메뉴 건너뛰기




Volumn 12, Issue 2, 2006, Pages 313-321

A general two-step strategy to synthesize lariat RNAs

Author keywords

Branched RNA; Debranching enzyme; Deoxyribozyme; Lariat RNA; T4 RNA ligase

Indexed keywords

DEOXYRIBOZYME; RNA; RNA LIGASE;

EID: 31044439368     PISSN: 13558382     EISSN: 14699001     Source Type: Journal    
DOI: 10.1261/rna.2259406     Document Type: Article
Times cited : (8)

References (46)
  • 1
    • 0001468848 scopus 로고    scopus 로고
    • Splicing of precursors to mRNAs by the spliceosomes
    • eds. R.F. Gesteland et al., Cold Spring Harbor Laboratory Press, Cold Spring Harbor, NY
    • Burge, C.B., Tuschl, T., and Sharp, P.A. 1999. Splicing of precursors to mRNAs by the spliceosomes. In The RNA world (eds. R.F. Gesteland et al.), pp. 525-560. Cold Spring Harbor Laboratory Press, Cold Spring Harbor, NY.
    • (1999) The RNA World , pp. 525-560
    • Burge, C.B.1    Tuschl, T.2    Sharp, P.A.3
  • 2
    • 0142196892 scopus 로고    scopus 로고
    • Template-mediated synthesis of lariat RNA and DNA
    • Carriero, S. and Damha, M.J. 2003. Template-mediated synthesis of lariat RNA and DNA. J. Org. Chem. 68: 8328-8338.
    • (2003) J. Org. Chem. , vol.68 , pp. 8328-8338
    • Carriero, S.1    Damha, M.J.2
  • 3
    • 1442286924 scopus 로고    scopus 로고
    • A DNA enzyme that mimics the first step of RNA splicing
    • Coppins, R.L. and Silverman, S.K. 2004. A DNA enzyme that mimics the first step of RNA splicing. Nat. Struct. Mol. Biol. 11: 270-274.
    • (2004) Nat. Struct. Mol. Biol. , vol.11 , pp. 270-274
    • Coppins, R.L.1    Silverman, S.K.2
  • 4
    • 14844285337 scopus 로고    scopus 로고
    • A deoxyribozyme that forms a three-helix-junction complex with its RNA substrates and has general RNA branchforming activity
    • _. 2005. A deoxyribozyme that forms a three-helix-junction complex with its RNA substrates and has general RNA branchforming activity. J. Am. Chem. Soc. 127: 2900-2907.
    • (2005) J. Am. Chem. Soc. , vol.127 , pp. 2900-2907
  • 5
    • 1142281951 scopus 로고    scopus 로고
    • Dinucleotide junction cleavage versatility of 8-17 deoxyribozyme
    • Cruz, R.P.G., Withers, J.B., and Li, Y. 2004. Dinucleotide junction cleavage versatility of 8-17 deoxyribozyme. Chem. Biol. 11: 57-67.
    • (2004) Chem. Biol. , vol.11 , pp. 57-67
    • Cruz, R.P.G.1    Withers, J.B.2    Li, Y.3
  • 6
    • 33845278826 scopus 로고
    • Synthesis and spectroscopic analysis of branched RNA fragments: Messenger RNA splicing intermediates
    • Damha, M.J. and Ogilvie, K.K. 1988. Synthesis and spectroscopic analysis of branched RNA fragments: Messenger RNA splicing intermediates. J. Org. Chem. 53: 3710-3722.
    • (1988) J. Org. Chem. , vol.53 , pp. 3710-3722
    • Damha, M.J.1    Ogilvie, K.K.2
  • 7
    • 0024455781 scopus 로고
    • Automated solid-phase synthesis of branched oligonucleotides
    • Damha, M.J. and Zabarylo, S. 1989. Automated solid-phase synthesis of branched oligonucleotides. Tetrahedron Lett. 30: 6295-6298.
