-
1
-
-
0031588542
-
Remarkable morphological variability of a common RNA folding motif: The GNRA tetraloop-receptor interaction
-
Abramovitz, D. L., and A. M. Pyle. 1997. Remarkable morphological variability of a common RNA folding motif: the GNRA tetraloop-receptor interaction. J. Mol. Biol. 266:493-506.
-
(1997)
J. Mol. Biol
, vol.266
, pp. 493-506
-
-
Abramovitz, D.L.1
Pyle, A.M.2
-
2
-
-
0345733992
-
Differential modes of recognition in N peptide-boxB complexes
-
Austin, R. J., T. Xia, J. Ren, T. T. Takahashi, and R. W. Roberts. 2003. Differential modes of recognition in N peptide-boxB complexes. Biochemistry 42:14957-14967.
-
(2003)
Biochemistry
, vol.42
, pp. 14957-14967
-
-
Austin, R.J.1
Xia, T.2
Ren, J.3
Takahashi, T.T.4
Roberts, R.W.5
-
4
-
-
0242592065
-
Achieving specificity in selected and wild-type N peptide-RNA complexes: The importance of discrimination against noncognate RNA targets
-
Barrick, J. E., and R. W. Roberts. 2003. Achieving specificity in selected and wild-type N peptide-RNA complexes: the importance of discrimination against noncognate RNA targets. Biochemistry 42:12998-13007.
-
(2003)
Biochemistry
, vol.42
, pp. 12998-13007
-
-
Barrick, J.E.1
Roberts, R.W.2
-
5
-
-
0031916834
-
Solution structure of P22 transcriptional antitermination N peptide-boxB RNA complex
-
Cai, Z., A. Gorin, R. Frederick, X. Ye, W. Hu, A. Majumdar, A. Kettani, and D. J. Patel. 1998. Solution structure of P22 transcriptional antitermination N peptide-boxB RNA complex. Nat. Struct. Biol. 5:203-212.
-
(1998)
Nat. Struct. Biol
, vol.5
, pp. 203-212
-
-
Cai, Z.1
Gorin, A.2
Frederick, R.3
Ye, X.4
Hu, W.5
Majumdar, A.6
Kettani, A.7
Patel, D.J.8
-
6
-
-
0029007110
-
Bipartite function of a small RNA hairpin in transcription antitermination in bacteriophage lambda
-
Chattopadhyay, S., J. Garcia-Mena, J. DeVito, K. Wolska, and A. Das. 1995. Bipartite function of a small RNA hairpin in transcription antitermination in bacteriophage lambda. Proc. Natl. Acad. Sci. USA 92:4061-4065.
-
(1995)
Proc. Natl. Acad. Sci. USA
, vol.92
, pp. 4061-4065
-
-
Chattopadhyay, S.1
Garcia-Mena, J.2
DeVito, J.3
Wolska, K.4
Das, A.5
-
7
-
-
0038813728
-
Structural mimicry in the phage phi21 N peptide-boxB RNA complex
-
Cilley, C. D., and J. R. Williamson. 2003. Structural mimicry in the phage phi21 N peptide-boxB RNA complex. RNA 9:663-676.
-
(2003)
RNA
, vol.9
, pp. 663-676
-
-
Cilley, C.D.1
Williamson, J.R.2
-
8
-
-
0031024660
-
Analysis of bacteriophage N protein and peptide binding to boxB RNA using polyacrylamide gel coelectrophoresis (PACE)
-
Cilley, C. D., and J. R. Williamson. 1997. Analysis of bacteriophage N protein and peptide binding to boxB RNA using polyacrylamide gel coelectrophoresis (PACE). RNA 3:57-67.
-
(1997)
RNA
, vol.3
, pp. 57-67
-
-
Cilley, C.D.1
Williamson, J.R.2
-
9
-
-
18044396557
-
-
8a.Conant, C. R., M. R. Van Gilst, S. E. Weitzel, W. A. Rees, and P. H. von Hippel. 2005. A quantitative description of the binding states and in vitro function of antitermination protein N of bacteriophage lambda. J. Mol. Biol. 348:1039-1057.
