-
1
-
-
0026593806
-
Thermodynamic parameters for loop formation in RNA and DNA hairpin tetraloops
-
Antao V. P., Tinoco I. Jr. Thermodynamic parameters for loop formation in RNA and DNA hairpin tetraloops. Nucl. Acids Res. 20:1992;819-824.
-
(1992)
Nucl. Acids Res.
, vol.20
, pp. 819-824
-
-
Antao, V.P.1
Tinoco I., Jr.2
-
2
-
-
0025942059
-
A thermodynamic study of unusually stable RNA and DNA hairpins
-
Antao V. P., Lai S. Y., Tinoco I. Jr. A thermodynamic study of unusually stable RNA and DNA hairpins. Nucl. Acids Res. 19:1991;5901-5905.
-
(1991)
Nucl. Acids Res.
, vol.19
, pp. 5901-5905
-
-
Antao, V.P.1
Lai, S.Y.2
Tinoco I., Jr.3
-
3
-
-
0027434244
-
Thermal unfolding of a group I ribozyme: The low temperature transition is primarily a disruption of tertiary structure
-
Banerjee A. R., Jaeger J. A., Turner D. H. Thermal unfolding of a group I ribozyme: the low temperature transition is primarily a disruption of tertiary structure. Biochemistry. 32:1993;153-163.
-
(1993)
Biochemistry
, vol.32
, pp. 153-163
-
-
Banerjee, A.R.1
Jaeger, J.A.2
Turner, D.H.3
-
4
-
-
0032506045
-
Thermodynamic analysis of an RNA combinatorial library contained in a short hairpin
-
Bevilacqua J. M., Bevilacqua P. C. Thermodynamic analysis of an RNA combinatorial library contained in a short hairpin. Biochemistry. 37:1998;15877-15884.
-
(1998)
Biochemistry
, vol.37
, pp. 15877-15884
-
-
Bevilacqua, J.M.1
Bevilacqua, P.C.2
-
6
-
-
0031841911
-
The ribonuclease P database
-
Brown J. W. The ribonuclease P database. Nucl. Acids Res. 26:1998;351-352.
-
(1998)
Nucl. Acids Res.
, vol.26
, pp. 351-352
-
-
Brown, J.W.1
-
7
-
-
0031029398
-
Flavin-dependent photocleavage of RNA at G·U base pairs
-
Burgstaller P., Famulok M. Flavin-dependent photocleavage of RNA at G·U base pairs. J. Am. Chem. Soc. 119:1997;1137-1138.
-
(1997)
J. Am. Chem. Soc.
, vol.119
, pp. 1137-1138
-
-
Burgstaller, P.1
Famulok, M.2
-
8
-
-
0030873521
-
Isoalloxazine derivatives promote photocleavage of natural RNAs at G·U base pairs embedded within helices
-
Burgstaller P., Hermann T., Huber C., Westhof E., Famulok M. Isoalloxazine derivatives promote photocleavage of natural RNAs at G·U base pairs embedded within helices. Nucl. Acids Res. 25:1997;4018-4027.
-
(1997)
Nucl. Acids Res.
, vol.25
, pp. 4018-4027
-
-
Burgstaller, P.1
Hermann, T.2
Huber, C.3
Westhof, E.4
Famulok, M.5
-
9
-
-
0031463994
-
Solution structure of a GAAA tetraloop receptor RNA
-
Butcher S. E., Dieckmann T., Feigon J. Solution structure of a GAAA tetraloop receptor RNA. EMBO J. 16:1997;7490-7499.
-
(1997)
EMBO J.
, vol.16
, pp. 7490-7499
-
-
Butcher, S.E.1
Dieckmann, T.2
Feigon, J.3
-
10
-
-
0029820625
-
Crystal structure of a group I ribozyme domain: Principles of RNA packing
-
Cate J. H., Gooding A. R., Podell E., Zhou K., Golden B. L., Kundrot C. E., Cech T. R., Doudna J. A. Crystal structure of a group I ribozyme domain: principles of RNA packing. Science. 273:1996;1678-1685.
-
(1996)
Science
, vol.273
, pp. 1678-1685
-
-
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
-
11
-
-
0030856333
-
Metals, motifs, and recognition in the crystal structure of a 5S rRNA domain
-
Correl C. C., Freeborn B., Moore P. B., Steitz T. A. Metals, motifs, and recognition in the crystal structure of a 5S rRNA domain. Cell. 91:1997;705-712.
