-
1
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0016354122
-
Structure of yeast phenylalanine tRNA at 3 Å resolution
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Robertus JD, Ladner JE, Finch JT, Rhodes D, Brown RS, Clark BF, Klug A. Structure of yeast phenylalanine tRNA at 3 Å resolution. Nature. 250:1974;546-551.
-
(1974)
Nature
, vol.250
, pp. 546-551
-
-
Robertus, J.D.1
Ladner, J.E.2
Finch, J.T.3
Rhodes, D.4
Brown, R.S.5
Clark, B.F.6
Klug, A.7
-
2
-
-
0015929511
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Three-dimensional structure of yeast phenylalanine transfer RNA: Folding of the polynucleotide chain
-
Kim SH, Quigley GJ, Suddath FL, McPherson A, Sneden D, Kim JJ, Weinzierl J, Rich A. Three-dimensional structure of yeast phenylalanine transfer RNA: folding of the polynucleotide chain. Science. 179:1973;285-288.
-
(1973)
Science
, vol.179
, pp. 285-288
-
-
Kim, S.H.1
Quigley, G.J.2
Suddath, F.L.3
McPherson, A.4
Sneden, D.5
Kim, J.J.6
Weinzierl, J.7
Rich, A.8
-
3
-
-
0028063567
-
Three-dimensional structure of a hammerhead ribozyme
-
Pley HW, Flaherty KM, McKay DB. Three-dimensional structure of a hammerhead ribozyme. Nature. 372:1994;68-74.
-
(1994)
Nature
, vol.372
, pp. 68-74
-
-
Pley, H.W.1
Flaherty, K.M.2
McKay, D.B.3
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4
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0030476765
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Capturing the structure of a catalytic RNA intermediate: The hammerhead ribozyme
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of outstanding interest. This paper presents three structures of hammerhead RNA in the absence and presence of divalent metal ions. The metal ions were infused into the crystals and a conformational intermediate, having a metal ion localized near the cleavage-site, was trapped by flash-freezing of the crystal. Only minor conformational changes near the active site occur upon activation of the ribozyme.
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Scott WG, Murray JB, Arnold JRP, Stoddard BL, Klug A. Capturing the structure of a catalytic RNA intermediate: the hammerhead ribozyme. of outstanding interest Science. 274:1996;2065-2069 This paper presents three structures of hammerhead RNA in the absence and presence of divalent metal ions. The metal ions were infused into the crystals and a conformational intermediate, having a metal ion localized near the cleavage-site, was trapped by flash-freezing of the crystal. Only minor conformational changes near the active site occur upon activation of the ribozyme.
-
(1996)
Science
, vol.274
, pp. 2065-2069
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Scott, W.G.1
Murray, J.B.2
Arnold, J.R.P.3
Stoddard, B.L.4
Klug, A.5
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5
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0029073091
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The crystal structure of an all-RNA hammerhead ribozyme: A proposed mechanism for RNA catalytic cleavage
-
Scott WG, Finch JT, Klug A. The crystal structure of an all-RNA hammerhead ribozyme: a proposed mechanism for RNA catalytic cleavage. Cell. 81:1995;991-1002.
-
(1995)
Cell
, vol.81
, pp. 991-1002
-
-
Scott, W.G.1
Finch, J.T.2
Klug, A.3
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6
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0028004607
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Crystal structure at 1.92 Å resolution of the RNA-binding domain of the U1A spliceosomal protein complexed with an RNA hairpin
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Oubridge C, Ito N, Evans PR, Teo CH, Nagai K. Crystal structure at 1.92 Å resolution of the RNA-binding domain of the U1A spliceosomal protein complexed with an RNA hairpin. Nature. 372:1994;432-438.
-
(1994)
Nature
, vol.372
, pp. 432-438
-
-
Oubridge, C.1
Ito, N.2
Evans, P.R.3
Teo, C.H.4
Nagai, K.5
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7
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0031213649
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The three-dimensional structures of two complexes between recombinant MS2 capsids and RNA operator fragments reveal sequence-specific protein-RNA interactions
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Valegard K, Murray JB, Stonehouse NJ, Den Worm S, Stockley PG, Liljas L. The three-dimensional structures of two complexes between recombinant MS2 capsids and RNA operator fragments reveal sequence-specific protein-RNA interactions. J Mol Biol. 270:1997;724-738.
-
(1997)
J Mol Biol
, vol.270
, pp. 724-738
-
-
Valegard, K.1
Murray, J.B.2
Stonehouse, N.J.3
Den Worm, S.4
Stockley, P.G.5
Liljas, L.6
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8
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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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of outstanding interest. The authors describe current state of the art X-ray crystallography on naked RNA. The 2.8 Å crystal structure is currently the largest solved structure and has provided detailed structural information on several novel RNA motifs, including the tetraloop receptor and ribose zipper, and has demonstrated a central role for metal ions in RNA folding.
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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. of outstanding interest Science. 273:1996;1678-1685 The authors describe current state of the art X-ray crystallography on naked RNA. The 2.8 Å crystal structure is currently the largest solved structure and has provided detailed structural information on several novel RNA motifs, including the tetraloop receptor and ribose zipper, and has demonstrated a central role for metal ions in RNA folding.
-
(1996)
Science
, vol.273
, pp. 1678-1685
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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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9
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0028902990
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Structure of an RNA double helix including uracil-uracil base pairs in an internal loop
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Baeyens KJ, De Bondt HL, Holbrook SR. Structure of an RNA double helix including uracil-uracil base pairs in an internal loop. Nat Struct Biol. 2:1995;56-62.