-
8a.Conant, C. R., M. R. Van Gilst, S. E. Weitzel, W. A. Rees, and P. H. von Hippel. 2005. A quantitative description of the binding states and in vitro function of antitermination protein N of bacteriophage lambda. J. Mol. Biol. 348:1039-1057.
-
-
-
-
10
-
-
0037370110
-
Common and distinctive features of GNRA tetraloops based on a GUAA tetraloop structure at 1.4 Å resolution
-
Correll, C. C., and K. Swinger. 2003. Common and distinctive features of GNRA tetraloops based on a GUAA tetraloop structure at 1.4 Å resolution. RNA 9:355-363.
-
(2003)
RNA
, vol.9
, pp. 355-363
-
-
Correll, C.C.1
Swinger, K.2
-
11
-
-
0015185520
-
A minor Q-independent pathway for the expression of the late genes in bacteriophage lambda
-
Dambly, C., and M. Couturier. 1971. A minor Q-independent pathway for the expression of the late genes in bacteriophage lambda. Mol. Gen. Genet. 113:244-250.
-
(1971)
Mol. Gen. Genet
, vol.113
, pp. 244-250
-
-
Dambly, C.1
Couturier, M.2
-
12
-
-
0024394611
-
Effects of all single base substitutions in the loop of boxB on antitermination of transcription by bacteriophage lambda's N protein
-
Duelling, J. H., and N. C. Franklin. 1989. Effects of all single base substitutions in the loop of boxB on antitermination of transcription by bacteriophage lambda's N protein. Nucleic Acids Res. 17:5565-5577.
-
(1989)
Nucleic Acids Res
, vol.17
, pp. 5565-5577
-
-
Duelling, J.H.1
Franklin, N.C.2
-
13
-
-
0029954443
-
Structural features of a six-nucleotide RNA hairpin loop found in ribosomal RNA
-
Fountain, M. A., M. J. Serra, T. R. Krugh, and D. H. Turner. 1996. Structural features of a six-nucleotide RNA hairpin loop found in ribosomal RNA. Biochemistry 35:6539-6548.
-
(1996)
Biochemistry
, vol.35
, pp. 6539-6548
-
-
Fountain, M.A.1
Serra, M.J.2
Krugh, T.R.3
Turner, D.H.4
-
14
-
-
2442595009
-
Morphing molecular specificities between Arm-peptide and NUT-RNA in the antitermination complexes of bacteriophages lambda and P22
-
Franklin, N. C. 2004. Morphing molecular specificities between Arm-peptide and NUT-RNA in the antitermination complexes of bacteriophages lambda and P22. Mol. Microbiol. 52:815-822.
-
(2004)
Mol. Microbiol
, vol.52
, pp. 815-822
-
-
Franklin, N.C.1
-
15
-
-
0027288664
-
Clustered arginine residues of bacteriophage lambda N protein are essential to antitermination of transcription, but their locale cannot compensate for boxB loop defects
-
Franklin, N. C. 1993. Clustered arginine residues of bacteriophage lambda N protein are essential to antitermination of transcription, but their locale cannot compensate for boxB loop defects. J. Mol. Biol. 231:343-360.
-
(1993)
J. Mol. Biol
, vol.231
, pp. 343-360
-
-
Franklin, N.C.1
-
16
-
-
0024671716
-
Overexprcssion of N antitermination proteins of bacteriophages λ, 21, and P22: Loss of N protein specificity
-
Franklin, N. C., and J. H. Doelling. 1989. Overexprcssion of N antitermination proteins of bacteriophages λ, 21, and P22: loss of N protein specificity. J. Bacteriol. 171:2513-2522.
