-
1
-
-
77952883423
-
Exploring RNA structure by integrative molecular modelling
-
Masquida B, Beckert B, Jossinet F (2010) Exploring RNA structure by integrative molecular modelling. New Biotechnol 27(3):170-183.
-
(2010)
New Biotechnol
, vol.27
, Issue.3
, pp. 170-183
-
-
Masquida, B.1
Beckert, B.2
Jossinet, F.3
-
2
-
-
34249278470
-
Control of alternative RNA splicing and gene expression by eukaryotic riboswitches
-
DOI 10.1038/nature05769, PII NATURE05769
-
Cheah MT, Wachter A, Sudarsan N, Breaker RR (2007) Control of alternative RNA splicing and gene expression by eukaryotic riboswitches. Nature 447(7143):497-500. (Pubitemid 46816734)
-
(2007)
Nature
, vol.447
, Issue.7143
, pp. 497-500
-
-
Cheah, M.T.1
Wachter, A.2
Sudarsan, N.3
Breaker, R.R.4
-
3
-
-
77955630859
-
An allosteric self-splicing ribozyme triggered by a bacterial second messenger
-
Lee ER, Baker JL, Weinberg Z, Sudarsan N, Breaker RR (2010) An allosteric self-splicing ribozyme triggered by a bacterial second messenger. Science 329(5993):845-848.
-
(2010)
Science
, vol.329
, Issue.5993
, pp. 845-848
-
-
Lee, E.R.1
Baker, J.L.2
Weinberg, Z.3
Sudarsan, N.4
Breaker, R.R.5
-
4
-
-
39449121705
-
The GIR1 branching ribozyme
-
eds Lilley DMJ, Eckstein F (Royal Society of Chemistry, London)
-
Nielsen H, Beckert B, Masquida B, Johansen SD (2008) The GIR1 branching ribozyme. Ribozymes and RNA catalysis, eds Lilley DMJ, Eckstein F (Royal Society of Chemistry, London), pp 229-252.
-
(2008)
Ribozymes and RNA Catalysis
, pp. 229-252
-
-
Nielsen, H.1
Beckert, B.2
Masquida, B.3
Johansen, S.D.4
-
5
-
-
24644492436
-
Molecular biology: An mRNA is capped by a 2′,5′ lariat catalyzed by a group I-like ribozyme
-
DOI 10.1126/science.1113645
-
Nielsen H, Westhof E, Johansen S (2005) An mRNA is capped by a 2′, 5′ lariat catalyzed by a group I-like ribozyme. Science 309(5740):1584-1587. (Pubitemid 41266488)
-
(2005)
Science
, vol.309
, Issue.5740
, pp. 1584-1587
-
-
Nielsen, H.1
Westhof, E.2
Johansen, S.3
-
6
-
-
34250661376
-
Expression of protein-coding genes embedded in ribosomal DNA
-
DOI 10.1515/BC.2007.089
-
Johansen SD, Haugen P, Nielsen H (2007) Expression of protein-coding genes embedded in ribosomal DNA. Biol Chem 388(7):679-686. (Pubitemid 46934172)
-
(2007)
Biological Chemistry
, vol.388
, Issue.7
, pp. 679-686
-
-
Johansen, S.D.1
Haugen, P.2
Nielsen, H.3
-
7
-
-
0033557745
-
In vivo expression of the nucleolar group I intron-encoded I-DirI homing endonuclease involves the removal of a spliceosomal intron
-
DOI 10.1093/emboj/18.4.1003
-
Vader A, Nielsen H, Johansen S (1999) In vivo expression of the nucleolar group I intron-encoded I-dirI homing endonuclease involves the removal of a spliceosomal intron. EMBO J 18(4):1003-1013. (Pubitemid 29082279)
-
(1999)
EMBO Journal
, vol.18
, Issue.4
, pp. 1003-1013
-
-
Vader, A.1
Nielsen, H.2
Johansen, S.3
-
8
-
-
18744363869
-
The group I-like ribozyme DiGIR1 mediates alternative processing of pre-rRNA transcripts in Didymium iridis
-
DOI 10.1046/j.1432-1033.2002.03283.x
-
Vader A, Johansen S, Nielsen H (2002) The group I-like ribozyme DiGIR1 mediates alternative processing of pre-rRNA transcripts in Didymium iridis. Eur J Biochem 269(23):5804-5812. (Pubitemid 35425578)
-
(2002)
