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0003604405
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R.F. Gesteland, Atkins J.F. Cold Spring Harbor, NY: Cold Spring Harbor Laboratory Press
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Gesteland RF, Atkins JF. The RNA World. 1993;Cold Spring Harbor Laboratory Press, Cold Spring Harbor, NY.
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The RNA World
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2
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0029820625
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Crystal structure of a group I ribozyme domain: Principles of RNA packing
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This paper represents a landmark advance in our understanding of RNA structure and reports the crystal structure of an 160-nucleotide, roughly U-shaped RNA domain. The structure richly illustrates tertiary packing in large RNAs. of outstanding interest
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Cate JH, Gooding AR, Podell E, Zhou K, Golden BL, Kundrot CE, Cech TR, Doudna JA. Crystal structure of a group I ribozyme domain: principles of RNA packing. Science. 273:1996;1678-1685 This paper represents a landmark advance in our understanding of RNA structure and reports the crystal structure of an 160-nucleotide, roughly U-shaped RNA domain. The structure richly illustrates tertiary packing in large RNAs. of outstanding interest.
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Science
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Cate, J.H.1
Gooding, A.R.2
Podell, E.3
Zhou, K.4
Golden, B.L.5
Kundrot, C.E.6
Cech, T.R.7
Doudna, J.A.8
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4
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0002664413
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RNA tectonics: Towards RNA design
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This review, together with complementary reviews [5,6], lays out the arguments for a hierarchy of RNA folding, in which much of the RNA secondary structure forms before tertiary folding. of outstanding interest
-
Westhof E, Masquida B, Jaeger L. RNA tectonics: towards RNA design. Fold Des. 1:1996;78-88 This review, together with complementary reviews [5,6], lays out the arguments for a hierarchy of RNA folding, in which much of the RNA secondary structure forms before tertiary folding. of outstanding interest.
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(1996)
Fold des
, vol.1
, pp. 78-88
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Westhof, E.1
Masquida, B.2
Jaeger, L.3
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5
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0029149905
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RNA folding
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See annotation [4]. of special interest
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Pyle AM, Green JB. RNA folding. Curr Opin Struct Biol. 5:1995;303-310 See annotation [4]. of special interest.
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(1995)
Curr Opin Struct Biol
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Pyle, A.M.1
Green, J.B.2
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6
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0029877099
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Parallel worlds
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See annotation [4]. of special interest
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Draper DE. Parallel worlds. Nat Struct Biol. 3:1996;397-400 See annotation [4]. of special interest.
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(1996)
Nat Struct Biol
, vol.3
, pp. 397-400
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Draper, D.E.1
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7
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0029258928
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Keeping RNA happy
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This is a lively, historical review of RNA misfolding. of special interest
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Uhlenbeck OC. Keeping RNA happy. RNA. 1:1995;4-6 This is a lively, historical review of RNA misfolding. of special interest.
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(1995)
RNA
, vol.1
, pp. 4-6
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Uhlenbeck, O.C.1
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8
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0029163563
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RNA chaperones and the RNA folding problem
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An authoritative review of RNA chaperone activities. of special interest
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Herschlag D. RNA chaperones and the RNA folding problem. J Biol Chem. 270:1995;20871-20874 An authoritative review of RNA chaperone activities. of special interest.
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(1995)
J Biol Chem
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Herschlag, D.1
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9
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0029050588
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Efficient protein-facilitated splicing of the yeast mitochondrial b15 intron
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Weeks KM, Cech TR. Efficient protein-facilitated splicing of the yeast mitochondrial b15 intron. Biochemistry. 34:1995;7728-7738.
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(1995)
Biochemistry
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Weeks, K.M.1
Cech, T.R.2
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10
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0028276865
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Escherichia coli proteins, including ribosomal protein S12, facilitate in vitro splicing of phage T4 introns by acting as RNA chaperones
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Coetzee T, Herschlag D, Belfort M. Escherichia coli proteins, including ribosomal protein S12, facilitate in vitro splicing of phage T4 introns by acting as RNA chaperones. Genes Dev. 8:1994;1575-1588.
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Genes Dev
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Coetzee, T.1
Herschlag, D.2
Belfort, M.3
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11
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0028904152
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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 Jr, 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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Biochemistry
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, pp. 2965-2977
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Michels W.J., Jr.1
Pyle, A.M.2
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12
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0026580844
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Evidence for processivity and two-step binding of the RNA substrate from studies of J1/2 mutants of the Tetrahymena ribozyme
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Herschlag D. Evidence for processivity and two-step binding of the RNA substrate from studies of J1/2 mutants of the Tetrahymena ribozyme. Biochemistry. 31:1992;1386-1399.