-
(1997)
Cell
, vol.91
, pp. 705-712
-
-
Correl, C.C.1
Freeborn, B.2
Moore, P.B.3
Steitz, T.A.4
-
12
-
-
0028921811
-
Frequent use of the same tertiary motif by self-folding RNAs
-
Costa M., Michel F. Frequent use of the same tertiary motif by self-folding RNAs. EMBO J. 14:1995;1276-1285.
-
(1995)
EMBO J.
, vol.14
, pp. 1276-1285
-
-
Costa, M.1
Michel, F.2
-
13
-
-
0016169138
-
The molecular mechanism of thermal unfolding of Escherichia coli formylmethionine transfer RNA
-
Crothers D. M., Cole P. E., Hilbers C. W., Schulman R. G. The molecular mechanism of thermal unfolding of Escherichia coli formylmethionine transfer RNA. J. Mol. Biol. 87:1974;63-88.
-
(1974)
J. Mol. Biol
, vol.87
, pp. 63-88
-
-
Crothers, D.M.1
Cole, P.E.2
Hilbers, C.W.3
Schulman, R.G.4
-
14
-
-
0028146967
-
A comparative database of group I intron structures
-
Damberger S. H., Gutell R. R. A comparative database of group I intron structures. Nucl. Acids Res. 22:1994;3508-3510.
-
(1994)
Nucl. Acids Res.
, vol.22
, pp. 3508-3510
-
-
Damberger, S.H.1
Gutell, R.R.2
-
15
-
-
0023665268
-
Probing the structure of RNAs in solution
-
Ehresmann C., Baudin F., Mougel M., Romby P., Ebel J., Ehresmann B. Probing the structure of RNAs in solution. Nucl. Acids Res. 15:1987;9109-9128.
-
(1987)
Nucl. Acids Res.
, vol.15
, pp. 9109-9128
-
-
Ehresmann, C.1
Baudin, F.2
Mougel, M.3
Romby, P.4
Ebel, J.5
Ehresmann, B.6
-
16
-
-
0031014984
-
Probing the structure of the Escherichia coli 10Sa (tmRNA)
-
Felden B., Himeno H., Muto A., McCutcheon J. P., Atkins J. F., Gesteland R. F. Probing the structure of the Escherichia coli 10Sa (tmRNA). RNA. 3:1997;89-104.
-
(1997)
RNA
, vol.3
, pp. 89-104
-
-
Felden, B.1
Himeno, H.2
Muto, A.3
McCutcheon, J.P.4
Atkins, J.F.5
Gesteland, R.F.6
-
17
-
-
0015526994
-
Free energy of imperfect nucleic acid helices. I. The bulge defect
-
Fink T. R., Crothers D. M. Free energy of imperfect nucleic acid helices. I. The bulge defect. J. Mol. Biol. 66:1972;1-12.
-
(1972)
J. Mol. Biol.
, vol.66
, pp. 1-12
-
-
Fink, T.R.1
Crothers, D.M.2
-
18
-
-
0026108692
-
Light-directed, spatially addressable parallel chemical synthesis
-
Fodor S. P. A., Read J. L., Pirrung M. C., Stryer L., Lu A. T., Solas D. Light-directed, spatially addressable parallel chemical synthesis. Science. 251:1991;767-773.
-
(1991)
Science
, vol.251
, pp. 767-773
-
-
Fodor, S.P.A.1
Read, J.L.2
Pirrung, M.C.3
Stryer, L.4
Lu, A.T.5
Solas, D.6
-
19
-
-
0027640931
-
Genetic algorithms: Principles of natural selection applied to computation
-
Forrest S. Genetic algorithms: principles of natural selection applied to computation. Science. 261:1993;872-878.
-
(1993)
Science
, vol.261
, pp. 872-878
-
-
Forrest, S.1
-
20
-
-
0032520637
-
Parallel thermodynamic analysis of duplexes on oligodeoxyribonucleotide microchips
-
Fotin A. V., Drobyshev A. L., Proudnikov D. Y., Perov A. N., Mirzabekov A. D. Parallel thermodynamic analysis of duplexes on oligodeoxyribonucleotide microchips. Nucl. Acids Res. 26:1998;1515-1521.
-
(1998)
Nucl. Acids Res.
, vol.26
, pp. 1515-1521
-
-
Fotin, A.V.1
Drobyshev, A.L.2
Proudnikov, D.Y.3
Perov, A.N.4
Mirzabekov, A.D.5
-
21
-
-
0001613489
-
Effects of 3′ dangling end stacking on the stability of GGCC and CCGG double helices
-
Freier S. M., Burger B. J., Alkema D., Neilson T., Turner D. H. Effects of 3′ dangling end stacking on the stability of GGCC and CCGG double helices. Biochemistry. 22:1983;6198-6206.