European Journal of Biochemistry
, vol.269
, Issue.23
, pp. 5804-5812
-
-
Vader, A.1
Johansen, S.2
Nielsen, H.3
-
9
-
-
0344442429
-
The ability to form full-length intron RNA circles is a general property of nuclear group I introns
-
DOI 10.1261/rna.5290903
-
Nielsen H, et al. (2003) The ability to form full-length intron RNA circles is a general property of nuclear group I introns. RNA 9(12):1464-1475. (Pubitemid 37463473)
-
(2003)
RNA
, vol.9
, Issue.12
, pp. 1464-1475
-
-
Nielsen, H.1
Fiskaa, T.2
Birgisdottir, A.B.3
Haugen, P.4
Einvik, C.5
Johansen, S.6
-
10
-
-
0028208494
-
An intron in the nuclear ribosomal DNA of Didymium iridis codes for a group I ribozyme and a novel ribozyme that cooperate in self-splicing
-
DOI 10.1016/0092-8674(94)90511-8
-
Johansen S, Vogt VM (1994) An intron in the nuclear ribosomal DNA of Didymium iridis codes for a group I ribozyme and a novel ribozyme that cooperate in self-splicing. Cell 76(4):725-734. (Pubitemid 24070656)
-
(1994)
Cell
, vol.76
, Issue.4
, pp. 725-734
-
-
Johansen, S.1
Vogt, V.M.2
-
11
-
-
0036761518
-
DiGIR1 and NaGIR1: Naturally occurring group I-like ribozymes with unique core organization and evolved biological role
-
DOI 10.1016/S0300-9084(02)01443-8, PII S0300908402014438
-
Johansen S, Einvik C, Nielsen H (2002) DiGIR1 and NaGIR1: Naturally occurring group I-like ribozymes with unique core organization and evolved biological role. Biochimie 84(9):905-912. (Pubitemid 35422917)
-
(2002)
Biochimie
, vol.84
, Issue.9
, pp. 905-912
-
-
Johansen, S.1
Einvik, C.2
Nielsen, H.3
-
12
-
-
39449136567
-
Molecular modelling of the GIR1 branching ribozyme gives new insight into evolution of structurally related ribozymes
-
DOI 10.1038/emboj.2008.4, PII EMBOJ20084
-
Beckert B, et al. (2008) Molecular modelling of the GIR1 branching ribozyme gives new insight into evolution of structurally related ribozymes. EMBO J 27(4):667-678. (Pubitemid 351273126)
-
(2008)
EMBO Journal
, vol.27
, Issue.4
, pp. 667-678
-
-
Beckert, B.1
Nielsen, H.2
Einvik, C.3
Johansen, S.D.4
Westhof, E.5
Masquida, B.6
-
13
-
-
65249177277
-
A conformational switch in the DiGIR1 ribozyme involved in release and folding of the downstream I-DirI mRNA
-
Nielsen H, Einvik C, Lentz TE, Hedegaard MM, Johansen SD (2009) A conformational switch in the DiGIR1 ribozyme involved in release and folding of the downstream I-DirI mRNA. RNA 15(5):958-967.
-
(2009)
RNA
, vol.15
, Issue.5
, pp. 958-967
-
-
Nielsen, H.1
Einvik, C.2
Lentz, T.E.3
Hedegaard, M.M.4
Johansen, S.D.5
-
14
-
-
84934436067
-
Cis-Acting 5′ hammerhead ribozyme optimization for in vitro transcription of highly structured RNAs
-
Meyer M, Masquida B (2014) cis-Acting 5′ hammerhead ribozyme optimization for in vitro transcription of highly structured RNAs. Methods Mol Biol 1086:21-40.
-
(2014)
Methods Mol Biol
, vol.1086
, pp. 21-40
-
-
Meyer, M.1
Masquida, B.2
-
15
-
-
0029020003
-
Crystallization of RNA-protein complexes. I. Methods for the large-scale preparation of RNA suitable for crystallo-graphic studies
-
Price SR, Ito N, Oubridge C, Avis JM, Nagai K (1995) Crystallization of RNA-protein complexes. I. Methods for the large-scale preparation of RNA suitable for crystallo-graphic studies. J Mol Biol 249(2):398-408.
