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2
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0030864852
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Group II intron from Pseudomonas alcaligenes NCIB 9867 (P25X): Entrapment in plasmid RP4 and sequence analysis
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Yeo CC, Tham JM, Yap MW-C, Poh CL. Group II intron from Pseudomonas alcaligenes NCIB 9867 (P25X): entrapment in plasmid RP4 and sequence analysis. Microbiology. 143:1997;2833-2840.
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0030808127
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Knoop V, Altwasser M, Brennicke A. A tripartite group II intron in mitochondria of an angiosperm plant. Mol Gen Genet. 255:1997;269-276.
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The mitochondrial LSU rDNA of the brown alga Phylaiella littoralis reveals α-proteobacterial features and is split by four group IIB introns with an atypical phylogeny
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Fontaine JM, Rousvoal S, Leblanc S, Kloareg S, Goer SL. The mitochondrial LSU rDNA of the brown alga Phylaiella littoralis reveals α-proteobacterial features and is split by four group IIB introns with an atypical phylogeny. J Mol Biol. 251:1995;378-389.
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Fontaine, J.M.1
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5
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0030832614
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Group II intron endonucleases use both RNA and protein subunits for recognition of specific sequences in double-stranded DNA
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of special interest. See annotation to [10].
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Guo H, Zimmerly S, Penman PS, Lambowitz AM. Group II intron endonucleases use both RNA and protein subunits for recognition of specific sequences in double-stranded DNA. of special interest EMBO J. 16:1997;6835-6848 See annotation to [10].
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Guo, H.1
Zimmerly, S.2
Penman, P.S.3
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6
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0031106356
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of special interest. See annotation to [7].
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Jenkins BD, Kulhanek DJ, Barkan A. Nuclear mutations that block group II RNA splicing in maize chloroplasts reveal several intron classes with distinct requirements for splicing factors. of special interest Plant Cell. 9:1997;283-296 See annotation to [7].
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Jenkins, B.D.1
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Barkan, A.3
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7
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17044461720
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Splicing and intron-internal RNA editing of trnK-matK transcripts in barley plastids: Support for matK as an essential splicing factor
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of special interest. This paper and [6] describe genetic approaches for uncovering splicing factors that are required for group II intron functions in vivo.
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Vogel J, Hubschmann T, Bornerand T, Hess WR. Splicing and intron-internal RNA editing of trnK-matK transcripts in barley plastids: support for matK as an essential splicing factor. of special interest J Mol Biol. 270:1997;179-187 This paper and [6] describe genetic approaches for uncovering splicing factors that are required for group II intron functions in vivo.
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Vogel, J.1
Hubschmann, T.2
Bornerand, T.3
Hess, W.R.4
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8
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The reverse-transcriptase-like proteins encoded by group II introns in the mitochondrial genome of the brown alga Phylaiella littoralis belong to two different lineages which apparently coevolved with the group II ribosyme lineages
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Fontaine JM, Goux D, Kloareg B, Goer SL. The reverse-transcriptase-like proteins encoded by group II introns in the mitochondrial genome of the brown alga Phylaiella littoralis belong to two different lineages which apparently coevolved with the group II ribosyme lineages. J Mol Evol. 44:1997;33-42.
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Fontaine, J.M.1
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Goer, S.L.4
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9
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0027430128
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A multitude of suppressors of group II intron-splicing defects in yeast
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Walcherr M, Ragnin A, Jank B, Teply R, Wiesenberger G, Schweyen RJ. A multitude of suppressors of group II intron-splicing defects in yeast. Curr Genet. 24:1993;301-306.
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Walcherr, M.1
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Teply, R.4
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10
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Efficient integration of an intron RNA into double-stranded DNA by reverse-splicing
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of special interest. This paper, together with [5] and [28], describes studies of homing, or mobility, by ribonucleoprotein (RNP) complexes composed of group II introns and their incoded proteins. These RNP complexes provide a unique system for studying RNA - protein interactions, as both RNA and protein subunits are involved in recognition of specific homing sites and catalyzing intron integration.