-
(1983)
Biochemistry
, vol.22
, pp. 6198-6206
-
-
Freier, S.M.1
Burger, B.J.2
Alkema, D.3
Neilson, T.4
Turner, D.H.5
-
23
-
-
0023040892
-
Free energy contributions of G·U and other terminal mismatches to helix stability
-
Freier S. M., Kierzek R., Caruthers M. H., Neilson T., Turner D. H. Free energy contributions of G·U and other terminal mismatches to helix stability. Biochemistry. 25:1986a;3209-3213.
-
(1986)
Biochemistry
, vol.25
, pp. 3209-3213
-
-
Freier, S.M.1
Kierzek, R.2
Caruthers, M.H.3
Neilson, T.4
Turner, D.H.5
-
24
-
-
0000075467
-
Improved free-energy parameters for predictions of RNA duplex stability
-
Freier S. M., Kierzek R., Jaeger J. A., Sugimoto N., Caruthers M. H., Neilson T., Turner D. H. Improved free-energy parameters for predictions of RNA duplex stability. Proc. Natl Acad. Sci. USA. 83:1986b;9373-9377.
-
(1986)
Proc. Natl Acad. Sci. USA
, vol.83
, pp. 9373-9377
-
-
Freier, S.M.1
Kierzek, R.2
Jaeger, J.A.3
Sugimoto, N.4
Caruthers, M.H.5
Neilson, T.6
Turner, D.H.7
-
25
-
-
0023040885
-
Stability of XGCGCp, GCGCYp, and XGCGCYp helixes: An empirical estimate of the energetics of hydrogen bonds in nucleic acids
-
Freier S. M., Sugimoto N., Sinclair A., Alkema D., Neilson T., Kierzek R., Caruthers M. H., Turner D. H. Stability of XGCGCp, GCGCYp, and XGCGCYp helixes: an empirical estimate of the energetics of hydrogen bonds in nucleic acids. Biochemistry. 25:1986c;3214-3219.
-
(1986)
Biochemistry
, vol.25
, pp. 3214-3219
-
-
Freier, S.M.1
Sugimoto, N.2
Sinclair, A.3
Alkema, D.4
Neilson, T.5
Kierzek, R.6
Caruthers, M.H.7
Turner, D.H.8
-
26
-
-
0028823370
-
An interactive framework for RNA secondary structure prediction with a dynamical treatment of constraints
-
Gaspin C., Westhof E. An interactive framework for RNA secondary structure prediction with a dynamical treatment of constraints. J. Mol. Biol. 254:1995;163-174.
-
(1995)
J. Mol. Biol.
, vol.254
, pp. 163-174
-
-
Gaspin, C.1
Westhof, E.2
-
27
-
-
0032570280
-
Stability of RNA hairpins closed by wobble base-pairs
-
Giese M. R., Betschart K., Dale T., Riley C. K., Rowan C., Sprouse K. J., Serra M. J. Stability of RNA hairpins closed by wobble base-pairs. Biochemistry. 37:1998;1094-1100.
-
(1998)
Biochemistry
, vol.37
, pp. 1094-1100
-
-
Giese, M.R.1
Betschart, K.2
Dale, T.3
Riley, C.K.4
Rowan, C.5
Sprouse, K.J.6
Serra, M.J.7
-
28
-
-
0024295554
-
Characterization of RNA hairpin loop stability
-
Groebe D. R., Uhlenbeck O. C. Characterization of RNA hairpin loop stability. Nucl. Acids Res. 16:1988;11725-11735.
-
(1988)
Nucl. Acids Res.
, vol.16
, pp. 11725-11735
-
-
Groebe, D.R.1
Uhlenbeck, O.C.2
-
29
-
-
0024579255
-
Thermal stability of RNA hairpins containing a four-membered loop and a bulge nucleotide
-
Groebe D. R., Uhlenbeck O. C. Thermal stability of RNA hairpins containing a four-membered loop and a bulge nucleotide. Biochemistry. 28:1989;742-747.
-
(1989)
Biochemistry
, vol.28
, pp. 742-747
-
-
Groebe, D.R.1
Uhlenbeck, O.C.2
-
30
-
-
0029061125
-
The computer simulation of RNA folding pathways using a genetic algorithm
-
Gultyaev A. P., van Batenburg F. H. D., Pleij C. W. A. The computer simulation of RNA folding pathways using a genetic algorithm. J. Mol. Biol. 250:1995;37-51.