-
(1989)
J. Bacteriol
, vol.171
, pp. 2513-2522
-
-
Franklin, N.C.1
Doelling, J.H.2
-
17
-
-
0036600739
-
RNA-protein interactions
-
Hall, K. B. 2002. RNA-protein interactions. Curr. Opin. Struct. Biol. 12:283-288.
-
(2002)
Curr. Opin. Struct. Biol
, vol.12
, pp. 283-288
-
-
Hall, K.B.1
-
18
-
-
0029868515
-
Selection of RNA-binding peptides in vivo
-
Harada, K., S. S. Martin, and A. D. Frankel. 1996. Selection of RNA-binding peptides in vivo. Nature 380:175-179.
-
(1996)
Nature
, vol.380
, pp. 175-179
-
-
Harada, K.1
Martin, S.S.2
Frankel, A.D.3
-
19
-
-
0041832289
-
Evolutionary landscapes for the acquisition of new ligand recognition by RNA aptamers
-
Held, D. M., S. T. Greathouse, A. Agrawal, and D. H. Burke. 2003. Evolutionary landscapes for the acquisition of new ligand recognition by RNA aptamers. J. Mol. Evol. 57:299-308.
-
(2003)
J. Mol. Evol
, vol.57
, pp. 299-308
-
-
Held, D.M.1
Greathouse, S.T.2
Agrawal, A.3
Burke, D.H.4
-
20
-
-
0016679661
-
An early regulatory gene of Salmonella phage P22 analogous to gene N of coliphage lambda
-
Hilliker, S., and D. Botstein. 1975. An early regulatory gene of Salmonella phage P22 analogous to gene N of coliphage lambda. Virology 68:510-524.
-
(1975)
Virology
, vol.68
, pp. 510-524
-
-
Hilliker, S.1
Botstein, D.2
-
21
-
-
15444372483
-
The application of cluster analysis in the intercomparison of loop structures in RNA
-
Huang, H. C., U. Nagaswamy, and G. E. Fox. 2005. The application of cluster analysis in the intercomparison of loop structures in RNA. RNA 11:412-423.
-
(2005)
RNA
, vol.11
, pp. 412-423
-
-
Huang, H.C.1
Nagaswamy, U.2
Fox, G.E.3
-
22
-
-
0030030533
-
Smoothness within ruggedness: The role of neutrality in adaptation
-
Huynen, M. A., P. F. Stadler, and W. Fontana. 1996. Smoothness within ruggedness: the role of neutrality in adaptation. Proc. Natl. Acad. Sci. USA 93:397-401.
-
(1996)
Proc. Natl. Acad. Sci. USA
, vol.93
, pp. 397-401
-
-
Huynen, M.A.1
Stadler, P.F.2
Fontana, W.3
-
23
-
-
0037336430
-
Putative intermediary stages for the molecular evolution from a ribozyme to a catalytic RNP
-
Ikawa, Y., K. Tsuda, S. Matsumura, S. Atsumi, and T. Inoue. 2003. Putative intermediary stages for the molecular evolution from a ribozyme to a catalytic RNP. Nucleic Acids Res. 31:1488-1496.
-
(2003)
Nucleic Acids Res
, vol.31
, pp. 1488-1496
-
-
Ikawa, Y.1
Tsuda, K.2
Matsumura, S.3
Atsumi, S.4
Inoue, T.5
-
24
-
-
24044528558
-
Evolvability of the mode of peptide binding by an RNA
-
Iwazaki, T., X. Li, and K. Harada. 2005. Evolvability of the mode of peptide binding by an RNA. RNA 11:1364-1373.
-
(2005)
RNA
, vol.11
, pp. 1364-1373
-
-
Iwazaki, T.1
Li, X.2
Harada, K.3
-
25
-
-
25444481051
-
Low energy CD of RNA hairpin unveils a loop conformation required for lambda N antitermination activity
-
Johnson, N. P., W. A. Baase, and P. H. von Hippel. 2005. Low energy CD of RNA hairpin unveils a loop conformation required for lambda N antitermination activity. J. Biol. Chem. 280:32177-32183.