-
(1995)
Nat Struct Biol
, vol.2
, pp. 56-62
-
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Baeyens, K.J.1
De Bondt, H.L.2
Holbrook, S.R.3
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10
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0029822046
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A curved RNA helix incorporating an internal loop with G·A and A·A non-Watson-Crick base pairing
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Baeyens KJ, De Bondt HL, Pardi A, Holbrook SR. A curved RNA helix incorporating an internal loop with G·A and A·A non-Watson-Crick base pairing. Proc Natl Acad Sci USA. 93:1996;12851-12855.
-
(1996)
Proc Natl Acad Sci USA
, vol.93
, pp. 12851-12855
-
-
Baeyens, K.J.1
De Bondt, H.L.2
Pardi, A.3
Holbrook, S.R.4
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13
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0025817050
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A hammerhead ribozym allows synthesis of a new form of the tetrahedron ribozyme homogeneous in length with a 3′ end blocked for transesterification
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Grosshans CA, Cech TR. A hammerhead ribozym allows synthesis of a new form of the tetrahedron ribozyme homogeneous in length with a 3′ end blocked for transesterification. Nucleic Acids Res. 19:1991;3875-3880.
-
(1991)
Nucleic Acids Res
, vol.19
, pp. 3875-3880
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Grosshans, C.A.1
Cech, T.R.2
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14
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0031213875
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Crystals by design: A strategy for crystallization of a ribozyme derived from the Tetrahymena group I intron
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Golden BL, Podell ER, Gooding AR, Cech TR. Crystals by design: a strategy for crystallization of a ribozyme derived from the Tetrahymena group I intron. J Mol Biol. 270:1997;711-723.
-
(1997)
J Mol Biol
, vol.270
, pp. 711-723
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Golden, B.L.1
Podell, E.R.2
Gooding, A.R.3
Cech, T.R.4
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15
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0031588925
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How accurately and precisely can RNA structure be determined by NMR?
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of special interest. Distance constraints and dihedral angles were extracted from a known structure. Subsets of these parameters were used to predict the structure by algorithms normally used in NMR experiments. The calculations demonstrated that a complete assignment based on isotopically labeled RNA, may predict the structure with a resolution of 1-1.5 Å.
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Allain FH, Varani G. How accurately and precisely can RNA structure be determined by NMR? of special interest J Mol Biol. 267:1997;338-351 Distance constraints and dihedral angles were extracted from a known structure. Subsets of these parameters were used to predict the structure by algorithms normally used in NMR experiments. The calculations demonstrated that a complete assignment based on isotopically labeled RNA, may predict the structure with a resolution of 1-1.5 Å.
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(1997)
J Mol Biol
, vol.267
, pp. 338-351
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Allain, F.H.1
Varani, G.2
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16
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0030916603
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Recent solution structures of RNA and its complexes with drugs, peptides and proteins
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of special interest. This excellent review summarizes the latest NMR structures of natural and in vitro evolved RNAs. Instructive illustrations of common RNA folding patterns, alone and in complex with different ligands, are presented.
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Ramos A, Gubser CC, Varani G. Recent solution structures of RNA and its complexes with drugs, peptides and proteins. of special interest Curr Opin Struct Biol. 7:1997;317-323 This excellent review summarizes the latest NMR structures of natural and in vitro evolved RNAs. Instructive illustrations of common RNA folding patterns, alone and in complex with different ligands, are presented.
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(1997)
Curr Opin Struct Biol
, vol.7
, pp. 317-323
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Ramos, A.1
Gubser, C.C.2
Varani, G.3
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17
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0030602904
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A characteristic bent conformation of RNA pseudoknots promotes -1 frameshifting during translation of retroviral RNA
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Chen X, Kang H, Shen LX, Chamorro M, Varmus HE, Tinoco I Jr. A characteristic bent conformation of RNA pseudoknots promotes -1 frameshifting during translation of retroviral RNA. J Mol Biol. 260:1996;479-483.
-
(1996)
J Mol Biol
, vol.260
, pp. 479-483
-
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Chen, X.1
Kang, H.2
Shen, L.X.3
Chamorro, M.4
Varmus, H.E.5
Tinoco I., Jr.6
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18
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0031591383
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The structure of an RNA 'kissing' hairpin complex of the HIV TAR hairpin loop and its complement
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Chang KY, Tinoco I Jr. The structure of an RNA 'kissing' hairpin complex of the HIV TAR hairpin loop and its complement. J Mol Biol. 269:1997;52-66.
-
(1997)
J Mol Biol
, vol.269
, pp. 52-66
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Chang, K.Y.1
Tinoco I., Jr.2
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20
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0029920331
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Specificity of ribonucleoprotein interaction determined by RNA folding during complex formation
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of special interest. This study demonstrates significant conformational changes in both U1A and U1A-3′ UTR regulatory element upon complex formation.
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Allain FH-T, Gubser CC, Howe PWA, Nagai K, Neuhaus D, Varani G. Specificity of ribonucleoprotein interaction determined by RNA folding during complex formation. of special interest Nature. 380:1996;646-650 This study demonstrates significant conformational changes in both U1A and U1A-3′ UTR regulatory element upon complex formation.
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(1996)
Nature
, vol.380
, pp. 646-650
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Allain Fh-T1
Gubser, C.C.2
Howe, P.W.A.3
Nagai, K.4
Neuhaus, D.5
Varani, G.6
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21
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0029825658
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Structure of the A site of Escherichia coli 16S ribosomal RNA complexed with an aminoglycoside antibiotic
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of special interest. This is the first example of an native antibiotic - RNA complex, and it illustrates characteristic major groove interactions of drugs, which also have been observed in aptamer complexes.
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Fourmy D, Recht MI, Blanchard SC, Puglisi JD. Structure of the A site of Escherichia coli 16S ribosomal RNA complexed with an aminoglycoside antibiotic. of special interest Science. 274:1996;1367-1371 This is the first example of an native antibiotic - RNA complex, and it illustrates characteristic major groove interactions of drugs, which also have been observed in aptamer complexes.