    • (1989) Tetrahedron Lett. , vol.30 , pp. 6295-6298
    • Damha, M.J.1    Zabarylo, S.2
  • 8
    • 0027058286 scopus 로고
    • Solid-phase synthesis of branched oligoribonucleotides related to messenger RNA splicing intermediates
    • Damha, M.J., Ganeshan, K., Hudson, R.H., and Zabarylo, S.V. 1992. Solid-phase synthesis of branched oligoribonucleotides related to messenger RNA splicing intermediates. Nucleic Acids Res. 20: 6565-6573.
    • (1992) Nucleic Acids Res. , vol.20 , pp. 6565-6573
    • Damha, M.J.1    Ganeshan, K.2    Hudson, R.H.3    Zabarylo, S.V.4
  • 9
    • 0034655641 scopus 로고    scopus 로고
    • Test of intron predictions reveals novel splice sites, alternatively spliced mRNAs and new introns in meiotically regulated genes of yeast
    • Davis, C.A., Grate, L., Spingola, M., and Ares Jr., M. 2000. Test of intron predictions reveals novel splice sites, alternatively spliced mRNAs and new introns in meiotically regulated genes of yeast. Nucleic Acids Res. 28: 1700-1706.
    • (2000) Nucleic Acids Res. , vol.28 , pp. 1700-1706
    • Davis, C.A.1    Grate, L.2    Spingola, M.3    Ares Jr., M.4
  • 11
    • 0017889065 scopus 로고
    • Enzymatic oligoribonucleotide synthesis with T4 RNA ligase
    • England, T.E. and Uhlenbeck, O.C. 1978. Enzymatic oligoribonucleotide synthesis with T4 RNA ligase. Biochemistry 17: 2069-2076.
    • (1978) Biochemistry , vol.17 , pp. 2069-2076
    • England, T.E.1    Uhlenbeck, O.C.2
  • 12
    • 0036436750 scopus 로고    scopus 로고
    • Group II introns: Highly specific endonucleases with modular structures and diverse catalytic functions
    • Fedorova, O., Su, L.J., and Pyle, A.M. 2002. Group II introns: Highly specific endonucleases with modular structures and diverse catalytic functions. Methods 28: 323-335.
    • (2002) Methods , vol.28 , pp. 323-335
    • Fedorova, O.1    Su, L.J.2    Pyle, A.M.3
  • 13
    • 0029919746 scopus 로고    scopus 로고
    • Use of cis- and transribozymes to remove 5′ and 3′ heterogeneities from milligrams of in vitro transcribed RNA
    • Ferré-D'Amaré, A.R., and Doudna, J.A. 1996. Use of cis- and transribozymes to remove 5′ and 3′ heterogeneities from milligrams of in vitro transcribed RNA. Nucleic Acids Res. 24: 977-978.
    • (1996) Nucleic Acids Res. , vol.24 , pp. 977-978
    • Ferré-D'Amaré, A.R.1    Doudna, J.A.2
  • 16
    • 0036270548 scopus 로고    scopus 로고
    • Searching yeast intron data at Ares lab Web site
    • Grate, L. and Ares Jr., M. 2002. Searching yeast intron data at Ares lab Web site. Methods Enzymol. 350: 380-392.
    • (2002) Methods Enzymol. , vol.350 , pp. 380-392
    • Grate, L.1    Ares Jr., M.2
  • 17
    • 0025817050 scopus 로고
    • A hammerhead ribozyme allows synthesis of a new form of the Tetrahymena ribozyme homogeneous in length with a 3′ end blocked for transesterification
    • Grosshans, C.A. and Cech, T.R. 1991. A hammerhead ribozyme allows synthesis of a new form of the Tetrahymena ribozyme homogeneous in length with a 3′ end blocked for transesterification. Nucleic Acids Res. 19: 3875-3880.