-
(1995)
J Mol Biol
, vol.249
, Issue.2
, pp. 398-408
-
-
Price, S.R.1
Ito, N.2
Oubridge, C.3
Avis, J.M.4
Nagai, K.5
-
16
-
-
0031978817
-
Group I-like ribozymes with a novel core organization perform obligate sequential hydrolytic cleavages at two processing sites
-
DOI 10.1017/S1355838298971758
-
Einvik C, Nielsen H, Westhof E, Michel F, Johansen S (1998) Group I-like ribozymes with a novel core organization perform obligate sequential hydrolytic cleavages at two processing sites. RNA 4(5):530-541. (Pubitemid 28225421)
-
(1998)
RNA
, vol.4
, Issue.5
, pp. 530-541
-
-
Einvik, C.1
Nielsen, H.2
Westhof, E.3
Michel, F.4
Johansen, S.5
-
17
-
-
81255176950
-
A natural fast-cleaving branching ribozyme from the amoeboflagellate Naegleria pringsheimi
-
Tang Y, Nielsen H, Birgisdottir AB, Johansen S (2011) A natural fast-cleaving branching ribozyme from the amoeboflagellate Naegleria pringsheimi. RNA Biol 8(6): 997-1004.
-
(2011)
RNA Biol
, vol.8
, Issue.6
, pp. 997-1004
-
-
Tang, Y.1
Nielsen, H.2
Birgisdottir, A.B.3
Johansen, S.4
-
18
-
-
0035942248
-
RNA tertiary interactions in the large ribosomal subunit: The A-minor motif
-
DOI 10.1073/pnas.081082398
-
Nissen P, Ippolito JA, Ban N, Moore PB, Steitz TA (2001) RNA tertiary interactions in the large ribosomal subunit: The A-minor motif. Proc Natl Acad Sci USA 98(9): 4899-4903. (Pubitemid 32397054)
-
(2001)
Proceedings of the National Academy of Sciences of the United States of America
, vol.98
, Issue.9
, pp. 4899-4903
-
-
Nissen, P.1
Ippolito, J.A.2
Ban, N.3
Moore, P.B.4
Steitz, T.A.5
-
19
-
-
0032505999
-
Crystal structure of the ribosomal RNA domain essential for binding elongation factors
-
DOI 10.1073/pnas.95.23.13436
-
Correll CC, et al. (1998) Crystal structure of the ribosomal RNA domain essential for binding elongation factors. Proc Natl Acad Sci USA 95(23):13436-13441. (Pubitemid 28522990)
-
(1998)
Proceedings of the National Academy of Sciences of the United States of America
, vol.95
, Issue.23
, pp. 13436-13441
-
-
Correll, C.C.1
Munishkin, A.2
Chan, Y.-L.3
Ren, Z.4
Wool, I.G.5
Steitz, T.A.6
-
20
-
-
3042848954
-
Crystal structure of a self-splicing group I intron with both exons
-
DOI 10.1038/nature02642
-
Adams PL, Stahley MR, Kosek AB, Wang J, Strobel SA (2004) Crystal structure of a self-splicing group I intron with both exons. Nature 430(6995):45-50. (Pubitemid 38915218)
-
(2004)
Nature
, vol.430
, Issue.6995
, pp. 45-50
-
-
Adams, P.L.1
Stahley, M.R.2
Kosek, A.B.3
Wang, J.4
Strobel, S.A.5
-
22
-
-
0033598755
-
Recurrent invasion and extinction of a selfish gene
-
Goddard MR, Burt A (1999) Recurrent invasion and extinction of a selfish gene. Proc Natl Acad Sci USA 96(24):13880-13885.
-
(1999)
Proc Natl Acad Sci USA
, vol.96
, Issue.24
, pp. 13880-13885
-
-
Goddard, M.R.1
Burt, A.2
-
23
-
-
84875588195
-
The mtDNA rns gene landscape in the Ophiostomatales and other fungal taxa: Twintrons, introns, and intron-encoded proteins
-
Hafez M, et al. (2013) The mtDNA rns gene landscape in the Ophiostomatales and other fungal taxa: Twintrons, introns, and intron-encoded proteins. Fungal Genet Biol 53:71-83.
-
(2013)
Fungal Genet Biol
, vol.53
, pp. 71-83
-
-
Hafez, M.1
-
24
-
-
79958829880
-
The 2′-OH group of the peptidyl-tRNA stabilizes an active conformation of the ribosomal PTC
-
Zaher HS, Shaw JJ, Strobel SA, Green R (2011) The 2′-OH group of the peptidyl-tRNA stabilizes an active conformation of the ribosomal PTC. EMBO J 30(12):2445-2453.
-
(2011)
EMBO J
, vol.30
, Issue.12
, pp. 2445-2453
-
-
Zaher, H.S.1
Shaw, J.J.2
Strobel, S.A.3
Green, R.4
-
25
-
-
78651267394
-
Improved deoxyribozymes for synthesis of co-valently branched DNA and RNA
-
Lee CS, Mui TP, Silverman SK (2011) Improved deoxyribozymes for synthesis of co-valently branched DNA and RNA. Nucleic Acids Res 39(1):269-279.