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(1996)
Science
, vol.274
, pp. 1367-1371
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Fourmy, D.1
Recht, M.I.2
Blanchard, S.C.3
Puglisi, J.D.4
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22
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0029784592
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α helix - RNA major groove recognition in an HIV-1 Rev peptide-RRE RNA complex
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of special interest. The NMR structure of helix IIB from HIV-1 RNA interacting with the basic domain of HIV-1 Rev protein is an instructive example of how purine-purine base pairs in internal loops can displace the phosphate backbone and expose the major groove for direct interactions with the peptide.
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Battiste JL, Mao H, Rao S, 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. of special interest Science. 273:1996;1547-1551 The NMR structure of helix IIB from HIV-1 RNA interacting with the basic domain of HIV-1 Rev protein is an instructive example of how purine-purine base pairs in internal loops can displace the phosphate backbone and expose the major groove for direct interactions with the peptide.
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(1996)
Science
, vol.273
, pp. 1547-1551
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Battiste, J.L.1
Mao, H.2
Rao, S.3
Tan, R.4
Muhandiram, D.R.5
Kay, L.E.6
Frankel, A.D.7
Williamson, J.R.8
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23
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0028858599
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Solution structure of a bovine immunodeficiency virus Tat-TAR peptide-RNA complex
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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.
-
(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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24
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0029946537
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Structural basis of RNA folding and recognition in an AMP - RNA aptamer complex
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of special interest. The aptamer forms a highly complex internal bulge structure which interacts with ATP through hydrogen binding and stacking. The RNA structure is not formed in the absence of ATP, demonstrating that small molecules can play an important role in stabilizing RNA structures.
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Jiang F, Kumar RA, Jones RA, Patel DJ. Structural basis of RNA folding and recognition in an AMP - RNA aptamer complex. of special interest Nature. 382:1996;183-186 The aptamer forms a highly complex internal bulge structure which interacts with ATP through hydrogen binding and stacking. The RNA structure is not formed in the absence of ATP, demonstrating that small molecules can play an important role in stabilizing RNA structures.
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(1996)
Nature
, vol.382
, pp. 183-186
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Jiang, F.1
Kumar, R.A.2
Jones, R.A.3
Patel, D.J.4
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25
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0029904020
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Solution structure of an ATP-binding RNA aptamer reveals a novel fold
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Dieckmann T, Suzuki E, Nakamura GK, Feigon J. Solution structure of an ATP-binding RNA aptamer reveals a novel fold. RNA. 2:1996;628-640.
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(1996)
RNA
, vol.2
, pp. 628-640
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Dieckmann, T.1
Suzuki, E.2
Nakamura, G.K.3
Feigon, J.4
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26
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0029972909
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Structural basis of ligand discrimination by two related RNA aptamers resolved by NMR spectroscopy
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of special interest. This paper describes the structure of an aptamer that can bind citrulline with amazingly high specificity, thus distinguishing it from the structurally similar arginine molecule.
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Yang Y, Kochoyan M, Burgstaller P, Westhof E, Famulok M. Structural basis of ligand discrimination by two related RNA aptamers resolved by NMR spectroscopy. of special interest Science. 272:1996;1343-1347 This paper describes the structure of an aptamer that can bind citrulline with amazingly high specificity, thus distinguishing it from the structurally similar arginine molecule.
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(1996)
Science
, vol.272
, pp. 1343-1347
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Yang, Y.1
Kochoyan, M.2
Burgstaller, P.3
Westhof, E.4
Famulok, M.5
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27
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0030752211
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Interlocking structural motifs mediate molecular discrimination by a theophylline-binding RNA
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of outstanding interest. The authors investigate the structure of an aptamer that has been selected for theophylline binding and counter selected for binding to the related compound caffeine. They demonstrate that sterical hinderance by a unique methyl group in caffeine accounts for the inability of the aptamer to bind this compound.
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Zimmermann GR, Jenison RD, Wick CL, Simorre JP, Pardi A. Interlocking structural motifs mediate molecular discrimination by a theophylline-binding RNA. of outstanding interest Nat Struct Biol. 4:1997;644-649 The authors investigate the structure of an aptamer that has been selected for theophylline binding and counter selected for binding to the related compound caffeine. They demonstrate that sterical hinderance by a unique methyl group in caffeine accounts for the inability of the aptamer to bind this compound.
-
(1997)
Nat Struct Biol
, vol.4
, pp. 644-649
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Zimmermann, G.R.1
Jenison, R.D.2
Wick, C.L.3
Simorre, J.P.4
Pardi, A.5
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28
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0031589498
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RNA structure. A molecular contortionist
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Doudna JA. RNA structure. A molecular contortionist. Nature. 388:1997;830-831.
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(1997)
Nature
, vol.388
, pp. 830-831
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Doudna, J.A.1
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29
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0030959348
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Rules for RNA recognition of GNRA tetraloops deduced by in vitro selection comparison with in vivo evolution
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of special interest. In vitro selection methods were employed to search for tetra loop receptors containing a GNRA sequence. A remarkable conservation of the GAAA receptor was found and the interaction between other GNRA tetraloops and their receptors was rationalized with emphasis on the second nucleotide in the loop for the specific recognition.
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Costa M, Michel F. Rules for RNA recognition of GNRA tetraloops deduced by in vitro selection comparison with in vivo evolution. of special interest EMBO J. 16:1997;3289-3302 In vitro selection methods were employed to search for tetra loop receptors containing a GNRA sequence. A remarkable conservation of the GAAA receptor was found and the interaction between other GNRA tetraloops and their receptors was rationalized with emphasis on the second nucleotide in the loop for the specific recognition.