-
(2005)
J. Biol. Chem
, vol.280
, pp. 32177-32183
-
-
Johnson, N.P.1
Baase, W.A.2
von Hippel, P.H.3
-
26
-
-
0034716946
-
Genomic sequences of bacteriophages HK97 and HK022: Pervasive genetic mosaicism in the lambdoid bacteriophages
-
Juhala, R. J., M. E. Ford, R. L. Duda, A. Youlton, G. F. Hatfull, and R. W. Hendrix. 2000. Genomic sequences of bacteriophages HK97 and HK022: pervasive genetic mosaicism in the lambdoid bacteriophages. J. Mol. Biol. 299:27-51.
-
(2000)
J. Mol. Biol
, vol.299
, pp. 27-51
-
-
Juhala, R.J.1
Ford, M.E.2
Duda, R.L.3
Youlton, A.4
Hatfull, G.F.5
Hendrix, R.W.6
-
27
-
-
0025912824
-
Recent development of the neutral theory viewed from the Wrightian tradition of theoretical population genetics
-
Kimura, M. 1991. Recent development of the neutral theory viewed from the Wrightian tradition of theoretical population genetics. Proc. Natl. Acad. Sci. USA 88:5969-5973.
-
(1991)
Proc. Natl. Acad. Sci. USA
, vol.88
, pp. 5969-5973
-
-
Kimura, M.1
-
28
-
-
0035423087
-
The kink-turn: A new RNA secondary structure motif
-
Klein, D. J., T. M. Schmeing, P. B. Moore, and T. A. Steitz. 2001. The kink-turn: a new RNA secondary structure motif. EMBO J. 20:4214-4221.
-
(2001)
EMBO J
, vol.20
, pp. 4214-4221
-
-
Klein, D.J.1
Schmeing, T.M.2
Moore, P.B.3
Steitz, T.A.4
-
29
-
-
0024434420
-
Sequence-specific recognition of RNA hairpins by bacteriophage antiterminators requires a conserved arginine-rich motif
-
Lazinski, D., E. Grzadzielska, and A. Das. 1989. Sequence-specific recognition of RNA hairpins by bacteriophage antiterminators requires a conserved arginine-rich motif. Cell 59:207-218.
-
(1989)
Cell
, vol.59
, pp. 207-218
-
-
Lazinski, D.1
Grzadzielska, E.2
Das, A.3
-
30
-
-
0032540286
-
NMR structure of the bacteriophage lambda N peptide/boxB RNA complex: Recognition of a GNRA fold by an arginine-rich motif
-
Legault, P., J. Li, J. Mogridge, L. E. Kay, and J. Greenblatt. 1998. NMR structure of the bacteriophage lambda N peptide/boxB RNA complex: recognition of a GNRA fold by an arginine-rich motif. Cell 93:289-299.
-
(1998)
Cell
, vol.93
, pp. 289-299
-
-
Legault, P.1
Li, J.2
Mogridge, J.3
Kay, L.E.4
Greenblatt, J.5
-
31
-
-
0036470051
-
Protein Explorer: Easy yet powerful macromolecular visualization
-
Martz, E. 2002. Protein Explorer: easy yet powerful macromolecular visualization. Trends Biochem. Sci. 27:107-109.
-
(2002)
Trends Biochem. Sci
, vol.27
, pp. 107-109
-
-
Martz, E.1
-
33
-
-
0028880310
-
A protein-RNA interaction network facilitates the template-independent cooperative assembly on RNA polymerase of a stable antitermination complex containing the lambda N protein
-
Mogridge, J., T. F. Mah, and J. Greenblatt. 1995. A protein-RNA interaction network facilitates the template-independent cooperative assembly on RNA polymerase of a stable antitermination complex containing the lambda N protein. Genes Dev. 9:2831-2845.