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Biochemistry
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Herschlag, D.1
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13
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0029904022
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Kinetic pathway for folding of the Tetrahymena ribozyme revealed by three UV-inducible crosslinks
-
The thermodynamics and kinetics of RNA folding are monitored by UV cross-linking. The authors identify a non-native structure that accumulates at intermediate times and a rate-limiting conformational change that has a half life of two minutes. of outstanding interest
-
Downs WD, Cech TR. Kinetic pathway for folding of the Tetrahymena ribozyme revealed by three UV-inducible crosslinks. RNA. 2:1996;718-732 The thermodynamics and kinetics of RNA folding are monitored by UV cross-linking. The authors identify a non-native structure that accumulates at intermediate times and a rate-limiting conformational change that has a half life of two minutes. of outstanding interest.
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(1996)
RNA
, vol.2
, pp. 718-732
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Downs, W.D.1
Cech, T.R.2
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14
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0029155840
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Protein facilitation of group I intron splicing by assembly of the catalytic core and the 5′ splice site domain
-
Protein binding specifically stabilizes two distinct RNA folding transitions in a group I intron. The CBP2 binds to one face of the RNA and sandwiches the 5′ splice site between itself and the rest of the catalytic core. of outstanding interest
-
Weeks KM, Cech TR. Protein facilitation of group I intron splicing by assembly of the catalytic core and the 5′ splice site domain. Cell. 82:1995;221-230 Protein binding specifically stabilizes two distinct RNA folding transitions in a group I intron. The CBP2 binds to one face of the RNA and sandwiches the 5′ splice site between itself and the rest of the catalytic core. of outstanding interest.
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(1995)
Cell
, vol.82
, pp. 221-230
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Weeks, K.M.1
Cech, T.R.2
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15
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0027930184
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A kinetic mechanism for cleavage of precursor tRNA(Asp) catalyzed by the RNA component of Bacillus subtilis ribonuclease P
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Beebe JA, Fierke CA. A kinetic mechanism for cleavage of precursor tRNA(Asp) catalyzed by the RNA component of Bacillus subtilis ribonuclease P. Biochemistry. 33:1994;10294-10304.
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Biochemistry
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Beebe, J.A.1
Fierke, C.A.2
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16
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0029384106
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Escherichia coli protein StpA stimulates self-splicing by promoting RNA assembly in vitro
-
The StpA protein facilitates RNA strand exchange and promotes group I intron splicing. The authors also provide a clear comparison of protein facilitation by StpA with CYT-18, a splicing cofactor. of outstanding interest
-
Zhang A, Derbyshire V, Salvo JL, Belfort M. Escherichia coli protein StpA stimulates self-splicing by promoting RNA assembly in vitro. RNA. 1:1995;783-793 The StpA protein facilitates RNA strand exchange and promotes group I intron splicing. The authors also provide a clear comparison of protein facilitation by StpA with CYT-18, a splicing cofactor. of outstanding interest.
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(1995)
RNA
, vol.1
, pp. 783-793
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Zhang, A.1
Derbyshire, V.2
Salvo, J.L.3
Belfort, M.4
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17
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0026639175
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The neurospora CYT-18 protein suppresses defects in the phage T4 td intron by stabilizing the catalytically active structure of the intron core
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Mohr G, Zhang A, Gianelos JA, Belfort M, Lambowitz AM. The neurospora CYT-18 protein suppresses defects in the phage T4 td intron by stabilizing the catalytically active structure of the intron core. Cell. 69:1992;483-494.
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Cell
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Mohr, G.1
Zhang, A.2
Gianelos, J.A.3
Belfort, M.4
Lambowitz, A.M.5
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18
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0030595381
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A tyrosyl-tRNA synthetase suppresses structural defects in the two major helical domains of the group I intron catalytic core
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Myers CA, Wallweber GJ, Rennard R, Kemel Y, Caprara MG, Mohr G, Lambowitz AM. A tyrosyl-tRNA synthetase suppresses structural defects in the two major helical domains of the group I intron catalytic core. J Mol Biol. 262:1996;87-104.