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(1997)
EMBO J
, vol.16
, pp. 3289-3302
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Costa, M.1
Michel, F.2
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30
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0028037302
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Model for an RNA tertiary interaction from the structure of an intermolecular complex between a GAAA tetraloop and an RNA helix
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Pley HW, Flaherty KM, McKay DB. Model for an RNA tertiary interaction from the structure of an intermolecular complex between a GAAA tetraloop and an RNA helix. Nature. 372:1994;111-113.
-
(1994)
Nature
, vol.372
, pp. 111-113
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Pley, H.W.1
Flaherty, K.M.2
McKay, D.B.3
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31
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0029796982
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RNA tertiary structure mediation by adenosine platforms
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of special interest. Demonstration of a novel motif, the adenosine platform, where adjacent adenosines lie side-by-site and form hydrogen bonds between N3 and N6 of the 5′- and 3′-adenosine, respectively. The platform opens the minor groove for interactions. Upon interaction, the accessible N1 of the 5′-adenosine becomes protected - a feature which may be useful for identification of adenosine platforms in other RNAs by chemical probing.
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Cate JH, Gooding AR, Podell E, Zhou K, Golden BL, Szewczak AA, Kundrot CE, Cech TR, Doudna JA. RNA tertiary structure mediation by adenosine platforms. of special interest Science. 273:1996;1696-1699 Demonstration of a novel motif, the adenosine platform, where adjacent adenosines lie side-by-site and form hydrogen bonds between N3 and N6 of the 5′- and 3′-adenosine, respectively. The platform opens the minor groove for interactions. Upon interaction, the accessible N1 of the 5′-adenosine becomes protected - a feature which may be useful for identification of adenosine platforms in other RNAs by chemical probing.
-
(1996)
Science
, vol.273
, pp. 1696-1699
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-
Cate, J.H.1
Gooding, A.R.2
Podell, E.3
Zhou, K.4
Golden, B.L.5
Szewczak, A.A.6
Kundrot, C.E.7
Cech, T.R.8
Doudna, J.A.9
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32
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0030929889
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A magnesium ion core at the heart of a ribozyme domain
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Cate JH, Hanna RL, Doudna JA. A magnesium ion core at the heart of a ribozyme domain. Nat Struct Biol. 4:1997;553-558.
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(1997)
Nat Struct Biol
, vol.4
, pp. 553-558
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Cate, J.H.1
Hanna, R.L.2
Doudna, J.A.3
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33
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0030968993
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RNA structures and folding: From conventional to new issues in structure predictions
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Schuster P, Stadler PF, Renner A. RNA structures and folding: from conventional to new issues in structure predictions. Curr Opin Struct Biol. 7:1997;229-235.
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(1997)
Curr Opin Struct Biol
, vol.7
, pp. 229-235
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Schuster, P.1
Stadler, P.F.2
Renner, A.3
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34
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0030324880
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An analysis of large rRNA sequences folded by a thermodynamic method
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Fields DS, Gutell RR. An analysis of large rRNA sequences folded by a thermodynamic method. Fold Des. 1:1996;419-430.
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(1996)
Fold des
, vol.1
, pp. 419-430
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Fields, D.S.1
Gutell, R.R.2
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35
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0030866522
-
Mutagenesis and comparative sequence analysis of a base triple joining the two domains of group I ribozymes
-
of special interest. A hydrogen bonding model is proposed for triple base pairing between two domains of group I intron. A comparison of 450 different group 1 intron structures was compatible with the proposed triple base pair.
-
Tanner MA, Anderson EM, Gutell RR, Cech TR. Mutagenesis and comparative sequence analysis of a base triple joining the two domains of group I ribozymes. of special interest RNA. 3:1997;1037-1051 A hydrogen bonding model is proposed for triple base pairing between two domains of group I intron. A comparison of 450 different group 1 intron structures was compatible with the proposed triple base pair.
-
(1997)
RNA
, vol.3
, pp. 1037-1051
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Tanner, M.A.1
Anderson, E.M.2
Gutell, R.R.3
Cech, T.R.4
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36
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0031025796
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Joining the two domains of a group I ribozyme to form the catalytic core
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Tanner MA, Cech TR. Joining the two domains of a group I ribozyme to form the catalytic core. Science. 275:1997;847-849.
-
(1997)
Science
, vol.275
, pp. 847-849
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Tanner, M.A.1
Cech, T.R.2
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37
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0029866211
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The ribosomal database project (RDP)
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Maidak BL, Olsen GJ, Larsen N, Overbeek R, McCaughey MJ, Woese CR. The ribosomal database project (RDP). Nucleic Acids Res. 24:1996;109-110.
-
(1996)
Nucleic Acids Res
, vol.24
, pp. 109-110
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-
Maidak, B.L.1
Olsen, G.J.2
Larsen, N.3
Overbeek, R.4
McCaughey, M.J.5
Woese, C.R.6
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38
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0029147392
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Structurally complex and highly active RNA ligases derived from random RNA sequences
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Ekland EH, Szostak JW, Bartel DP. Structurally complex and highly active RNA ligases derived from random RNA sequences. Science. 269:1995;364-370.
-
(1995)
Science
, vol.269
, pp. 364-370
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Ekland, E.H.1
Szostak, J.W.2
Bartel, D.P.3
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39
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0029011424
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Mapping important nucleotides in the peptidyl transferase centre of 23 S rRNA using a random mutagenesis approach
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Porse BT, Garrett RA. Mapping important nucleotides in the peptidyl transferase centre of 23 S rRNA using a random mutagenesis approach. J Mol Biol. 249:1995;1-10.