-
(2011)
Nucleic Acids Res
, vol.39
, Issue.1
, pp. 269-279
-
-
Lee, C.S.1
Mui, T.P.2
Silverman, S.K.3
-
26
-
-
84875425784
-
Structural principles of RNA catalysis in a 2′-5′ lariat-forming ribozyme
-
Carlomagno T, et al. (2013) Structural principles of RNA catalysis in a 2′-5′ lariat-forming ribozyme. J Am Chem Soc 135(11):4403-4411.
-
(2013)
J Am Chem Soc
, vol.135
, Issue.11
, pp. 4403-4411
-
-
Carlomagno, T.1
-
27
-
-
84887115772
-
RNA structure analysis of human spliceosomes reveals a compact 3D arrangement of snRNAs at the catalytic core
-
Anokhina M, et al. (2013) RNA structure analysis of human spliceosomes reveals a compact 3D arrangement of snRNAs at the catalytic core. EMBO J 32(21):2804-2818.
-
(2013)
EMBO J
, vol.32
, Issue.21
, pp. 2804-2818
-
-
Anokhina, M.1
-
28
-
-
0022409013
-
Intermolecular exon ligation of the rRNA precursor of tetrahymena: Oligonucleotides can function as 5' exons
-
Inoue T, Sullivan FX, Cech TR (1985) Intermolecular exon ligation of the rRNA precursor of Tetrahymena: Oligonucleotides can function as 5′ exons. Cell 43(2 Pt 1): 431-437. (Pubitemid 16213268)
-
(1985)
Cell
, vol.43
, Issue.2
, pp. 431-437
-
-
Inoue, T.1
Sullivan, F.X.2
Cech, T.R.3
-
29
-
-
58249123666
-
A natural ribozyme with 3′, 5′ RNA ligase activity
-
Vicens Q, Cech TR (2009) A natural ribozyme with 3′, 5′ RNA ligase activity. Nat Chem Biol 5(2):97-99.
-
(2009)
Nat Chem Biol
, vol.5
, Issue.2
, pp. 97-99
-
-
Vicens, Q.1
Cech, T.R.2
-
30
-
-
39149143346
-
Mechanisms of covalent self-assembly of the Azoarcus ribozyme from four fragment oligonucleotides
-
DOI 10.1093/nar/gkm1055
-
Draper WE, Hayden EJ, Lehman N (2008) Mechanisms of covalent self-assembly of the Azoarcus ribozyme from four fragment oligonucleotides. Nucleic Acids Res 36(2): 520-531. (Pubitemid 351250443)
-
(2008)
Nucleic Acids Research
, vol.36
, Issue.2
, pp. 520-531
-
-
Draper, W.E.1
Hayden, E.J.2
Lehman, N.3
-
31
-
-
84868368844
-
Spontaneous network formation among cooperative RNA replicators
-
Vaidya N, et al. (2012) Spontaneous network formation among cooperative RNA replicators. Nature 491(7422):72-77.
-
(2012)
Nature
, vol.491
, Issue.7422
, pp. 72-77
-
-
Vaidya, N.1
-
32
-
-
9344232753
-
Crystal structure of a group I intron splicing intermediate
-
DOI 10.1261/rna.7140504
-
Adams PL, et al. (2004) Crystal structure of a group I intron splicing intermediate. RNA 10(12):1867-1887. (Pubitemid 39557825)
-
(2004)
RNA
, vol.10
, Issue.12
, pp. 1867-1887
-
-
Adams, P.L.1
Stahley, M.R.2
Gill, M.L.3
Kosek, A.B.4
Wang, J.5
Strobel, S.A.6
-
33
-
-
11444263264
-
Crystal structure of a phage Twort group I ribozyme-product complex
-
DOI 10.1038/nsmb868
-
Golden BL, Kim H, Chase E (2005) Crystal structure of a phage Twort group I ribo-zyme-product complex. Nat Struct Mol Biol 12(1):82-89. (Pubitemid 40082921)
-
(2005)
Nature Structural and Molecular Biology
, vol.12
, Issue.1
, pp. 82-89
-
-
Golden, B.L.1
Kim, H.2
Chase, E.3
-
34
-
-
8644229237
-
Structure of the tetrahymena ribozyme: Base triple sandwich and metal ion at the active site
-
DOI 10.1016/j.molcel.2004.10.003, PII S1097276504005921
-
Guo F, Gooding AR, Cech TR (2004) Structure of the Tetrahymena ribozyme: Base triple sandwich and metal ion at the active site. Mol Cell 16(3):351-362. (Pubitemid 39504790)
-
(2004)
Molecular Cell
, vol.16
, Issue.3
, pp. 351-362
-
-
Guo, F.1
Gooding, A.R.2
Cech, T.R.3
-
35
-
-
41749109563
-
Crystal structure of a self-spliced group II intron
-
DOI 10.1126/science.1153803
-
Toor N, Keating KS, Taylor SD, Pyle AM (2008) Crystal structure of a self-spliced group II intron. Science 320(5872):77-82. (Pubitemid 351490756)
-
(2008)
Science
, vol.320
, Issue.5872
, pp. 77-82
-
-
Toor, N.1
Keating, K.S.2
Taylor, S.D.3
Pyle, A.M.4
-
36
-
-
78650175123
-
Structure of a bacterial ribonuclease P holoenzyme in complex with tRNA
-
Reiter NJ, et al. (2010) Structure of a bacterial ribonuclease P holoenzyme in complex with tRNA. Nature 468(7325):784-789.