-
(1995)
J. Mol. Biol.
, vol.250
, pp. 37-51
-
-
Gultyaev, A.P.1
Van Batenburg, F.H.D.2
Pleij, C.W.A.3
-
31
-
-
0028071557
-
Collection of small subunit (16 S- And 16 S-like) ribosomal RNA structures
-
Gutell R. R. Collection of small subunit (16 S- and 16 S-like) ribosomal RNA structures. Nucl. Acids Res. 22:1994;3502-3507.
-
(1994)
Nucl. Acids Res.
, vol.22
, pp. 3502-3507
-
-
Gutell, R.R.1
-
32
-
-
0027225783
-
A compilation of large subunit (23 S- And 23 S-like) ribosomal RNA structures
-
Gutell R. R., Gray M. W., Schnare M. N. A compilation of large subunit (23 S- and 23 S-like) ribosomal RNA structures. Nucl. Acids Res. 21:1993;3055-3074.
-
(1993)
Nucl. Acids Res.
, vol.21
, pp. 3055-3074
-
-
Gutell, R.R.1
Gray, M.W.2
Schnare, M.N.3
-
33
-
-
0031010235
-
Analysis of the tertiary structure of the ribonuclease P ribozyme-substrate complex by photoaffinity crosslinking
-
Harris M. E., Kazantchev A. V., Chen J. L., Pace N. R. Analysis of the tertiary structure of the ribonuclease P ribozyme-substrate complex by photoaffinity crosslinking. RNA. 3:1997;561-574.
-
(1997)
RNA
, vol.3
, pp. 561-574
-
-
Harris, M.E.1
Kazantchev, A.V.2
Chen, J.L.3
Pace, N.R.4
-
34
-
-
0026335264
-
Nearest-neighbor parameters for G·U mismatches
-
He L., Kierzek R., SantaLucia J. Jr, Walter A. E., Turner D. H. Nearest-neighbor parameters for G·U mismatches. Biochemistry. 30:1991;11124-11132.
-
(1991)
Biochemistry
, vol.30
, pp. 11124-11132
-
-
He, L.1
Kierzek, R.2
Santalucia J., Jr.3
Walter, A.E.4
Turner, D.H.5
-
35
-
-
0017158334
-
Thermal unfolding of yeast glycine transfer RNA
-
Hilbers C. W., Robillard G. T., Shulman R. G., Blake R. D., Webb P. K., Fresco R., Riesner D. Thermal unfolding of yeast glycine transfer RNA. Biochemistry. 15:1976;1874-1882.
-
(1976)
Biochemistry
, vol.15
, pp. 1874-1882
-
-
Hilbers, C.W.1
Robillard, G.T.2
Shulman, R.G.3
Blake, R.D.4
Webb, P.K.5
Fresco, R.6
Riesner, D.7
-
36
-
-
34249772381
-
Fast folding and comparison of RNA secondary structures
-
Hofacker I. L., Fontana W., Stadler P. F., Bonhoeffer L. S., Tacker M., Schuster P. Fast folding and comparison of RNA secondary structures. Monatsh. Chem. 125:1994;167-188.
-
(1994)
Monatsh. Chem.
, vol.125
, pp. 167-188
-
-
Hofacker, I.L.1
Fontana, W.2
Stadler, P.F.3
Bonhoeffer, L.S.4
Tacker, M.5
Schuster, P.6
-
38
-
-
0031576996
-
Assessing the reliability of RNA folding using statistical mechanics
-
Huynen M., Gutell R., Konings D. Assessing the reliability of RNA folding using statistical mechanics. J. Mol. Biol. 267:1997;1104-1112.
-
(1997)
J. Mol. Biol.
, vol.267
, pp. 1104-1112
-
-
Huynen, M.1
Gutell, R.2
Konings, D.3
-
39
-
-
0031414413
-
Kinetic and secondary structure analysis of Naegleria anderson: GIR1, a group I ribozyme whose putative biological function is site-specific hydrolysis
-
Jabri E., Aigner S., Cech T. R. Kinetic and secondary structure analysis of Naegleria anderson: GIR1, a group I ribozyme whose putative biological function is site-specific hydrolysis. Biochemistry. 36:1997;16345-16354.
-
(1997)
Biochemistry
, vol.36
, pp. 16345-16354
-
-
Jabri, E.1
Aigner, S.2
Cech, T.R.3
-
40
-
-
3843114319
-
Intramolecular reaction in polycondensations. I. The theory of linear systems
-
Jacobson H., Stockmayer W. H. Intramolecular reaction in polycondensations. I. The theory of linear systems. J. Chem. Phys. 18:1950;1600-1606.