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J Mol Biol
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Myers, C.A.1
Wallweber, G.J.2
Rennard, R.3
Kemel, Y.4
Caprara, M.G.5
Mohr, G.6
Lambowitz, A.M.7
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19
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0028000994
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Coaxial stacking of helixes enhances binding of oligoribonucleotides and improves predictions of RNA folding
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Walter AE, Turner DH, Kim J, Lyttle MH, Muller P, Mathews DH, Zuker M. Coaxial stacking of helixes enhances binding of oligoribonucleotides and improves predictions of RNA folding. Proc Natl Acad Sci USA. 91:1994;9218-9222.
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Proc Natl Acad Sci USA
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Walter, A.E.1
Turner, D.H.2
Kim, J.3
Lyttle, M.H.4
Muller, P.5
Mathews, D.H.6
Zuker, M.7
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20
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0002617993
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A simple model of chaperonin-mediated protein folding
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Chan HS, Dill KA. A simple model of chaperonin-mediated protein folding. Proteins. 24:1996;345-351.
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Proteins
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, pp. 345-351
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Chan, H.S.1
Dill, K.A.2
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21
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0030006212
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Chaperonin-facilitated protein folding: Optimization of rate and yield by an interative annealing mechanism
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Todd MJ, Lorimer GH, Thirumalai D. Chaperonin-facilitated protein folding: optimization of rate and yield by an interative annealing mechanism. Proc Natl Acad Sci USA. 93:1996;4030-4035.
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Proc Natl Acad Sci USA
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, pp. 4030-4035
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Todd, M.J.1
Lorimer, G.H.2
Thirumalai, D.3
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22
-
-
0028858599
-
Solution structure of a bovine immunodeficiency virus Tat-TAR peptide - RNA complex
-
A 14-residue, arginine-rich peptide adopts a β-hairpin conformation and interacts in the RNA major groove. of special interest
-
Puglisi JD, Chen L, Blanchard S, Frankel AD. Solution structure of a bovine immunodeficiency virus Tat-TAR peptide - RNA complex. Science. 270:1995;1200-1203 A 14-residue, arginine-rich peptide adopts a β-hairpin conformation and interacts in the RNA major groove. of special interest.
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(1995)
Science
, vol.270
, pp. 1200-1203
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Puglisi, J.D.1
Chen, L.2
Blanchard, S.3
Frankel, A.D.4
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23
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0029613238
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Molecular recognition in the bovine immunodeficiency virus Tat peptide - TAR RNA complex
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See annotation [22]. of special interest
-
Ye X, Kumar RA, Patel DJ. Molecular recognition in the bovine immunodeficiency virus Tat peptide - TAR RNA complex. Chem Biol. 2:1995;827-840 See annotation [22]. of special interest.
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(1995)
Chem Biol
, vol.2
, pp. 827-840
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-
Ye, X.1
Kumar, R.A.2
Patel, D.J.3
-
24
-
-
0029784592
-
α helix - RNA major groove recognition in an HIV-1 Rev peptide - RRE RNA complex
-
The Rev peptide is embedded in the RNA major groove. Two purine - purine base pairs are essential for specific interaction: one widens the major groove; and the other forms a specific interaction with a aspariginyl sidechain. of special interest
-
Battiste JL, Mao H, Rao NS, Tan R, Muhandiram DR, Kay LE, Frankel AD, Williamson JR. α helix - RNA major groove recognition in an HIV-1 Rev peptide - RRE RNA complex. Science. 273:1996;1547-1551 The Rev peptide is embedded in the RNA major groove. Two purine - purine base pairs are essential for specific interaction: one widens the major groove; and the other forms a specific interaction with a aspariginyl sidechain. of special interest.
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(1996)
Science
, vol.273
, pp. 1547-1551
-
-
Battiste, J.L.1
Mao, H.2
Rao, N.S.3
Tan, R.4
Muhandiram, D.R.5
Kay, L.E.6
Frankel, A.D.7
Williamson, J.R.8
-
25
-
-
0030475417
-
Deep penetration of an α-helix into a widened RNA major groove in the HIV-1 rev peptide - RNA aptamer complex
-
Compare with [24]. In this case, a Rev peptide is bound to a high affinity RNA aptamer; overall, the structures for the natural and selected substrates are similar with the exception that the aptamer forms a distinctive U·AU base triple. of special interest
-
Ye X, Gorin A, Ellington AD, Patel DJ. Deep penetration of an α-helix into a widened RNA major groove in the HIV-1 rev peptide - RNA aptamer complex. Nat Struct Biol. 3:1996;1026-1033 Compare with [24]. In this case, a Rev peptide is bound to a high affinity RNA aptamer; overall, the structures for the natural and selected substrates are similar with the exception that the aptamer forms a distinctive U·AU base triple. of special interest.