-
(1995)
Genes Dev
, vol.9
, pp. 2831-2845
-
-
Mogridge, J.1
Mah, T.F.2
Greenblatt, J.3
-
34
-
-
0031614914
-
Independent ligand-induced folding of the RNA-binding domain and two functionally distinct antitermination regions in the phage lambda N protein
-
Mogridge, J., P. Legault, J. Li, M. D. Van Oene, L. E. Kay, and J. Greenblatt. 1998. Independent ligand-induced folding of the RNA-binding domain and two functionally distinct antitermination regions in the phage lambda N protein. Mol. Cell 1:265-275.
-
(1998)
Mol. Cell
, vol.1
, pp. 265-275
-
-
Mogridge, J.1
Legault, P.2
Li, J.3
Van Oene, M.D.4
Kay, L.E.5
Greenblatt, J.6
-
35
-
-
7344259635
-
Evolution by nearly-neutral mutations
-
Ohta, T. 1998. Evolution by nearly-neutral mutations. Genetica 102-103:83-90.
-
(1998)
Genetica
, vol.102
, Issue.103
, pp. 83-90
-
-
Ohta, T.1
-
36
-
-
0032864043
-
Adaptive recognition in RNA complexes with peptides and protein modules
-
Patel, D. J. 1999. Adaptive recognition in RNA complexes with peptides and protein modules. Curr. Opin. Struct. Biol. 9:74-87.
-
(1999)
Curr. Opin. Struct. Biol
, vol.9
, pp. 74-87
-
-
Patel, D.J.1
-
37
-
-
0033648752
-
Screening RNA-binding libraries by transcriptional antitermination in bacteria
-
Peled-Zehavi, H., C. A. Smith, K. Harada, and A. D. Frankel. 2000. Screening RNA-binding libraries by transcriptional antitermination in bacteria. Methods Enzymol. 318:297-308.
-
(2000)
Methods Enzymol
, vol.318
, pp. 297-308
-
-
Peled-Zehavi, H.1
Smith, C.A.2
Harada, K.3
Frankel, A.D.4
-
38
-
-
0031558773
-
Regulation of the elongation-termination decision at intrinsic terminators by antitermination protein N of phage lambda
-
Rees, W. A., S. E. Weitzel, A. Das, and P. H. von Hippel. 1997. Regulation of the elongation-termination decision at intrinsic terminators by antitermination protein N of phage lambda. J. Mol. Biol. 273:797-813.
-
(1997)
J. Mol. Biol
, vol.273
, pp. 797-813
-
-
Rees, W.A.1
Weitzel, S.E.2
Das, A.3
von Hippel, P.H.4
-
39
-
-
0034968504
-
Replication and mutation on neutral networks
-
Reidys, C., C. V. Forst, and P. Schuster. 2001. Replication and mutation on neutral networks. Bull. Math. Biol. 63:57-94.
-
(2001)
Bull. Math. Biol
, vol.63
, pp. 57-94
-
-
Reidys, C.1
Forst, C.V.2
Schuster, P.3
-
40
-
-
0000641399
-
Antitermination in bacteriophage lambda. The structure of the N36 peptide-boxB RNA complex
-
Scharpf, M., H. Sticht, K. Schweimer, M. Boehm, S. Hoffmann, and P. Rosch. 2000. Antitermination in bacteriophage lambda. The structure of the N36 peptide-boxB RNA complex. Eur. J. Biochem. 267:2397-2408.
-
(2000)
Eur. J. Biochem
, vol.267
, pp. 2397-2408
-
-
Scharpf, M.1
Sticht, H.2
Schweimer, K.3
Boehm, M.4
Hoffmann, S.5
Rosch, P.6
-
41
-
-
0034698298
-
-
Schultes, E. A, and D. P. Bartel. 2000. One sequence, two ribozymes: implications for the emergence of new ribozyme folds. Science 289:448-452.
-
Schultes, E. A, and D. P. Bartel. 2000. One sequence, two ribozymes: implications for the emergence of new ribozyme folds. Science 289:448-452.