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Yang J, Zimmerly S, Perlman PS, Lambowitz AM. Efficient integration of an intron RNA into double-stranded DNA by reverse-splicing. of special interest Nature. 381:1996;332-335 This paper, together with [5] and [28], describes studies of homing, or mobility, by ribonucleoprotein (RNP) complexes composed of group II introns and their incoded proteins. These RNP complexes provide a unique system for studying RNA - protein interactions, as both RNA and protein subunits are involved in recognition of specific homing sites and catalyzing intron integration.
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Nature
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Yang, J.1
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11
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Identification of splicing signals in introns of yeast mitochondrial split genes: Mutational alterations in intron bl1 and secondary structures in related introns
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Schmelzer C, Schmidt C, Schweyen RJ. Identification of splicing signals in introns of yeast mitochondrial split genes: mutational alterations in intron bl1 and secondary structures in related introns. Nucleic Acids Res. 10:1982;6797-6808.
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Schmidt, C.2
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Michel F, Jacquier A, Dujon B. Comparison of fungal mitochondrial introns reveals extensive homologies in RNA secondary structure. Biochimie. 64:1982;867-881.
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0025165413
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Structural analysis of a group II intron by chemical modifications and minimal energy calculations
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Kwakman JH, Konings DA, Hogeweg P, Pel HJ, Grivell LA. Structural analysis of a group II intron by chemical modifications and minimal energy calculations. J Biomol Struct Dynamics. 8:1990;413-430.
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14
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0028569768
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Chanfreau G, Jacquier A. Catalytic site components common to both splicing steps of a group II intron. Science. 266:1994;1383-1387.
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15
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Comparative and functional anatomy of group II catalytic introns-a review
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Michel F, Umesono K, Ozeki H. Comparative and functional anatomy of group II catalytic introns-a review. Gene. 82:1989;5-30.
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Cech TR. Conserved sequences and structure of group I introns: building an active site for RNA catalysis- a review. Gene. 73:1988;259-271.
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Cech, T.R.1
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Stereochemical selectivity of group II intron splicing, reverse-splicing and hydrolysis reactions
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Podar M, Perlman PS, Padgett RA. Stereochemical selectivity of group II intron splicing, reverse-splicing and hydrolysis reactions. Mol Cell Biol. 15:1995;4466-4478.
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Podar, M.1
Perlman, P.S.2
Padgett, R.A.3
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18
-
-
0030015953
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An RNA conformational change between the two chemical steps of group II self-splicing
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of special interest. Modification interference approaches were used to identify important sites in the first and second step of group II intron splicing. The interaction between D2 and D6 (η-η′) is proposed to play a role in conformational change between the two steps.
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Chanfreau G, Jacquier A. An RNA conformational change between the two chemical steps of group II self-splicing. of special interest EMBO J. 15:1996;3466-3476 Modification interference approaches were used to identify important sites in the first and second step of group II intron splicing. The interaction between D2 and D6 (η-η′) is proposed to play a role in conformational change between the two steps.
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EMBO J
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Chanfreau, G.1
Jacquier, A.2
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19
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0027173193
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An independently folding domain of RNA tertiary structure withithe Tetrahymena ribozyme
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Murphy FL, Cech TR. An independently folding domain of RNA tertiary structure withithe Tetrahymena ribozyme. Biochemistry. 32:1993;5291-5300.
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Biochemistry
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Murphy, F.L.1
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0024022167
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Group II intron domain 5 facilitates a trans-splicing reaction
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Jarrell KA, Dietrich RC, Perlman PS. Group II intron domain 5 facilitates a trans-splicing reaction. Mol Cell Biol. 8:1988;2361-2366.
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Jarrell, K.A.1
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21
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Kinetic analysis of the 5-'splice junction hydrolysis of a group II intron promoted by domain 5
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Franzen JS, Zhang M, Peebles CL. Kinetic analysis of the 5-'splice junction hydrolysis of a group II intron promoted by domain 5. Nucleic Acids Res. 21:1993;627-634.