-
(1950)
J. Chem. Phys.
, vol.18
, pp. 1600-1606
-
-
Jacobson, H.1
Stockmayer, W.H.2
-
42
-
-
0027433710
-
Monitoring of cooperative unfolding of the sunY group I intron of bacteriophage T4
-
Jaeger L., Westhof E., Michel F. Monitoring of cooperative unfolding of the sunY group I intron of bacteriophage T4. J. Mol. Biol. 234:1993;331-346.
-
(1993)
J. Mol. Biol
, vol.234
, pp. 331-346
-
-
Jaeger, L.1
Westhof, E.2
Michel, F.3
-
43
-
-
0028294458
-
Involvement of a GNRA tetraloop in long-range RNA tertiary interactions
-
Jaeger L., Michel F., Westhof E. Involvement of a GNRA tetraloop in long-range RNA tertiary interactions. J. Mol. Biol. 236:1994;1271-1276.
-
(1994)
J. Mol. Biol.
, vol.236
, pp. 1271-1276
-
-
Jaeger, L.1
Michel, F.2
Westhof, E.3
-
44
-
-
0024827733
-
Phylogenetic comparative analysis of RNA secondary structure
-
James B. D., Olsen G. J., Pace N. R. Phylogenetic comparative analysis of RNA secondary structure. Methods Enzymol. 180:1989;227-239.
-
(1989)
Methods Enzymol.
, vol.180
, pp. 227-239
-
-
James, B.D.1
Olsen, G.J.2
Pace, N.R.3
-
45
-
-
0028866812
-
Solution structure of the CUUG hairpin loop - A novel RNA tetraloop motif
-
Jucker F. M., Pardi A. Solution structure of the CUUG hairpin loop - a novel RNA tetraloop motif. Biochemistry. 34:1995;14416-14427.
-
(1995)
Biochemistry
, vol.34
, pp. 14416-14427
-
-
Jucker, F.M.1
Pardi, A.2
-
46
-
-
0021970326
-
Secondary structure of a 345-base RNA fragment covering the S8/S15 protein binding domain of Escherichia coli 16 S ribosomal RNA
-
Kean J. M., Draper D. E. Secondary structure of a 345-base RNA fragment covering the S8/S15 protein binding domain of Escherichia coli 16 S ribosomal RNA. Biochemistry. 24:1985;5052-5061.
-
(1985)
Biochemistry
, vol.24
, pp. 5052-5061
-
-
Kean, J.M.1
Draper, D.E.2
-
47
-
-
0029855518
-
Thermodynamics of coaxially stacked helices with GA and CC mismatches
-
Kim J., Walter A. E., Turner D. H. Thermodynamics of coaxially stacked helices with GA and CC mismatches. Biochemistry. 35:1996;13753-13761.
-
(1996)
Biochemistry
, vol.35
, pp. 13753-13761
-
-
Kim, J.1
Walter, A.E.2
Turner, D.H.3
-
48
-
-
0024841809
-
Enzymatic approaches to probing RNA secondary and tertiary structure
-
Knapp G. Enzymatic approaches to probing RNA secondary and tertiary structure. Methods Enzymol. 180:1989;192-212.
-
(1989)
Methods Enzymol.
, vol.180
, pp. 192-212
-
-
Knapp, G.1
-
49
-
-
0028234517
-
Thermodynamics of RNA folding in a conserved ribosomal RNA domain
-
Laing L. G., Draper D. E. Thermodynamics of RNA folding in a conserved ribosomal RNA domain. J. Mol. Biol. 237:1994;560-576.
-
(1994)
J. Mol. Biol.
, vol.237
, pp. 560-576
-
-
Laing, L.G.1
Draper, D.E.2
-
50
-
-
0031866668
-
The signal recognition particle database (SRPDB)
-
Larsen N., Samuelsson T., Zwieb C. The signal recognition particle database (SRPDB). Nucl. Acids Res. 26:1998;177-178.
-
(1998)
Nucl. Acids Res.
, vol.26
, pp. 177-178
-
-
Larsen, N.1
Samuelsson, T.2
Zwieb, C.3
-
51
-
-
0030452773
-
New loop-loop tertiary interactions in self-splicing introns of subgroup IC and ID: A complete 3D model of theTetrahymena thermophila ribozyme
-
Lehnert V., Jaeger L., Michel F., Westhof E. New loop-loop tertiary interactions in self-splicing introns of subgroup IC and ID: a complete 3D model of theTetrahymena thermophila ribozyme. Chem. Biol. 3:1996;993-1009.