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(1996)
Nat Struct Biol
, vol.3
, pp. 1026-1033
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-
Ye, X.1
Gorin, A.2
Ellington, A.D.3
Patel, D.J.4
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26
-
-
0029920331
-
Specificity of ribonucleoprotein interaction determined by RNA folding during complex formulation
-
Protein binding induces large conformational changes in an asymmetric internal loop and dramatically changes the overall trajectory of the RNA. of outstanding interest
-
Allain FH, Gubser CC, Howe PW, Nagai K, Neuhaus D, Varani G. Specificity of ribonucleoprotein interaction determined by RNA folding during complex formulation. Nature. 380:1996;646-650 Protein binding induces large conformational changes in an asymmetric internal loop and dramatically changes the overall trajectory of the RNA. of outstanding interest.
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(1996)
Nature
, vol.380
, pp. 646-650
-
-
Allain, F.H.1
Gubser, C.C.2
Howe, P.W.3
Nagai, K.4
Neuhaus, D.5
Varani, G.6
-
27
-
-
0029001288
-
Bent helix formation between RNA hairpins with complementary loops
-
A complex formed between RNA hairpins, which have seven nucleotide complementary loops, is bent. The authors establish the bent structure using a nice combination of NMR and comparative electrophoretic methods. Protein binding increases RNA bending. of outstanding interest
-
Marino JP, Gregorian RS Jr, Csankovszki G, Crothers DM. Bent helix formation between RNA hairpins with complementary loops. Science. 268:1995;1448-1454 A complex formed between RNA hairpins, which have seven nucleotide complementary loops, is bent. The authors establish the bent structure using a nice combination of NMR and comparative electrophoretic methods. Protein binding increases RNA bending. of outstanding interest.
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(1995)
Science
, vol.268
, pp. 1448-1454
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Marino, J.P.1
Gregorian R.S., Jr.2
Csankovszki, G.3
Crothers, D.M.4
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28
-
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0030606876
-
Interaction of the Bacillus stearothermophilus ribosomal protein S15 with 16S RNA: II. Specificity determinants of RNA - protein recognition
-
The authors carefully define the minimal RNA recognition site for the ribosomal S12 protein. Protein binding is accompanied by a significant RNA conformational changes involving reorientation of helices at a three-helix junction. of special interest
-
Batey RT, Williamson JR. Interaction of the Bacillus stearothermophilus ribosomal protein S15 with 16S RNA: II. Specificity determinants of RNA - protein recognition. J Mol Biol. 261:1996;550-567 The authors carefully define the minimal RNA recognition site for the ribosomal S12 protein. Protein binding is accompanied by a significant RNA conformational changes involving reorientation of helices at a three-helix junction. of special interest.
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(1996)
J Mol Biol
, vol.261
, pp. 550-567
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Batey, R.T.1
Williamson, J.R.2
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29
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0024392753
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Structure of E. coli glutaminyl-tRNA synthetase complexed with tRNA(Gln) and ATP at 2.8 Å resolution
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Rould MA, Perona JJ, Soll D, Steitz TA. Structure of E. coli glutaminyl-tRNA synthetase complexed with tRNA(Gln) and ATP at 2.8 Å resolution. Science. 246:1989;1135-1142.
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Science
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Rould, M.A.1
Perona, J.J.2
Soll, D.3
Steitz, T.A.4
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30
-
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0029869019
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A tyrosyl-tRNA synthetase protein induces tertiary folding of the group I intron catalytic core
-
CYT-18 binds the group I intron catalytic core on the side opposite the active-site cleft, primarily at a triple-helical structure involving the P4 and P6 helices. of special interest
-
Caprara MG, Mohr G, Lambowitz AM. A tyrosyl-tRNA synthetase protein induces tertiary folding of the group I intron catalytic core. J Mol Biol. 257:1996;512-531 CYT-18 binds the group I intron catalytic core on the side opposite the active-site cleft, primarily at a triple-helical structure involving the P4 and P6 helices. of special interest.
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(1996)
J Mol Biol
, vol.257
, pp. 512-531
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Caprara, M.G.1
Mohr, G.2
Lambowitz, A.M.3
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0027370486
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Major groove accessibility of RNA
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Weeks KM, Crothers DM. Major groove accessibility of RNA. Science. 261:1993;1574-1577.