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(1995)
J Mol Biol
, vol.249
, pp. 1-10
-
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Porse, B.T.1
Garrett, R.A.2
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40
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0030842451
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Forced evolution of a regulatory RNA helix in the HIV-1 genome
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of special interest. The authors provide an interesting example of forced evolution in HIV-1 viral RNA. The data suggest that the thermodynamic stability of an RNA helix is fine-tuned in response to growth temperature. This method provides an opportunity to study the intrinsic relationship between structure and function of RNA under physiological conditions.
-
Berkhout B, Klaver B, Das AT. Forced evolution of a regulatory RNA helix in the HIV-1 genome. of special interest Nucleic Acid Res. 25:1997;940-947 The authors provide an interesting example of forced evolution in HIV-1 viral RNA. The data suggest that the thermodynamic stability of an RNA helix is fine-tuned in response to growth temperature. This method provides an opportunity to study the intrinsic relationship between structure and function of RNA under physiological conditions.
-
(1997)
Nucleic Acid Res
, vol.25
, pp. 940-947
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Berkhout, B.1
Klaver, B.2
Das, A.T.3
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41
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0028962525
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Ionic intreactions and the global conformations of the hammerhead ribozyme
-
Bassi GS, Mollegaard NE, Murchie AI, von Kitzing E, Lilley DM. Ionic intreactions and the global conformations of the hammerhead ribozyme. Nat Struct Biol. 2:1995;45-55.
-
(1995)
Nat Struct Biol
, vol.2
, pp. 45-55
-
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Bassi, G.S.1
Mollegaard, N.E.2
Murchie, A.I.3
Von Kitzing, E.4
Lilley, D.M.5
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42
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0029903452
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The ion-induced folding of the hammerhead ribozyme: Core sequence changes that perturb folding into the active conformation
-
2+-dependent catalytically active 'wish bone structure', in which helix I and II only are separated by a small angle. Single nucleotide mutations at the three-way junction were identified which block the conformational change.
-
2+-dependent catalytically active 'wish bone structure', in which helix I and II only are separated by a small angle. Single nucleotide mutations at the three-way junction were identified which block the conformational change.
-
(1996)
RNA
, vol.2
, pp. 756-768
-
-
Bassi, G.S.1
Murchie, A.I.2
Lilley, D.M.3
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43
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0030272594
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Sometimes a great motion: The application of transient electric birefringence to the study of macromolecular structure
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of special interest. The author reviews the application of transient electric birefringence in studies of the hammerhead ribozyme which shows that the structure largely remains unchanged upon cleavage. RNA bending in response to ionic conditions and amino acid binding is discussed for different RNAs containing irregular base pairs.
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Hagerman PJ. Sometimes a great motion: the application of transient electric birefringence to the study of macromolecular structure. of special interest Curr Opin Struct Biol. 6:1996;643-649 The author reviews the application of transient electric birefringence in studies of the hammerhead ribozyme which shows that the structure largely remains unchanged upon cleavage. RNA bending in response to ionic conditions and amino acid binding is discussed for different RNAs containing irregular base pairs.
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(1996)
Curr Opin Struct Biol
, vol.6
, pp. 643-649
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Hagerman, P.J.1
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44
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0030921417
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The angle between the anticodon and aminoacyl acceptor stems of yeast tRNA(Phe) is strongly modulated by magnesium ions
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Friederich MW, Hagerman PJ. The angle between the anticodon and aminoacyl acceptor stems of yeast tRNA(Phe) is strongly modulated by magnesium ions. Biochemistry. 36:1997;6090-6099.
-
(1997)
Biochemistry
, vol.36
, pp. 6090-6099
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Friederich, M.W.1
Hagerman, P.J.2
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45
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0027973506
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A three-dimensional model for the hammerhead ribozyme based on fluorescence measurements
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Tuschl T, Gohlke C, Jovin TM, Westhof E, Eckstein F. A three-dimensional model for the hammerhead ribozyme based on fluorescence measurements. Science. 266:1994;785-789.
-
(1994)
Science
, vol.266
, pp. 785-789
-
-
Tuschl, T.1
Gohlke, C.2
Jovin, T.M.3
Westhof, E.4
Eckstein, F.5
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46
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0029100264
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Relative orientation of RNA helices in a group 1 ribozyme determined by helix extension electron microscopy
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Nakamura TM, Wang YH, Zaug AJ, Griffith JD, Cech TR. Relative orientation of RNA helices in a group 1 ribozyme determined by helix extension electron microscopy. EMBO J. 14:1995;4849-4859.
-
(1995)
EMBO J
, vol.14
, pp. 4849-4859
-
-
Nakamura, T.M.1
Wang, Y.H.2
Zaug, A.J.3
Griffith, J.D.4
Cech, T.R.5
-
47
-
-
0030990359
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The ribosome at higher resolution - The donut takes shape
-
Frank J. The ribosome at higher resolution - the donut takes shape. Curr Opin Struct Biol. 7:1997;266-272.
-
(1997)
Curr Opin Struct Biol
, vol.7
, pp. 266-272
-
-
Frank, J.1
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48
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0029100747
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A model of protein synthesis based on cryo-electron microscopy of the E. coli ribosome
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Frank J, Zhu J, Penczek P, Li Y, Srivastava S, Verschoor A, Radermacher M, Grassucci R, Lata RK, Agrawal RK. A model of protein synthesis based on cryo-electron microscopy of the E. coli ribosome. Nature. 376:1995;441-444.
-
(1995)
Nature
, vol.376
, pp. 441-444
-
-
Frank, J.1
Zhu, J.2
Penczek, P.3
Li, Y.4
Srivastava, S.5
Verschoor, A.6
Radermacher, M.7
Grassucci, R.8
Lata, R.K.9
Agrawal, R.K.10
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49
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0029645318
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The 70S Escherichia coli ribosome at 23 Å resolution: Fitting the ribosomal RNA
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Stark H, Mueller F, Orlova EV, Schatz M, Dube P, Erdemir T, Zemlin F, Brimacombe R, van Heel M. The 70S Escherichia coli ribosome at 23 Å resolution: fitting the ribosomal RNA. Structure. 3:1995;815-821.