-
(1996)
Chem. Biol.
, vol.3
, pp. 993-1009
-
-
Lehnert, V.1
Jaeger, L.2
Michel, F.3
Westhof, E.4
-
52
-
-
0025186882
-
Thermodynamic and spectroscopic study of bulge loops in oligoribonucleotides
-
Longfellow C. E., Kierzek R., Turner D. H. Thermodynamic and spectroscopic study of bulge loops in oligoribonucleotides. Biochemistry. 29:1990;278-285.
-
(1990)
Biochemistry
, vol.29
, pp. 278-285
-
-
Longfellow, C.E.1
Kierzek, R.2
Turner, D.H.3
-
53
-
-
0039161225
-
Thermodynamic prediction of conserved secondary structure: Application to the RRE element of HIV, the tRNA-like element of CMV and the mRNA of prion protein
-
Lück R., Steger G., Riesner D. Thermodynamic prediction of conserved secondary structure: application to the RRE element of HIV, the tRNA-like element of CMV and the mRNA of prion protein. J. Mol. Biol. 258:1996;813-826.
-
(1996)
J. Mol. Biol.
, vol.258
, pp. 813-826
-
-
Lück, R.1
Steger, G.2
Riesner, D.3
-
54
-
-
0032546728
-
Derivation of the three-dimensional architecture of bacterial ribonuclease P RNAs from comparative sequence analysis
-
Massire C., Jaeger L., Westhof E. Derivation of the three-dimensional architecture of bacterial ribonuclease P RNAs from comparative sequence analysis. J. Mol. Biol. 279:1998;773-793.
-
(1998)
J. Mol. Biol.
, vol.279
, pp. 773-793
-
-
Massire, C.1
Jaeger, L.2
Westhof, E.3
-
55
-
-
0031014702
-
Secondary structure model of the RNA recognized by the reverse transcriptase from the R2 retrotransposable element
-
Mathews D. H., Banerjee A. R., Luan D. D., Eickbush T. H., Turner D. H. Secondary structure model of the RNA recognized by the reverse transcriptase from the R2 retrotransposable element. RNA. 3:1997;1-16.
-
(1997)
RNA
, vol.3
, pp. 1-16
-
-
Mathews, D.H.1
Banerjee, A.R.2
Luan, D.D.3
Eickbush, T.H.4
Turner, D.H.5
-
56
-
-
0004286966
-
An updated recursive algorithm for RNA secondary structure prediction with improved thermodynamic parameters
-
N. B. Leontis, & J. Jr. SantaLucia. New York: American Chemical Society
-
Mathews D. H., Andre T. C., Kim J., Turner D. H., Zuker M. An updated recursive algorithm for RNA secondary structure prediction with improved thermodynamic parameters. Leontis N. B., SantaLucia J. Jr. Molecular Modeling of Nucleic Acids. 1998;246-257 American Chemical Society, New York.
-
(1998)
Molecular Modeling of Nucleic Acids
, pp. 246-257
-
-
Mathews, D.H.1
Andre, T.C.2
Kim, J.3
Turner, D.H.4
Zuker, M.5
-
57
-
-
0025264854
-
The equilibrium partition function and base-pair probabilities for RNA secondary structure
-
McCaskill J. S. The equilibrium partition function and base-pair probabilities for RNA secondary structure. Biopolymers. 29:1990;1105-1119.
-
(1990)
Biopolymers
, vol.29
, pp. 1105-1119
-
-
McCaskill, J.S.1
-
58
-
-
0029805937
-
2by two-dimensional NMR and simulated annealing
-
2by two-dimensional NMR and simulated annealing. Biochemistry. 35:1996;14077-14089.
-
(1996)
Biochemistry
, vol.35
, pp. 14077-14089
-
-
McDowell, J.A.1
Turner, D.H.2
-
60
-
-
0033557138
-
Thermodynamics of RNA hairpins containing single internal mismatches
-
Meroueh M., Chow C. S. Thermodynamics of RNA hairpins containing single internal mismatches. Nucl. Acids Res. 27:1999;1118-1125.
-
(1999)
Nucl. Acids Res.
, vol.27
, pp. 1118-1125
-
-
Meroueh, M.1
Chow, C.S.2
-
61
-
-
0025678737
-
Modeling of the three-dimensional architecture of group I catalytic introns based on comparative sequence analysis
-
Michel F., Westhof E. Modeling of the three-dimensional architecture of group I catalytic introns based on comparative sequence analysis. J. Mol. Biol. 216:1990;585-610.