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Science
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Weeks, K.M.1
Crothers, D.M.2
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32
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0029866752
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Mapping in three dimensions of regions in a catalytic RNA protected from attack by an Fe(II)-EDTA reagent
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Westhof E, Wesolowski D, Altman S. Mapping in three dimensions of regions in a catalytic RNA protected from attack by an Fe(II)-EDTA reagent. J Mol Biol. 258:1996;600-613.
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J Mol Biol
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Westhof, E.1
Wesolowski, D.2
Altman, S.3
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33
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0028945859
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Higher order folding and domain analysis of the ribozyme from Bacillus subtilis ribonuclease P
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Pan T. Higher order folding and domain analysis of the ribozyme from Bacillus subtilis ribonuclease P. Biochemistry. 34:1995;902-909.
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Biochemistry
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Pan, T.1
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35
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0027433710
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Monitoring of the cooperative unfolding of the sunY group I intron of bacteriophage T4. The active form of the sunY ribozyme is stabilized by multiple interactions with 3′ terminal intron components
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Jaeger L, Westhof E, Michel F. Monitoring of the cooperative unfolding of the sunY group I intron of bacteriophage T4. The active form of the sunY ribozyme is stabilized by multiple interactions with 3′ terminal intron components. J Mol Biol. 234:1993;331-346.
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J Mol Biol
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, pp. 331-346
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Jaeger, L.1
Westhof, E.2
Michel, F.3
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36
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0029007094
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The time dependence of chemical modification reveals slow steps in the folding of a group I ribozyme
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Banerjee AR, Turner DH. The time dependence of chemical modification reveals slow steps in the folding of a group I ribozyme. Biochemistry. 340:1995;6504-6512.
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(1995)
Biochemistry
, vol.340
, pp. 6504-6512
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Banerjee, A.R.1
Turner, D.H.2
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0027991626
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Kinetic intermediates in RNA folding
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Zarrinkar PP, Williamson JR. Kinetic intermediates in RNA folding. Science. 265:1994;918-924.
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Science
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Zarrinkar, P.P.1
Williamson, J.R.2
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38
-
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0029874598
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The kinetic folding pathway of the Tetrahymena ribozyme reveals possible similarities between RNA and protein folding
-
Having demonstrated that there is a slow step for folding the Tetrahymena ribozyme [37], the authors focus in on the specific nature of the rate-limiting step. Formation of a triple helical scaffold that orients two RNA domains with respect to each other occurs during the slow step. of special interest
-
Zarrinkar PP, Williamson JR. The kinetic folding pathway of the Tetrahymena ribozyme reveals possible similarities between RNA and protein folding. Nat Struct Biol. 3:1996;432-438 Having demonstrated that there is a slow step for folding the Tetrahymena ribozyme [37], the authors focus in on the specific nature of the rate-limiting step. Formation of a triple helical scaffold that orients two RNA domains with respect to each other occurs during the slow step. of special interest.
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(1996)
Nat Struct Biol
, vol.3
, pp. 432-438
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-
Zarrinkar, P.P.1
Williamson, J.R.2
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39
-
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0030593036
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Assembly of a ribonucleoprotein catalyst by tertiary structure capture
-
CBP2 must wait for its cognate RNA to fold before it can bind. This mechanism illustrates one way that RNA folding can govern RNA - protein complex formation. The CBP2 - RNA complex dissociates slowly; slow dissociation is shown to be a general problem for some RNA-binding proteins. of outstanding interest
-
Weeks KM, Cech TR. Assembly of a ribonucleoprotein catalyst by tertiary structure capture. Science. 271:1996;345-348 CBP2 must wait for its cognate RNA to fold before it can bind. This mechanism illustrates one way that RNA folding can govern RNA - protein complex formation. The CBP2 - RNA complex dissociates slowly; slow dissociation is shown to be a general problem for some RNA-binding proteins. of outstanding interest.
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(1996)
Science
, vol.271
, pp. 345-348
-
-
Weeks, K.M.1
Cech, T.R.2
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40
-
-
0028884596
-
Cotranscriptional splicing of a group I intron is facilitated by the Cbp2 protein
-
This paper illustrates an interesting twist on the theme of protein-facilitated RNA splicing. Mutations in some purified RNAs are not suppressed by the simple addition of CBP2; these RNAs do splice if CBP2 is present during transcription. CBP2 may modulate folding of nascent transcripts. of special interest
-
Lewin AS, Thomas J Jr, Tirupati HK. Cotranscriptional splicing of a group I intron is facilitated by the Cbp2 protein. Mol Cell Biol. 15:1995;6971-6978 This paper illustrates an interesting twist on the theme of protein-facilitated RNA splicing. Mutations in some purified RNAs are not suppressed by the simple addition of CBP2; these RNAs do splice if CBP2 is present during transcription. CBP2 may modulate folding of nascent transcripts. of special interest.