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22
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Pyle AM, Green JB. Building a kinetic framework for group II intron ribozyme activity: quantitation of interdomain binding and reaction rate. Biochemistry. 33:1994;2716-2725.
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Green, J.B.2
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23
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Conversion of a group II intron into a new multiple-turnover ribozyme that selectively cleaves oligonucleotides: Elucidation of reaction mechanism and structure/function relationships
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Michels WJ, Pyle AM. Conversion of a group II intron into a new multiple-turnover ribozyme that selectively cleaves oligonucleotides: elucidation of reaction mechanism and structure/function relationships. Biochemistry. 34:1995;2965-2977.
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Michels, W.J.1
Pyle, A.M.2
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24
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0029382528
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2+-dependent cross-link traps an active form of domain 3 of a self-splicing group II intron
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2+-dependent cross-link traps an active form of domain 3 of a self-splicing group II intron. RNA. 1:1995;828-840.
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Podar, M.1
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25
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0027263683
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Domain 5 interacts with domain 6 and influences the second transesterification reaction of group II intron self-splicing
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Dib-Hajj SD, Boulanger SC, Hebbar SK, Peebles CL, Franzen JS, Perlman PS. Domain 5 interacts with domain 6 and influences the second transesterification reaction of group II intron self-splicing. Nucleic Acids Res. 21:1993;1797-1804.
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Dib-Hajj, S.D.1
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Peebles, C.L.4
Franzen, J.S.5
Perlman, P.S.6
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Branch-point attack in group II introns is a highly reversible transesterification, providing a possible proof-reading mechanism for 5′-splice site selection
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Chin K, Pyle AM. Branch-point attack in group II introns is a highly reversible transesterification, providing a possible proof-reading mechanism for 5′-splice site selection. RNA. 1:1995;391-406.
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Chin, K.1
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27
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F. Eckstein, Lilley D.M.J. New York: Springer Verlag
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Pyle AM. Catalytic reaction mechanisms and structural features of group II intron ribozymes. Eckstein F, Lilley DMJ. Nucleic Acids and Molecular Biology. 1996;75-107 Springer Verlag, New York.
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Pyle, A.M.1
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28
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0030894573
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Mobility of yeast mitochondrial group II introns: Engineering a new site specificity and retrohoming via full reverse splicing
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of special interest. See annotation to [10].
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Eskes R, Yang J, Lambowitz AM, Perlman PS. Mobility of yeast mitochondrial group II introns: engineering a new site specificity and retrohoming via full reverse splicing. of special interest Cell. 88:1997;865-874 See annotation to [10].
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Cell
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Eskes, R.1
Yang, J.2
Lambowitz, A.M.3
Perlman, P.S.4
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29
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0026695012
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Group II introns deleted for multiple substructures retain self-splicing activity
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Koch JL, Boulanger SC, Dib-Hajj SD, Hebbar SD, Perlman SD. Group II introns deleted for multiple substructures retain self-splicing activity. Mol Cell Biol. 12:1992;1950-1958.
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Perlman, S.D.5
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Harris-Kerr CL, Zhang M, Peebles CL. The phylogenetically predicted base-pairing interaction between α and α′ is required for group II splicing in vitro. Proc Natl Acad Sci USA. 90:1993;10658-10662.
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Michel F, Ferat J-L. Structure and activities of group II introns. Annu Rev Biochem. 64:1995;435-461.
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Jacquier A, Michel F. Base-pairing interactions involving the 5′ and 3′ terminal nucleotides of group II self-splicing introns. J Mol Biol. 213:1990;437-447.
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Jacquier A, Michel F. Multiple exon-binding sites in class II self-splicing introns. Cell. 50:1987;17-29.