-
-
-
-
42
-
-
0032575334
-
Altering the context of an RNA bulge switches the binding specificities of two viral Tat proteins
-
Smith, C. A., S. Crotty, Y. Harada, and A. D. Frankel. 1998. Altering the context of an RNA bulge switches the binding specificities of two viral Tat proteins. Biochemistry 37:10808-10814.
-
(1998)
Biochemistry
, vol.37
, pp. 10808-10814
-
-
Smith, C.A.1
Crotty, S.2
Harada, Y.3
Frankel, A.D.4
-
43
-
-
17844397456
-
A novel RNA pentaloop fold involved in targeting ADAR2
-
Stell, R., and F. H. Allain. 2005. A novel RNA pentaloop fold involved in targeting ADAR2. RNA 11:592-597.
-
(2005)
RNA
, vol.11
, pp. 592-597
-
-
Stell, R.1
Allain, F.H.2
-
44
-
-
0030931149
-
An RNA enhancer in a phage transcriptional antitermination complex functions as a structural switch
-
Su, L., J. T. Radek, L. A. Labeots, K. Hallenga, P. Hermanto, H. Chen, S. Nakagawa, M. Zhao, S. Kates, and M. A. Weiss. 1997. An RNA enhancer in a phage transcriptional antitermination complex functions as a structural switch. Genes Dev. 11:2214-2226.
-
(1997)
Genes Dev
, vol.11
, pp. 2214-2226
-
-
Su, L.1
Radek, J.T.2
Labeots, L.A.3
Hallenga, K.4
Hermanto, P.5
Chen, H.6
Nakagawa, S.7
Zhao, M.8
Kates, S.9
Weiss, M.A.10
-
45
-
-
0029048796
-
Structural variety of arginine-rich RNA-binding peptides
-
Tan, R., and A. D. Frankel. 1995. Structural variety of arginine-rich RNA-binding peptides. Proc. Natl. Acad. Sci. USA 92:5282-5286.
-
(1995)
Proc. Natl. Acad. Sci. USA
, vol.92
, pp. 5282-5286
-
-
Tan, R.1
Frankel, A.D.2
-
47
-
-
4644255364
-
Stability of RNA hairpin loops closed by AU base pairs
-
Vecenie, C. J., and M. J. Serra. 2004. Stability of RNA hairpin loops closed by AU base pairs. Biochemistry 43:11813-11817.
-
(2004)
Biochemistry
, vol.43
, pp. 11813-11817
-
-
Vecenie, C.J.1
Serra, M.J.2
-
49
-
-
0032419957
-
RNA recognition by arginine-rich peptide motifs
-
Weiss, M. A., and N. Narayana. 1998. RNA recognition by arginine-rich peptide motifs. Biopolymers 48:167-180.
-
(1998)
Biopolymers
, vol.48
, pp. 167-180
-
-
Weiss, M.A.1
Narayana, N.2
-
50
-
-
0141730393
-
Context and conformation dictate function of a transcription antitermination switch
-
Xia, T., A. Frankel, T. T. Takahashi, J. Ren, and R. W. Roberts. 2003. Context and conformation dictate function of a transcription antitermination switch. Nat. Struct. Biol. 10:812-819.
-
(2003)
Nat. Struct. Biol
, vol.10
, pp. 812-819
-
-
Xia, T.1
Frankel, A.2
Takahashi, T.T.3
Ren, J.4
Roberts, R.W.5
-
51
-
-
0035019574
-
Structural characterization of the complex of the Rev response element RNA with a selected peptide
-
Zhang, Q., K. Harada, H. S. Cho, A. D. Frankel, and D. E. Wemmer. 2001. Structural characterization of the complex of the Rev response element RNA with a selected peptide. Chem. Biol. 8:511-520.
-
(2001)
Chem. Biol
, vol.8
, pp. 511-520
-
-
Zhang, Q.1
Harada, K.2
Cho, H.S.3
Frankel, A.D.4
Wemmer, D.E.5
|