-
(1995)
Mol Cell Biol
, vol.15
, pp. 6971-6978
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Lewin, A.S.1
Thomas J., Jr.2
Tirupati, H.K.3
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41
-
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0029958503
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Slow folding kinetics of RNase P RNA
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The authors show that the folding pathway of RNase P RNA includes a slow step. This work also defines characteristics of slow folding that may be common to other large RNAs. of outstanding interest
-
Zarrinkar PP, Wang J, Williamson JR. Slow folding kinetics of RNase P RNA. RNA. 2:1996;564-573 The authors show that the folding pathway of RNase P RNA includes a slow step. This work also defines characteristics of slow folding that may be common to other large RNAs. of outstanding interest.
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(1996)
RNA
, vol.2
, pp. 564-573
-
-
Zarrinkar, P.P.1
Wang, J.2
Williamson, J.R.3
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42
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0029410699
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Group II ribozymes that cleave DNA and RNA linkages with similar efficiency, and lack contacts with substrate 2'-hydroxyl groups
-
A kinetic lag in the kinetics of oligonucleotide-cleavage results from slow binding by ribozyme domain 5. Slow folding may be a characteristic of group II intron RNA assembly. of special interest
-
Griffin EA Jr, Qin Z, Michels WJ Jr, Pyle AM. Group II ribozymes that cleave DNA and RNA linkages with similar efficiency, and lack contacts with substrate 2'-hydroxyl groups. Chem Biol. 2:1995;761-770 A kinetic lag in the kinetics of oligonucleotide-cleavage results from slow binding by ribozyme domain 5. Slow folding may be a characteristic of group II intron RNA assembly. of special interest.
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(1995)
Chem Biol
, vol.2
, pp. 761-770
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Griffin E.A., Jr.1
Qin, Z.2
Michels W.J., Jr.3
Pyle, A.M.4
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43
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0027171312
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Dynamics of in vitro assembly of 16S rRNA into 30S ribosomal subunits
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Powers T, Daubresse G, Noller HF. Dynamics of in vitro assembly of 16S rRNA into 30S ribosomal subunits. J Mol Biol. 232:1993;362-374.
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J Mol Biol
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Powers, T.1
Daubresse, G.2
Noller, H.F.3
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44
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0028936110
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Involvement of Neurospora mitochondrial tyrosyl-tRNA synthetase in RNA splicing. A new method for purifying the protein and characterization of physical and enzymatic properties pertinent to splicing
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Saldanha RJ, Patel SS, Surendran R, Lee JC, Lambowitz AM. Involvement of Neurospora mitochondrial tyrosyl-tRNA synthetase in RNA splicing. A new method for purifying the protein and characterization of physical and enzymatic properties pertinent to splicing. Biochemistry. 34:1995;1275-1287.
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(1995)
Biochemistry
, vol.34
, pp. 1275-1287
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Saldanha, R.J.1
Patel, S.S.2
Surendran, R.3
Lee, J.C.4
Lambowitz, A.M.5
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45
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0030576507
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Analysis of the CYT-18 protein binding site at the junction of stacked helices in a group I intron RNA by quantitative binding assays and in vitro selection
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The CYT-18 splicing factor binds at the diffusion-controlled limit to a variety of group I intron deletion mutants as long as they include the P4-P6 triple-helical junction. Equilibrium binding affinities vary, however, which suggests that additional interactions are realized after the protein binds to the P4-P6 structure. A complex site spanning ten invariant residues is important for mediating specific complex formation. of outstanding interest
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Saldanha R, Ellington A, Lambowitz AM. Analysis of the CYT-18 protein binding site at the junction of stacked helices in a group I intron RNA by quantitative binding assays and in vitro selection. J Mol Biol. 261:1996;23-42 The CYT-18 splicing factor binds at the diffusion-controlled limit to a variety of group I intron deletion mutants as long as they include the P4-P6 triple-helical junction. Equilibrium binding affinities vary, however, which suggests that additional interactions are realized after the protein binds to the P4-P6 structure. A complex site spanning ten invariant residues is important for mediating specific complex formation. of outstanding interest.