    • (1991) Nucleic Acids Res. , vol.19 , pp. 3875-3880
    • Grosshans, C.A.1    Cech, T.R.2
  • 18
    • 0029827383 scopus 로고    scopus 로고
    • Group II introns: Elaborate ribozymes
    • Jacquier, A. 1996. Group II introns: Elaborate ribozymes. Biochimie 78: 474-487.
    • (1996) Biochimie , vol.78 , pp. 474-487
    • Jacquier, A.1
  • 19
    • 0032827799 scopus 로고    scopus 로고
    • A simple and efficient method to reduce nontemplated nucleotide addition at the 3′ terminus of RNAs transcribed by T7 RNA polymerase
    • Kao, C., Zheng, M., and Rudisser, S. 1999. A simple and efficient method to reduce nontemplated nucleotide addition at the 3′ terminus of RNAs transcribed by T7 RNA polymerase. RNA 5: 1268-1272.
    • (1999) RNA , vol.5 , pp. 1268-1272
    • Kao, C.1    Zheng, M.2    Rudisser, S.3
  • 20
    • 0016214623 scopus 로고
    • T4 RNA ligase: Substrate chain length requirements
    • Kaufmann, G., Klein, T., and Littauer, U.Z. 1974. T4 RNA ligase: Substrate chain length requirements. FEBS Lett. 46: 271-275.
    • (1974) FEBS Lett. , vol.46 , pp. 271-275
    • Kaufmann, G.1    Klein, T.2    Littauer, U.Z.3
  • 21
    • 0029845145 scopus 로고    scopus 로고
    • RNase H cleavage for processing of in vitro transcribed RNA for NMR studies and RNA ligation
    • Lapham, J. and Crothers, D.M. 1996. RNase H cleavage for processing of in vitro transcribed RNA for NMR studies and RNA ligation. RNA 2: 289-296.
    • (1996) RNA , vol.2 , pp. 289-296
    • Lapham, J.1    Crothers, D.M.2
  • 22
    • 0029066770 scopus 로고
    • Structure and activities of group II introns
    • Michel, F. and Ferat, J.L. 1995. Structure and activities of group II introns. Annu. Rev. Biochem. 64: 435-461.
    • (1995) Annu. Rev. Biochem. , vol.64 , pp. 435-461
    • Michel, F.1    Ferat, J.L.2
  • 23
    • 0024819449 scopus 로고
    • Synthesis of small RNAs using T7 RNA polymerase
    • Milligan, J.F. and Uhlenbeck, O.C. 1989. Synthesis of small RNAs using T7 RNA polymerase. Methods Enzymol. 180: 51-62.
    • (1989) Methods Enzymol. , vol.180 , pp. 51-62
    • Milligan, J.F.1    Uhlenbeck, O.C.2
  • 24
    • 0023651444 scopus 로고
    • Oligoribonucleotide synthesis using T7 RNA polymerase and synthetic DNA templates
    • Milligan, J.F., Groebe, D.R., Witherell, G.W., and Uhlenbeck, O.C. 1987. Oligoribonucleotide synthesis using T7 RNA polymerase and synthetic DNA templates. Nucleic Acids Res. 15: 8783-8798.
    • (1987) Nucleic Acids Res. , vol.15 , pp. 8783-8798
    • Milligan, J.F.1    Groebe, D.R.2    Witherell, G.W.3    Uhlenbeck, O.C.4
  • 26
    • 0031779553 scopus 로고    scopus 로고
    • Influence of substrate structure on in vitro ribozyme activity of a group II intron
    • Nolte, A., Chanfreau, G., and Jacquier, A. 1998. Influence of substrate structure on in vitro ribozyme activity of a group II intron. RNA 4: 694-708.
    • (1998) RNA , vol.4 , pp. 694-708
    • Nolte, A.1    Chanfreau, G.2    Jacquier, A.3
  • 29
    • 0026315514 scopus 로고
    • Folding of circularly permuted transfer RNAs