-
(1995)
Structure
, vol.3
, pp. 815-821
-
-
Stark, H.1
Mueller, F.2
Orlova, E.V.3
Schatz, M.4
Dube, P.5
Erdemir, T.6
Zemlin, F.7
Brimacombe, R.8
Van Heel, M.9
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50
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0030040661
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Direct visualization of A-, P-, and E-site transfer RNAs in the Escherichia coli ribosome
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Agrawal RK, Penczek P, Grassucci RA, Li Y, Leith A, Nierhaus KH, Frank J. Direct visualization of A-, P-, and E-site transfer RNAs in the Escherichia coli ribosome. Science. 271:1996;1000-1002.
-
(1996)
Science
, vol.271
, pp. 1000-1002
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-
Agrawal, R.K.1
Penczek, P.2
Grassucci, R.A.3
Li, Y.4
Leith, A.5
Nierhaus, K.H.6
Frank, J.7
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51
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0030887834
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Arrangement of tRNAs in pre- And post-translocational ribosomes revealed by electron cryomicroscopy
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of special interest. tRNAs positioned in the P- and E-site of post-translocational ribosomes and at the A- and P-site of pretranslocational ribosomes were visualized at 20 Å resolution. In the paper by Agrawal et al. 1996 [50] all three A-, P-, and E- sites were co-occupied by tRNAs. The significant discrepancies between the proposed models in Agrawal et al. 1996 [50] and this paper may be a consequence of the non-physiological simultaneous binding of three tRNAs in Agrawal et al. [50].
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Stark H, Orlova EV, Rinke-Appel J, Junke N, Mueller F, Rodnina M, Wintermeyer W, Brimacombe R, van Heel M. Arrangement of tRNAs in pre- and post-translocational ribosomes revealed by electron cryomicroscopy. of special interest Cell. 88:1997;19-28 tRNAs positioned in the P- and E-site of post-translocational ribosomes and at the A- and P-site of pretranslocational ribosomes were visualized at 20 Å resolution. In the paper by Agrawal et al. 1996 [50] all three A-, P-, and E- sites were co-occupied by tRNAs. The significant discrepancies between the proposed models in Agrawal et al. 1996 [50] and this paper may be a consequence of the non-physiological simultaneous binding of three tRNAs in Agrawal et al. [50].
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(1997)
Cell
, vol.88
, pp. 19-28
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Stark, H.1
Orlova, E.V.2
Rinke-Appel, J.3
Junke, N.4
Mueller, F.5
Rodnina, M.6
Wintermeyer, W.7
Brimacombe, R.8
Van Heel, M.9
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52
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0031581825
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Direct localization of the tRNAs within the elongating ribosome by means of neutron scattering (proto-spin contrast-variation)
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of special interest. Neutron scattering has mostly been used for measuring distances between proteins in the ribosome. In this paper a novel technique is employed to measure the movement of the tRNA - mRNA complex within the ribosomal model.
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Wadzack J, Burkhardt N, Junemann R, Diedrich G, Nierhaus KH, Frank J, Penczek P, Meerwinck W, Schmitt M, Willumeit R, Stuhrmann HB. Direct localization of the tRNAs within the elongating ribosome by means of neutron scattering (proto-spin contrast-variation). of special interest J Mol Biol. 266:1997;343-356 Neutron scattering has mostly been used for measuring distances between proteins in the ribosome. In this paper a novel technique is employed to measure the movement of the tRNA - mRNA complex within the ribosomal model.
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(1997)
J Mol Biol
, vol.266
, pp. 343-356
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-
Wadzack, J.1
Burkhardt, N.2
Junemann, R.3
Diedrich, G.4
Nierhaus, K.H.5
Frank, J.6
Penczek, P.7
Meerwinck, W.8
Schmitt, M.9
Willumeit, R.10
Stuhrmann, H.B.11
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53
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0031010235
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Analysis of the tertiary structure of the ribonuclease P ribozyme - Substrate complex by site-specific photoaffinity crosslinking
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of special interest. A three-dimensional model for RNase P RNA is proposed based on structural constraints obtained by crosslinks. The photo-reactive groups were introduced using the circular permutation method. Circular permutated RNA was transcribed from a genetically engineered template which is initiated at a selected internal site to produce an RNA with joint native 5′- and 3′-ends. The photo-reactive labels were attached cotranscriptionally or by ligation at the termini. Importantly, it was demonstrated that the crosslinked RNA species retained functionality.
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Harris ME, Kazantsev AV, Chen J-L, Pace NR. Analysis of the tertiary structure of the ribonuclease P ribozyme - substrate complex by site-specific photoaffinity crosslinking. of special interest RNA. 3:1997;561-576 A three-dimensional model for RNase P RNA is proposed based on structural constraints obtained by crosslinks. The photo-reactive groups were introduced using the circular permutation method. Circular permutated RNA was transcribed from a genetically engineered template which is initiated at a selected internal site to produce an RNA with joint native 5′- and 3′-ends. The photo-reactive labels were attached cotranscriptionally or by ligation at the termini. Importantly, it was demonstrated that the crosslinked RNA species retained functionality.