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(1996)
J Mol Biol
, vol.261
, pp. 23-42
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Saldanha, R.1
Ellington, A.2
Lambowitz, A.M.3
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46
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0029834485
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The Cbp2 protein suppresses splice site mutations in a group I intron
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Shaw LC, Thomas J Jr, Lewin AS. The Cbp2 protein suppresses splice site mutations in a group I intron. Nucleic Acids Res. 24:1996;3415-3423.
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(1996)
Nucleic Acids Res
, vol.24
, pp. 3415-3423
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Shaw, L.C.1
Thomas J., Jr.2
Lewin, A.S.3
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47
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0028268090
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Kinetic and thermodynamic analysis of RNA - protein interactions in the RNase P holoenzyme from Escherichia coli
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Talbot SJ, Altman S. Kinetic and thermodynamic analysis of RNA - protein interactions in the RNase P holoenzyme from Escherichia coli. Biochemistry. 33:1994;1406-1411.
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(1994)
Biochemistry
, vol.33
, pp. 1406-1411
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Talbot, S.J.1
Altman, S.2
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48
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0030034498
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The DExH box protein Suv3p is a component of a yeast mitochondrial 3′- to-5' exoribonuclease that suppresses group I intron toxicity
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The Suv3p protein, a DExH box helicase, is implicated in group I RNA degradation. The Suv3p-containing complex represents a neat way to recycle the protein components of group I intron-derived ribonucleoproteins. of outstanding interest
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Margossian SP, Li H, Zassenhaus HP, Butow RA. The DExH box protein Suv3p is a component of a yeast mitochondrial 3′- to-5' exoribonuclease that suppresses group I intron toxicity. Cell. 84:1996;199-209 The Suv3p protein, a DExH box helicase, is implicated in group I RNA degradation. The Suv3p-containing complex represents a neat way to recycle the protein components of group I intron-derived ribonucleoproteins. of outstanding interest.
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(1996)
Cell
, vol.84
, pp. 199-209
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Margossian, S.P.1
Li, H.2
Zassenhaus, H.P.3
Butow, R.A.4
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49
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0027512243
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Isolation and characterization of an NTP-dependent 3'-exoribonuclease from mitochondria of Saccharomyces cerevisiae
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Min JJ, Heuertz RM, Zassenhaus HP. Isolation and characterization of an NTP-dependent 3'-exoribonuclease from mitochondria of Saccharomyces cerevisiae. J Biol Chem. 268:1993;7350-7357.
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(1993)
J Biol Chem
, vol.268
, pp. 7350-7357
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Min, J.J.1
Heuertz, R.M.2
Zassenhaus, H.P.3
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50
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0030271457
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RNA turnover and the control of mitochondrial gene expression
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The authors thoughtfully review the problem of recycling the protein cofactors of group I introns. of special interest
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Margossian SP, Butow RA. RNA turnover and the control of mitochondrial gene expression. Trends Biochem Sci. 21:1996;392-396 The authors thoughtfully review the problem of recycling the protein cofactors of group I introns. of special interest.
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(1996)
Trends Biochem Sci
, vol.21
, pp. 392-396
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Margossian, S.P.1
Butow, R.A.2
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51
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0029792919
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An RNA topoisomerase
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The authors find that E. coli DNA topoisomerase III possesses RNA topoi-somerase activity, raising the possibility that strand passage activities might contribute to RNA folding. of special interest
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Wang H, Gate RJ, Seeman NC. An RNA topoisomerase. Proc Natl Acad Sci USA. 93:1996;9477-9482 The authors find that E. coli DNA topoisomerase III possesses RNA topoi-somerase activity, raising the possibility that strand passage activities might contribute to RNA folding. of special interest.
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(1996)
Proc Natl Acad Sci USA
, vol.93
, pp. 9477-9482
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Wang, H.1
Gate, R.J.2
Seeman, N.C.3
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52
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0028859580
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A group II intron RNA is a catalytic component of a DNA endonuclease involved in intron mobility
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In this and in a related paper [53], the authors show that the group II intron RNA al2 and its polyprotein cofactor collaborate to cleave double-stranded DNA. One DNA strand is cleaved by the RNA in a reverse splicing reaction, whereas the other strand is cleaved by one domain of the protein. A different domain of the protein enhances the RNA-splicing activity of the intron. Yet another domain of the protein possesses reverse transcriptase activity that contributes to intron mobility. of outstanding interest
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Zimmerly S, Guo H, Eskes R, Yang J, Perlman PS, Lambowitz AM. A group II intron RNA is a catalytic component of a DNA endonuclease involved in intron mobility. Cell. 83:1995;529-538 In this and in a related paper [53], the authors show that the group II intron RNA al2 and its polyprotein cofactor collaborate to cleave double-stranded DNA. One DNA strand is cleaved by the RNA in a reverse splicing reaction, whereas the other strand is cleaved by one domain of the protein. A different domain of the protein enhances the RNA-splicing activity of the intron. Yet another domain of the protein possesses reverse transcriptase activity that contributes to intron mobility. of outstanding interest.