    • Pan, T., Gutell, R.R., and Uhlenbeck, O.C. 1991. Folding of circularly permuted transfer RNAs. Science 254: 1361-1364.
    • (1991) Science , vol.254 , pp. 1361-1364
    • Pan, T.1    Gutell, R.R.2    Uhlenbeck, O.C.3
  • 30
    • 20444469324 scopus 로고    scopus 로고
    • A deoxyribozyme that synthesizes 2′,5′-branched RNA with any branch-site nucleotide
    • Pratico, E.D., Wang, Y., and Silverman, S.K. 2005. A deoxyribozyme that synthesizes 2′,5′-branched RNA with any branch-site nucleotide. Nucleic Acids Res. 33: 3503-3512.
    • (2005) Nucleic Acids Res. , vol.33 , pp. 3503-3512
    • Pratico, E.D.1    Wang, Y.2    Silverman, S.K.3
  • 31
    • 0029859430 scopus 로고    scopus 로고
    • Chemical methods of DNA and RNA fluorescent labeling
    • Proudnikov, D. and Mirzabekov, A. 1996. Chemical methods of DNA and RNA fluorescent labeling. Nucleic Acids Res. 24: 4535-4542.
    • (1996) Nucleic Acids Res. , vol.24 , pp. 4535-4542
    • Proudnikov, D.1    Mirzabekov, A.2
  • 32
    • 0034047698 scopus 로고    scopus 로고
    • Using DNAzymes to cut, process, and map RNA molecules for structural studies or modification
    • Pyle, A.M., Chu, V.T., Jankowsky, E., and Boudvillain, M. 2000. Using DNAzymes to cut, process, and map RNA molecules for structural studies or modification. Methods Enzymol. 317: 140-146.
    • (2000) Methods Enzymol. , vol.317 , pp. 140-146
    • Pyle, A.M.1    Chu, V.T.2    Jankowsky, E.3    Boudvillain, M.4
  • 33
    • 0033168572 scopus 로고    scopus 로고
    • A new approach to the synthesis of branched and branched cyclic oligoribonucleotides
    • Reese, C.B. and Song, Q. 1999. A new approach to the synthesis of branched and branched cyclic oligoribonucleotides. Nucleic Acids Res. 27: 2672-2681.
    • (1999) Nucleic Acids Res. , vol.27 , pp. 2672-2681
    • Reese, C.B.1    Song, Q.2
  • 34
    • 0020164793 scopus 로고
    • The effect of acceptor oligoribonucleotide sequence on the T4 RNA ligase reaction
    • Romaniuk, E., McLaughlin, L.W., Neilson, T., and Romaniuk, P.J. 1982. The effect of acceptor oligoribonucleotide sequence on the T4 RNA ligase reaction. Eur. J. Biochem. 125: 639-643.
    • (1982) Eur. J. Biochem. , vol.125 , pp. 639-643
    • Romaniuk, E.1    McLaughlin, L.W.2    Neilson, T.3    Romaniuk, P.J.4
  • 36
    • 0032539693 scopus 로고    scopus 로고
    • A unified view of polymer, dumbbell, and oligonucleotide DNA nearest-neighbor thermodynamics
    • SantaLucia Jr., J. 1998. A unified view of polymer, dumbbell, and oligonucleotide DNA nearest-neighbor thermodynamics. Proc. Natl. Acad. Sci. 95: 1460-1465.
    • (1998) Proc. Natl. Acad. Sci. , vol.95 , pp. 1460-1465
    • Santalucia Jr., J.1
  • 37
    • 0030898510 scopus 로고    scopus 로고
    • A general purpose RNA-cleaving DNA enzyme
    • Santoro, S.W. and Joyce, G.F. 1997. A general purpose RNA-cleaving DNA enzyme. Proc. Natl. Acad. Sci. 94: 4262-4266.
    • (1997) Proc. Natl. Acad. Sci. , vol.94 , pp. 4262-4266
    • Santoro, S.W.1    Joyce, G.F.2
  • 38