-
(1997)
RNA
, vol.3
, pp. 561-576
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Harris, M.E.1
Kazantsev, A.V.2
Chen J-L3
Pace, N.R.4
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54
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0030801742
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A new model for the three-dimensional folding of Escherichia coli 16 S ribosomal RNA. Fitting the RNA to a 3D electron microscopic map at 20 Å
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Mueller F, Brimacombe R. A new model for the three-dimensional folding of Escherichia coli 16 S ribosomal RNA. Fitting the RNA to a 3D electron microscopic map at 20 Å J Mol Biol. 271:1997;524-544.
-
(1997)
J Mol Biol
, vol.271
, pp. 524-544
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Mueller, F.1
Brimacombe, R.2
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55
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0030871279
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A new technique for the characterization of long-range tertiary contacts in large RNA molecules: Insertion of a photolabel at a selected position in 16S rRNA within the Escherichia coli ribosome
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of special interest. Description of the internal gap method where RNase H in the presence of a complementary chimeric oligonucleotide is used to cleave the RNA at a specified site. A photo-reactive label was attached at the termini using T4 RNA ligase.
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Baranov PV, Dokudovskaya SS, Oretskaya TS, Dontsova OA, Bogdanov AA, Brimacombe R. A new technique for the characterization of long-range tertiary contacts in large RNA molecules: insertion of a photolabel at a selected position in 16S rRNA within the Escherichia coli ribosome. of special interest Nucleic Acids Res. 25:1997;2266-2273 Description of the internal gap method where RNase H in the presence of a complementary chimeric oligonucleotide is used to cleave the RNA at a specified site. A photo-reactive label was attached at the termini using T4 RNA ligase.
-
(1997)
Nucleic Acids Res
, vol.25
, pp. 2266-2273
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-
Baranov, P.V.1
Dokudovskaya, S.S.2
Oretskaya, T.S.3
Dontsova, O.A.4
Bogdanov, A.A.5
Brimacombe, R.6
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56
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0026680843
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Site-specific modification of pre-mRNA: The 2′-hydroxyl groups at the splice sites
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Moore MJ, Sharp PA. Site-specific modification of pre-mRNA: the 2′-hydroxyl groups at the splice sites. Science. 256:1992;992-997.
-
(1992)
Science
, vol.256
, pp. 992-997
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Moore, M.J.1
Sharp, P.A.2
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57
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0030918785
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Site-specific crosslinking of mammalian U11 and u6atac to the 5′ splice site of an AT-AC intron
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of special interest. 365 nm UV irradiation of RNA with site specifically incorporated 4-thiouridine was used to identify RNAs associated with the 5′-splice site of AT-AC introns. 4-thiouridine has been used widely as a 'zero length' photo-reactive label.
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Yu YT, Steitz JA. Site-specific crosslinking of mammalian U11 and u6atac to the 5′ splice site of an AT-AC intron. of special interest Proc Natl Acad Sci USA. 94:1997;6030-6035 365 nm UV irradiation of RNA with site specifically incorporated 4-thiouridine was used to identify RNAs associated with the 5′-splice site of AT-AC introns. 4-thiouridine has been used widely as a 'zero length' photo-reactive label.
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(1997)
Proc Natl Acad Sci USA
, vol.94
, pp. 6030-6035
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Yu, Y.T.1
Steitz, J.A.2
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58
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0030020170
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Mapping the rRNA neighborhood of the acceptor end of tRNA in the ribosome
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of outstanding interest. This study demonstrates a novel approach to identify regions of an RNA molecule located in the vicinity of functional sites. Hydroxyl radicals generated in the vicinity of an Fe(II) metal ion tethered to the 5′- end of a tRNA, cleave the 23 S rRNA in the neighborhood of the tRNA bound to the ribosome. This method was used to map regions close to the A, P or E sites of the 23 S rRNA.
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Joseph S, Noller HF. Mapping the rRNA neighborhood of the acceptor end of tRNA in the ribosome. of outstanding interest EMBO J. 15:1996;910-916 This study demonstrates a novel approach to identify regions of an RNA molecule located in the vicinity of functional sites. Hydroxyl radicals generated in the vicinity of an Fe(II) metal ion tethered to the 5′- end of a tRNA, cleave the 23 S rRNA in the neighborhood of the tRNA bound to the ribosome. This method was used to map regions close to the A, P or E sites of the 23 S rRNA.
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(1996)
EMBO J
, vol.15
, pp. 910-916
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Joseph, S.1
Noller, H.F.2
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59
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0029896213
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Site-directed hydroxyl radical probing of the rRNA neighborhood of ribosomal protein S5
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of special interest. Fe(II) tethered to different position the ribosomal protein S5 was used to generate cleavage patterns on 16 S rRNA. Different locations were selected on the surface of S5 based on the X-ray structure and mutagenized to unique cysteine residues. These residues were used as targets to derivative with 1-(p-bromoacetamidobenzyl)-EDTA (BABE). The cleavage pattern was used to constrain the folding of 16 S rRNA and model S5 on the 16 S rRNA structure.
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Heilek GM, Noller HF. Site-directed hydroxyl radical probing of the rRNA neighborhood of ribosomal protein S5. of special interest Science. 272:1996;1659-1662 Fe(II) tethered to different position the ribosomal protein S5 was used to generate cleavage patterns on 16 S rRNA. Different locations were selected on the surface of S5 based on the X-ray structure and mutagenized to unique cysteine residues. These residues were used as targets to derivative with 1-(p-bromoacetamidobenzyl)-EDTA (BABE). The cleavage pattern was used to constrain the folding of 16 S rRNA and model S5 on the 16 S rRNA structure.
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(1996)
Science
, vol.272
, pp. 1659-1662
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Heilek, G.M.1
Noller, H.F.2
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60
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0029348087
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Probing RNA tertiary structure: Interhelical crosslinking of the hammerhead ribozyme
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Sigurdsson ST, Tuschl T, Eckstein F. Probing RNA tertiary structure: interhelical crosslinking of the hammerhead ribozyme. RNA. 1:1995;575-583.
