517-1523. (Pubitemid 36776538)
    • (2003) Molecular Cell , vol.11 , Issue.6 , pp. 1517-1523
    • Savelsbergh, A.1    Katunin, V.I.2    Mohr, D.3    Peske, F.4    Rodnina, M.V.5    Wintermeyer, W.6
  • 31
    • 0017822261 scopus 로고
    • Replacement of wybutine by hydrazines and its effect on the active conformation of yeast tRNA(Phe)
    • Schleich HG, Wintermeyer W, Zachau HG. 1978. Replacement of wybutine by hydrazines and its effect on the active conformation of yeast tRNAPhe. Nucleic Acids Res 5: 1701-1713. (Pubitemid 8398282)
    • (1978) Nucleic Acids Research , vol.5 , Issue.5 , pp. 1701-1713
    • Schleich, H.G.1    Wintermeyer, W.2    Zachau, H.G.3
  • 32
    • 0016717997 scopus 로고
    • On the interaction of 3,4,5,6- Tetrahydrouridine with human liver cytidine deaminase
    • Wentworth DF, Wolfenden R. 1975. On the interaction of 3,4,5,6- tetrahydrouridine with human liver cytidine deaminase. Biochemistry 23: 5099-5105.
    • (1975) Biochemistry , vol.23 , pp. 5099-5105
    • Wentworth, D.F.1    Wolfenden, R.2
  • 33
    • 49649150311 scopus 로고
    • Replacement of Y base, dihydrouracil, and 7-methylguanine in tRNA by artificial odd bases
    • Wintermeyer W, Zachau HG. 1971. Replacement of Y base, dihydrouracil, and 7-methylguanine in tRNA by artificial odd bases. FEBS Lett 18: 214-218.
    • (1971) FEBS Lett , vol.18 , pp. 214-218
    • Wintermeyer, W.1    Zachau, H.G.2
  • 34
    • 0016023632 scopus 로고
    • Replacement of odd bases in tRNA by fluorescent dyes
    • Wintermeyer W, Zachau HG. 1974. Replacement of odd bases in tRNA by fluorescent dyes. Methods Enzymol 29: 667-673.
    • (1974) Methods Enzymol , vol.29 , pp. 667-673
    • Wintermeyer, W.1    Zachau, H.G.2
  • 35
    • 0018510092 scopus 로고
    • Fluorescent derivatives of yeast tRNA
    • Wintermeyer W, Zachau HG. 1979. Fluorescent derivatives of yeast tRNA. Eur J Biochem 98: 465-475.
    • (1979) Eur J Biochem , vol.98 , pp. 465-475
    • Wintermeyer, W.1    Zachau, H.G.2
  • 36
    • 1542358892 scopus 로고    scopus 로고
    • Nascent membrane and secretory proteins differ in FRET-detected folding far inside the ribosome and in their exposure to ribosomal proteins
    • DOI 10.1016/S0092-8674(04)00169-2, PII S0092867404001692
    • Woolhead CA, McCormick PJ, Johnson AE. 2004. Nascent membrane and secretory proteins differ in FRET-detected folding far inside the ribosome and in their exposure to ribosomal proteins. Cell 116: 725-736. (Pubitemid 38326730)
    • (2004) Cell , vol.116 , Issue.5 , pp. 725-736
    • Woolhead, C.A.1    McCormick, P.J.2    Johnson, A.E.3
  • 37
    • 2442643944 scopus 로고    scopus 로고
    • Detection and quantitation of RNA base modifications
    • DOI 10.1261/rna.7110804
    • Zhao X, Yu YT. 2004. Detection and quantitation of RNA base modifications. RNA 10: 996-1002. (Pubitemid 38669772)
    • (2004) RNA , vol.10 , Issue.6 , pp. 996-1002
    • Zhao, X.1    Yu, Y.-T.2


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