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Cell
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Jacquier, A.1
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34
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0030936233
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Stopped-flow fluorescence spectroscopy reveals that domain 1 of a group II intron is an independent folding unit
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of outstanding interest. Stopped-flow fluorescence spectroscopy was applied for studying the folding of group II intron ribozymes. D1 was shown to be an independent folding unit, and it is proposed that D1 might serve as a folding core.
-
Qin PZ, Pyle AM. Stopped-flow fluorescence spectroscopy reveals that domain 1 of a group II intron is an independent folding unit. of outstanding interest Biochemistry. 36:1997;4718-4730 Stopped-flow fluorescence spectroscopy was applied for studying the folding of group II intron ribozymes. D1 was shown to be an independent folding unit, and it is proposed that D1 might serve as a folding core.
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Biochemistry
, vol.36
, pp. 4718-4730
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Qin, P.Z.1
Pyle, A.M.2
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35
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0032539968
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The sequence-specificity of a group II intron ribozyme: Multiple mechanisms for promoting unusually high discrimination against mismatched targets
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of outstanding interest. This paper describes how a group II intron ribozyme discriminates matched from mismatched substrate in both the ground state and the transition state to achieve high sequence specificity.
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Xiang Q, Qin PZ, Michels WJ, Freeland K, Pyle AM. The sequence-specificity of a group II intron ribozyme: multiple mechanisms for promoting unusually high discrimination against mismatched targets. of outstanding interest Biochemistry. 37:1998;3839-3849 This paper describes how a group II intron ribozyme discriminates matched from mismatched substrate in both the ground state and the transition state to achieve high sequence specificity.
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Biochemistry
, vol.37
, pp. 3839-3849
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Xiang, Q.1
Qin, P.Z.2
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Freeland, K.4
Pyle, A.M.5
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36
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0031003161
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Trans-activation of group II intron splicing by nuclear U5 snRNA
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of special interest. This paper provides evidence that the EBS1 element can function in trans, underlying the modular nature of group II introns.
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Hetzer M, Wurzer G, Schweyen RJ, Mueller MW. Trans-activation of group II intron splicing by nuclear U5 snRNA. of special interest Nature. 386:1997;417-420 This paper provides evidence that the EBS1 element can function in trans, underlying the modular nature of group II introns.
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Nature
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Hetzer, M.1
Wurzer, G.2
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Suchy M, Schmelzer C. Restoration of the self-splicing activity of a defective group II intron by a small trans-acting RNA. J Mol Biol. 222:1991;179-187.
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Suchy, M.1
Schmelzer, C.2
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0031552355
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Multiple tertiary interactions involving domain II of group II self-splicing introns
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of outstanding interest. Two tertiary interactions. η-η′ and 0-θ′, are proposed, both of which fall within the tetraloop - receptor motif. It is interesting to note that in the case of η-η′, the position of the tetraloop and its receptor could interchange in different introns.
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Costa M, Deme E, Jacquier A, Michel F. Multiple tertiary interactions involving domain II of group II self-splicing introns. of outstanding interest J Mol Biol. 267:1997;520-536 Two tertiary interactions. η-η′ and 0-θ′, are proposed, both of which fall within the tetraloop - receptor motif. It is interesting to note that in the case of η-η′, the position of the tetraloop and its receptor could interchange in different introns.
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J Mol Biol
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Costa, M.1
Deme, E.2
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Michel, F.4
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Griffin EA, Qin Z-F, Michels WA, Pyle AM. Group II intron ribozymes that cleave DNA and RNA linkages with similar efficiency, and lack contacts with substrate 2'-hydroxyl groups. Chem Biol. 2:1995;761-770.
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Griffin, E.A.1
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40
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0343742528
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Identification of structural elements critical for inter-domain interactions in a group II self-splicing intron
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of outstanding interest. The authors used modification interference to identify residues that are important for the interaction of domain 5 with domain 1 and domain 3.
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Jestin J-L, Deme E, Jacquier A. Identification of structural elements critical for inter-domain interactions in a group II self-splicing intron. of outstanding interest EMBO J. 16:1997;2945-2954 The authors used modification interference to identify residues that are important for the interaction of domain 5 with domain 1 and domain 3.