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(1995)
Cell
, vol.83
, pp. 529-538
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Zimmerly, S.1
Guo, H.2
Eskes, R.3
Yang, J.4
Perlman, P.S.5
Lambowitz, A.M.6
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53
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0029162089
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Group II intron mobility occurs by target DNA-primed reverse transcription
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See annotation [52]. of outstanding interest
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Zimmerly S, Guo H, Perlman PS, Lambowitz AM. Group II intron mobility occurs by target DNA-primed reverse transcription. Cell. 82:1995;545-554 See annotation [52]. of outstanding interest.
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(1995)
Cell
, vol.82
, pp. 545-554
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Zimmerly, S.1
Guo, H.2
Perlman, P.S.3
Lambowitz, A.M.4
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54
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0029417203
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The 'DEAD box' protein DbpA interacts specifically with the peptidyltransferase center in 23S rRNA
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The RNA binding site for DbpA, a putative helicase and demonstrated RNA-dependent ATPase, is localized to a 93-nucleotide and functionally critical region of 16S RNA. of special interest
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Nicol SM, Fuller-Pace FV. The 'DEAD box' protein DbpA interacts specifically with the peptidyltransferase center in 23S rRNA. Proc Natl Acad Sci USA. 92:1995;11681-11685 The RNA binding site for DbpA, a putative helicase and demonstrated RNA-dependent ATPase, is localized to a 93-nucleotide and functionally critical region of 16S RNA. of special interest.
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(1995)
Proc Natl Acad Sci USA
, vol.92
, pp. 11681-11685
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Nicol, S.M.1
Fuller-Pace, F.V.2
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55
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0029922992
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A DEAD-box RNA helicase in the Escherichia coli RNA degradosome
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The final stop for many RNAs is the degradosome - a complex that contains an essential ATP-dependent helicase. of special interest
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Py B, Higgins CF, Krisch HM, Carpousis AJ. A DEAD-box RNA helicase in the Escherichia coli RNA degradosome. Nature. 381:1996;169-172 The final stop for many RNAs is the degradosome - a complex that contains an essential ATP-dependent helicase. of special interest.
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(1996)
Nature
, vol.381
, pp. 169-172
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Py, B.1
Higgins, C.F.2
Krisch, H.M.3
Carpousis, A.J.4
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57
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0030582766
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A tyrosyl-tRNA synthetase recognizes a conserved tRNA-like structural motif in the group I intron catalytic core
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Tyr. Chemical footprinting and molecular modeling suggest CYT-18 recognizes overlapping structures that are centered at a stacked helix junction in both molecules. of special interest
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Tyr. Chemical footprinting and molecular modeling suggest CYT-18 recognizes overlapping structures that are centered at a stacked helix junction in both molecules. of special interest.
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(1996)
Cell
, vol.87
, pp. 1135-1145
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Caprara, M.G.1
Lehnert, V.2
Lambowitz, A.M.3
Westhof, E.4
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58
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0030452773
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New loop - loop tertiary interactions in self-splicing introns of subgroup IC and ID: A complete 3D model of the Tetrahymena thermophilia ribozyme
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The existence of good quality, medium resolution models for group I introns has been a boon to the ribozyme field. Models for group I RNAs belonging to four subgroups are now available and emphasize the modular organization of large RNAs. of special interest
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Lehnert V, Jaeger L, Michel F, Westhof E. New loop - loop tertiary interactions in self-splicing introns of subgroup IC and ID: a complete 3D model of the Tetrahymena thermophilia ribozyme. Chem Biol. 3:1996;993-1009 The existence of good quality, medium resolution models for group I introns has been a boon to the ribozyme field. Models for group I RNAs belonging to four subgroups are now available and emphasize the modular organization of large RNAs. of special interest.
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(1996)
Chem Biol
, vol.3
, pp. 993-1009
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Lehnert, V.1
Jaeger, L.2
Michel, F.3
Westhof, E.4
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