-
(1990)
J. Mol. Biol.
, vol.216
, pp. 585-610
-
-
Michel, F.1
Westhof, E.2
-
62
-
-
0024428420
-
Comparative and functional anatomy of group II catalytic introns - A review
-
Michel F., Umesono K., Ozeki H. Comparative and functional anatomy of group II catalytic introns - a review. Gene. 82:1989;5-30.
-
(1989)
Gene
, vol.82
, pp. 5-30
-
-
Michel, F.1
Umesono, K.2
Ozeki, H.3
-
63
-
-
0028897382
-
Purine-purine mismatches in RNA helixes: Evidence for protonated G·A pairs and next-nearest neighbor effects
-
Morse S. E., Draper D. E. Purine-purine mismatches in RNA helixes: evidence for protonated G·A pairs and next-nearest neighbor effects. Nucl. Acids Res. 23:1995;302-306.
-
(1995)
Nucl. Acids Res.
, vol.23
, pp. 302-306
-
-
Morse, S.E.1
Draper, D.E.2
-
64
-
-
0028301674
-
GAAA tetra loop and conserved bulge stabilize tertiary structure of a group I intron domain
-
Murphy F. L., Cech T. R. GAAA tetra loop and conserved bulge stabilize tertiary structure of a group I intron domain. J. Mol. Biol. 236:1994;49-63.
-
(1994)
J. Mol. Biol.
, vol.236
, pp. 49-63
-
-
Murphy, F.L.1
Cech, T.R.2
-
65
-
-
0030271495
-
The development of microfabricated arrays for DNA sequencing and analysis
-
O'Donnell-Maloney M. J., Smith C. L., Cantor C. R. The development of microfabricated arrays for DNA sequencing and analysis. Trends Biotechnol. 14:1996;401-407.
-
(1996)
Trends Biotechnol.
, vol.14
, pp. 401-407
-
-
O'Donnell-Maloney, M.J.1
Smith, C.L.2
Cantor, C.R.3
-
66
-
-
0001899745
-
Probing RNA structure, function, and history by comparative analysis
-
R. F. Gesteland, T. R. Cech, & J. F. Atkins. Cold Spring Harbor: Cold Spring Harbor Laboratory Press
-
Pace N. R., Thomas B. C., Woese C. R. Probing RNA structure, function, and history by comparative analysis. Gesteland R. F., Cech T. R., Atkins J. F. The RNA World. 1999;113-141 Cold Spring Harbor Laboratory Press, Cold Spring Harbor.
-
(1999)
The RNA World
, pp. 113-141
-
-
Pace, N.R.1
Thomas, B.C.2
Woese, C.R.3
-
67
-
-
0025900996
-
Thermodynamic study of internal loops in oligoribonucleotides: Symmetric loops are more stable than asymmetric loops
-
Peritz A. E., Kierzek R., Sugimoto N., Turner D. H. Thermodynamic study of internal loops in oligoribonucleotides: Symmetric loops are more stable than asymmetric loops. Biochemistry. 30:1991;6428-6436.
-
(1991)
Biochemistry
, vol.30
, pp. 6428-6436
-
-
Peritz, A.E.1
Kierzek, R.2
Sugimoto, N.3
Turner, D.H.4
-
68
-
-
0028037302
-
Model for an RNA tertiary interaction from the structure of an intermolecular complex between a GAAA tetraloop and an RNA helix
-
Pley H. W., Flaherty K. M., McKay D. B. Model for an RNA tertiary interaction from the structure of an intermolecular complex between a GAAA tetraloop and an RNA helix. Nature. 372:1994;111-114.
-
(1994)
Nature
, vol.372
, pp. 111-114
-
-
Pley, H.W.1
Flaherty, K.M.2
McKay, D.B.3
-
69
-
-
12044257509
-
Functional group substitutions as probes of hydrogen bonding between GA mismatches in RNA internal loops
-
SantaLucia J. Jr, Kierzek R., Turner D. H. Functional group substitutions as probes of hydrogen bonding between GA mismatches in RNA internal loops. J. Am. Chem. Soc. 113:1991a;4313-4322.