    • 1542365201 scopus 로고    scopus 로고
    • A universal method to produce in vitro transcripts with homogeneous 3′-ends
    • Schürer, H., Lang, K., Schuster, J., and Mörl, M. 2002. A universal method to produce in vitro transcripts with homogeneous 3′-ends. Nucleic Acids Res. 30: e56.
    • (2002) Nucleic Acids Res. , vol.30
    • Schürer, H.1    Lang, K.2    Schuster, J.3    Mörl, M.4
  • 39
    • 0015408606 scopus 로고
    • Purification and properties of bacteriophage T4-induced RNA ligase
    • Silber, R., Malathi, V.G., and Hurwitz, J. 1972. Purification and properties of bacteriophage T4-induced RNA ligase. Proc. Natl. Acad. Sci. 69: 3009-3013.
    • (1972) Proc. Natl. Acad. Sci. , vol.69 , pp. 3009-3013
    • Silber, R.1    Malathi, V.G.2    Hurwitz, J.3
  • 40
    • 1642569624 scopus 로고    scopus 로고
    • Practical and general synthesis of 5′-adenylated RNA (5′-AppRNA)
    • Silverman, S.K. 2004. Practical and general synthesis of 5′-adenylated RNA (5′-AppRNA). RNA 10: 731-746.
    • (2004) RNA , vol.10 , pp. 731-746
    • Silverman, S.K.1
  • 41
    • 0038210243 scopus 로고    scopus 로고
    • Deoxyribozymes that synthesize branched and lariat RNA
    • Wang, Y. and Silverman, S.K. 2003a. Deoxyribozymes that synthesize branched and lariat RNA. J. Am. Chem. Soc. 125: 6880-6881.
    • (2003) J. Am. Chem. Soc. , vol.125 , pp. 6880-6881
    • Wang, Y.1    Silverman, S.K.2
  • 42
    • 0347594188 scopus 로고    scopus 로고
    • Characterization of deoxyribozymes that synthesize branched RNA
    • _. 2003b. Characterization of deoxyribozymes that synthesize branched RNA. Biochemistry 42: 15252-15263.
    • (2003) Biochemistry , vol.42 , pp. 15252-15263
  • 43
    • 24944445132 scopus 로고    scopus 로고
    • Efficient one-step synthesis of biologically related lariat RNAs by a deoxyribozyme
    • _. 2005a. Efficient one-step synthesis of biologically related lariat RNAs by a deoxyribozyme. Angew. Chem. Int. Ed. 44: 5863-5866.
    • (2005) Angew. Chem. Int. Ed. , vol.44 , pp. 5863-5866
  • 44
    • 14344263295 scopus 로고    scopus 로고
    • Directing the outcome of deoxyribozyme selections to favor native 3′-5′ RNA ligation
    • _. 2005b. Directing the outcome of deoxyribozyme selections to favor native 3′-5′ RNA ligation. Biochemistry 44: 3017-3023.
    • (2005) Biochemistry , vol.44 , pp. 3017-3023
  • 45
    • 0347298816 scopus 로고    scopus 로고
    • Purification of histidine-tagged T4 RNA ligase from E. coli
    • Wang, Q.S. and Unrau, P.J. 2002. Purification of histidine-tagged T4 RNA ligase from E. coli. BioTechniques 33: 1256-1260.
    • (2002) BioTechniques , vol.33 , pp. 1256-1260
    • Wang, Q.S.1    Unrau, P.J.2
  • 46
    • 0042121256 scopus 로고    scopus 로고
    • Mfold web server for nucleic acid folding and hybridization prediction
    • Zuker, M. 2003. Mfold web server for nucleic acid folding and hybridization prediction. Nucleic Acids Res. 31: 3406-3415.
    • (2003) Nucleic Acids Res. , vol.31 , pp. 3406-3415
    • Zuker, M.1


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.