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EMBO J
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Jacquier, A.3
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Mohr G, Perlman PS, Lambowitz AM. Evolutionary relationships among group II intron-encoded proteins and identification of a conserved domain that may be related to maturase function. Nucleic Acids Res. 21:1993;4991-4997.
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Abromovitz DL, Friedman RA, Pyle AM. Catalytic role of 2'-hydroxyl groups within a group II intron active site. Science. 271:1996;1410-1413.
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43
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Ribozyme catalysis from the major groove of group II intron domain 5
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of outstanding interest. Single-atom changes were made to the most conserved nucleotide in D5, thus elucidating its function in binding and catalysis.
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Konforti BB, Abramovitz DL, Duarte CM, Karpeisky A, Beigelman L, Pyle AM. Ribozyme catalysis from the major groove of group II intron domain 5. of outstanding interest Mol Cell. 1:1998;433-441 Single-atom changes were made to the most conserved nucleotide in D5, thus elucidating its function in binding and catalysis.
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Konforti, B.B.1
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Boulanger SC, Belcher SM, Schmidt U, Dib-Hajj SD, Schmidt T, Perlman PS. Studies of point mutants define three essential paired nucleotides in the domain 5 substructure of a group II intron. Mol Cell Biol. 15:1995;4479-4488.
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Peebles CL, Zhang M, Perlman PS, Franzen JF. Identification of a catalytically critical trinucleotide in domain 5 of a group II intron. Proc Natl Acad Sci USA. 92:1995;4422-4426.
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Podar M, Chu VT, Pyle AM, Perlman PS. Group II intron splicing in vivo by first step hydrolysis. of special interest Nature. 391:1998;915-918 Hydrolysis was found to be a viable pathway for group II intron splicing in vivo, underscoring the versatile nature of the group II intron active site.
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50
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Branch-site selection in a group II intron mediated by active recognition of the adenine amino group and steric exclusion of non-adenine functionalities
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of outstanding interest. Mutations and single-atom changes of the branch point adenosine were used to reveal the mechanism of branch-site recognition.
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Liu Q, Green JB, Khodadadi A, Haeberli P, Beigelman L, Pyle AM. Branch-site selection in a group II intron mediated by active recognition of the adenine amino group and steric exclusion of non-adenine functionalities. of outstanding interest J Mol Biol. 267:1997;163-171 Mutations and single-atom changes of the branch point adenosine were used to reveal the mechanism of branch-site recognition.
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Doudna, J.A.8
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55
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Remarkable morphological variability of a common RNA folding motif: The GNRA tetraloop-receptor interaction
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of outstanding interest. The GNRA tetraloop - receptor interaction was found to tolerate many structural perturbations, including expanded loops.
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56
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0031939815
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Domain 5 binds near a highly-conserved dinucleotide in the joiner linking domains 2 and 3 of a group II intron
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of outstanding interest. The first piece of evidence that D5 is located near the site of chemical reaction (the 3′-splice site).
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Podar M, Zhou J, Zhang M, Franzen JS, Perlman PS, Peebles CL. Domain 5 binds near a highly-conserved dinucleotide in the joiner linking domains 2 and 3 of a group II intron. of outstanding interest RNA. 4:1998;151-166 The first piece of evidence that D5 is located near the site of chemical reaction (the 3′-splice site).
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57
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0031555476
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A group II self-splicing intron from the brown alga Phylaiella littoralis is active at unusually low magnesium concentrations and forms populations of molecules with a uniform conformation
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of outstanding interest. An active group II intron with higher stability, which might be a better candidate for structural analysis.
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Costa M, Fontaine JM, Goer SL, Michel F. A group II self-splicing intron from the brown alga Phylaiella littoralis is active at unusually low magnesium concentrations and forms populations of molecules with a uniform conformation. of outstanding interest J Mol Biol. 274:1997;353-364 An active group II intron with higher stability, which might be a better candidate for structural analysis.
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