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(1995)
RNA
, vol.1
, pp. 575-583
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Sigurdsson, S.T.1
Tuschl, T.2
Eckstein, F.3
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61
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0030805544
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Dynamics of thermal motion within a large catalytic RNA investigated by cross-linking with thioldisulfide interchange
-
of outstanding interest. The first direct demonstration of large thermal movements in RNA. Alkylphenyl disulfide and alkyl thiol were attached to a chemically incorporated amino group at the 2′-positions of specified nucleotides. The advantage of these disulfide crosslinking is that the crosslink can be generated under physiological conditions.
-
Cohen SB, Cech TR. Dynamics of thermal motion within a large catalytic RNA investigated by cross-linking with thioldisulfide interchange. of outstanding interest J Am Chem Soc. 119:1997;6259-6268 The first direct demonstration of large thermal movements in RNA. Alkylphenyl disulfide and alkyl thiol were attached to a chemically incorporated amino group at the 2′-positions of specified nucleotides. The advantage of these disulfide crosslinking is that the crosslink can be generated under physiological conditions.
-
(1997)
J Am Chem Soc
, vol.119
, pp. 6259-6268
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Cohen, S.B.1
Cech, T.R.2
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62
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0030833215
-
Metal ion catalysis during splicing of premessenger RNA
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2+ rescue assay to demonstrate that the two steps in pre-mRNA splicing proceed by different catalytic mechanisms. Pre-mRNA with a 3′-sulfur substitution at the 5′-splice was used to demonstrate that the spliceosome acts as an metalloenzyme in the first reaction step. A 3′-sulfur substitution at the 3′-splice site, however, provides no evidence for metal ion interaction at the second reaction step.
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2+ rescue assay to demonstrate that the two steps in pre-mRNA splicing proceed by different catalytic mechanisms. Pre-mRNA with a 3′-sulfur substitution at the 5′-splice was used to demonstrate that the spliceosome acts as an metalloenzyme in the first reaction step. A 3′-sulfur substitution at the 3′-splice site, however, provides no evidence for metal ion interaction at the second reaction step.
-
(1997)
Nature
, vol.388
, pp. 801-805
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-
Sontheimer, E.J.1
Sun, S.2
Piccirilli, J.A.3
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63
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0030800470
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A second catalytic metal ion in group I ribozyme
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of special interest. The same procedure described by Sontheimier et al. 1997 [62] was used to study the self-splicing of group I intron from Tetrahymena. Contrary to pre-mRNA splicing there is evidence that both steps in self-splicing of group I introns require metal ion interaction.
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Weinstein LB, Jones BC, Cosstick R, Cech TR. A second catalytic metal ion in group I ribozyme. of special interest Nature. 388:1997;805-808 The same procedure described by Sontheimier et al. 1997 [62] was used to study the self-splicing of group I intron from Tetrahymena. Contrary to pre-mRNA splicing there is evidence that both steps in self-splicing of group I introns require metal ion interaction.
-
(1997)
Nature
, vol.388
, pp. 805-808
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Weinstein, L.B.1
Jones, B.C.2
Cosstick, R.3
Cech, T.R.4
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64
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0030965811
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Defining the chemical groups essential for Tetrahymena group I intron function by nucleotide analog interference mapping
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of special interest. This paper reports the use of a nucleotide analogue interference mapping assay where random incorporation of 5′-O-(1-thio)inosine monophosphate (IMPaS) in RNA provides an efficient method for evaluating the contribution of N2 exocyclic amines of G. The concomitant incorporation of the phosphothioate with the base modification provides a general applicable method to test the role of modified nucleotides in RNA folding or function. The selective sensitivity of phosphothioates to iodine cleavage provides an easy identification of the modified nucleotide.
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Strobel SA, Shetty K. Defining the chemical groups essential for Tetrahymena group I intron function by nucleotide analog interference mapping. of special interest Proc Natl Acad Sci USA. 94:1997;2903-2908 This paper reports the use of a nucleotide analogue interference mapping assay where random incorporation of 5′-O-(1-thio)inosine monophosphate (IMPaS) in RNA provides an efficient method for evaluating the contribution of N2 exocyclic amines of G. The concomitant incorporation of the phosphothioate with the base modification provides a general applicable method to test the role of modified nucleotides in RNA folding or function. The selective sensitivity of phosphothioates to iodine cleavage provides an easy identification of the modified nucleotide.
-
(1997)
Proc Natl Acad Sci USA
, vol.94
, pp. 2903-2908
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-
Strobel, S.A.1
Shetty, K.2
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65
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0027295270
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Modification interference approach to detect ribose moieties important for the optimal activity of a ribozyme
-
Gaur RK, Krupp G. Modification interference approach to detect ribose moieties important for the optimal activity of a ribozyme. Nucleic Acids Res. 21:1993;21-26.
-
(1993)
Nucleic Acids Res
, vol.21
, pp. 21-26
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Gaur, R.K.1
Krupp, G.2
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66
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0029904022
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Kinetic pathway for folding of the Tetrahymena ribozyme revealed by three UV-inducible crosslinks
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Downs WD, Cech TR. Kinetic pathway for folding of the Tetrahymena ribozyme revealed by three UV-inducible crosslinks. RNA. 2:1996;718-732.
-
(1996)
RNA
, vol.2
, pp. 718-732
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-
Downs, W.D.1
Cech, T.R.2
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67
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0027991626
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Kinetic intermediates in RNA folding
-
Zarrinkar PP, Williamson JR. Kinetic intermediates in RNA folding. Science. 265:1994;918-924.
-
(1994)
Science
, vol.265
, pp. 918-924
-
-
Zarrinkar, P.P.1
Williamson, J.R.2
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