-
(2010)
Nature
, vol.468
, Issue.7325
, pp. 784-789
-
-
Reiter, N.J.1
-
37
-
-
0031455374
-
Substrate recognition by the leucyl/phenylalanyl-tRNA-protein transferase. Conservation within the enzyme family and localization to the trypsin-resistant domain
-
DOI 10.1074/jbc.272.52.33009
-
Ichetovkin IE, Abramochkin G, Shrader TE (1997) Substrate recognition by the leucyl/phenylalanyl-tRNA-protein transferase. Conservation within the enzyme family and localization to the trypsin-resistant domain. J Biol Chem 272(52):33009-33014. (Pubitemid 28023640)
-
(1997)
Journal of Biological Chemistry
, vol.272
, Issue.52
, pp. 33009-33014
-
-
Ichetovkin, I.E.1
Abramochkin, G.2
Shrader, T.E.3
-
39
-
-
37549039510
-
A short history of SHELX
-
Sheldrick GM (2008) A short history of SHELX. Acta Crystallogr A 64(Pt 1):112-122.
-
(2008)
Acta Crystallogr A
, vol.64
, Issue.PART 1
, pp. 112-122
-
-
Sheldrick, G.M.1
-
41
-
-
76449098262
-
PHENIX: A comprehensive Python-based system for macro-molecular structure solution
-
Adams PD, et al. (2010) PHENIX: A comprehensive Python-based system for macro-molecular structure solution. Acta Crystallogr D Biol Crystallogr 66(Pt 2):213-221.
-
(2010)
Acta Crystallogr D Biol Crystallogr
, vol.66
, Issue.PART 2
, pp. 213-221
-
-
Adams, P.D.1
-
42
-
-
84858642798
-
-
Global Phasing Ltd, Cambridge, U.K.), Version 2.11.5
-
Bricogne G, et al. (2011) BUSTER (Global Phasing Ltd, Cambridge, U.K.), Version 2.11.5.
-
(2011)
BUSTER
-
-
Bricogne, G.1
-
44
-
-
0030760922
-
Naegleria nucleolar introns contain two group I ribozymes with different functions in RNA splicing and processing
-
Einvik C, Decatur WA, Embley TM, Vogt VM, Johansen S (1997) Naegleria nucleolar introns contain two group I ribozymes with different functions in RNA splicing and processing. RNA 3(7):710-720. (Pubitemid 27291116)
-
(1997)
RNA
, vol.3
, Issue.7
, pp. 710-720
-
-
Einvik, C.1
Decatur, W.A.2
Embley, T.M.3
Vogt, V.M.4
Johansen, S.5
-
45
-
-
0031731440
-
In vitro selection of the Naegleria GIR1 ribozyme identifies three base changes that dramatically improve activity
-
DOI 10.1017/S1355838298981237
-
Jabri E, Cech TR (1998) In vitro selection of the Naegleria GIR1 ribozyme identifies three base changes that dramatically improve activity. RNA 4(12):1481-1492. (Pubitemid 28555211)
-
(1998)
RNA
, vol.4
, Issue.12
, pp. 1481-1492
-
-
Jabri, E.1
Cech, T.R.2
-
46
-
-
0035010211
-
Geometric nomenclature and classification of RNA base pairs
-
DOI 10.1017/S1355838201002515
-
Leontis NB, Westhof E (2001) Geometric nomenclature and classification of RNA base pairs. RNA 7(4):499-512. (Pubitemid 32416808)
-
(2001)
RNA
, vol.7
, Issue.4
, pp. 499-512
-
-
Leontis, N.B.1
Westhof, E.2
|