-
(1991)
J. Am. Chem. Soc.
, vol.113
, pp. 4313-4322
-
-
Santalucia J., Jr.1
Kierzek, R.2
Turner, D.H.3
-
70
-
-
0025925206
-
Stabilities of consecutive A·C, C·C, G·G, U·C, and U·U mismatches in RNA internal loops: Evidence for stable hydrogen-bonded U·U and C·C+ pairs
-
SantaLucia J. Jr, Kierzek R., Turner D. H. Stabilities of consecutive A·C, C·C, G·G, U·C, and U·U mismatches in RNA internal loops: evidence for stable hydrogen-bonded U·U and C·C+ pairs. Biochemistry. 30:1991b;8242-8251.
-
(1991)
Biochemistry
, vol.30
, pp. 8242-8251
-
-
Santalucia J., Jr.1
Kierzek, R.2
Turner, D.H.3
-
71
-
-
0029877001
-
Comprehensive comparison of structural characteristics in Eukaryotic cytoplasmic large subunit (23S-like) ribosomal RNA
-
Schnare M. N., Damberger S. H., Gray M. W., Gutell R. R. Comprehensive comparison of structural characteristics in Eukaryotic cytoplasmic large subunit (23S-like) ribosomal RNA. J. Mol. Biol. 256:1996;701-719.
-
(1996)
J. Mol. Biol.
, vol.256
, pp. 701-719
-
-
Schnare, M.N.1
Damberger, S.H.2
Gray, M.W.3
Gutell, R.R.4
-
72
-
-
0030299990
-
G·A and U·U mismatches can stabilize RNA internal loops of three nucleotides
-
Schroeder S., Kim J., Turner D. H. G·A and U·U mismatches can stabilize RNA internal loops of three nucleotides. Biochemistry. 35:1996;16105-16109.
-
(1996)
Biochemistry
, vol.35
, pp. 16105-16109
-
-
Schroeder, S.1
Kim, J.2
Turner, D.H.3
-
73
-
-
0029100233
-
Predicting thermodynamic properties of RNA
-
Serra M. J., Turner D. H. Predicting thermodynamic properties of RNA. Methods Enzymol. 259:1995;242-261.
-
(1995)
Methods Enzymol.
, vol.259
, pp. 242-261
-
-
Serra, M.J.1
Turner, D.H.2
-
74
-
-
0027247971
-
RNA hairpin loop stability depends on closing pair
-
Serra M. J., Lyttle M. H., Axenson T. J., Schadt C. A., Turner D. H. RNA hairpin loop stability depends on closing pair. Nucl. Acids Res. 21:1993;3845-3849.
-
(1993)
Nucl. Acids Res.
, vol.21
, pp. 3845-3849
-
-
Serra, M.J.1
Lyttle, M.H.2
Axenson, T.J.3
Schadt, C.A.4
Turner, D.H.5
-
75
-
-
0027992843
-
A model for the stabilities of RNA hairpins based on a study of the sequence dependence of stability for hairpins of six nucleotides
-
Serra M. J., Axenson T. J., Turner D. H. A model for the stabilities of RNA hairpins based on a study of the sequence dependence of stability for hairpins of six nucleotides. Biochemistry. 33:1994;14289-14296.
-
(1994)
Biochemistry
, vol.33
, pp. 14289-14296
-
-
Serra, M.J.1
Axenson, T.J.2
Turner, D.H.3
-
76
-
-
0030890755
-
Improved parameters for the prediction of RNA hairpin stability
-
Serra M. J., Barnes T. W., Betschart K., Gutierrez M. J., Sprouse K. J., Riley C. K., Stewart L., Temel R. E. Improved parameters for the prediction of RNA hairpin stability. Biochemistry. 36:1997;4844-4851.
-
(1997)
Biochemistry
, vol.36
, pp. 4844-4851
-
-
Serra, M.J.1
Barnes, T.W.2
Betschart, K.3
Gutierrez, M.J.4
Sprouse, K.J.5
Riley, C.K.6
Stewart, L.7
Temel, R.E.8
-
77
-
-
0020480145
-
Structural analyses of E. coli 5S RNA fragments, their associates and complexes with proteins L18 and L25
-
Speek M., Lind A. Structural analyses of E. coli 5S RNA fragments, their associates and complexes with proteins L18 and L25. Nucl. Acids Res. 10:1982;947-965.
-
(1982)
Nucl. Acids Res.
, vol.10
, pp. 947-965
-
-
Speek, M.1
Lind, A.2
-
78
-
-
0031804156
-
Compilation of tRNA sequences and sequences of tRNA genes
-
Sprinzl M., Horn C., Brown M., Ioudovitch A., Steinberg S. Compilation of tRNA sequences and sequences of tRNA genes. Nucl. Acids Res. 26:1998;148-153.
-
(1998)
Nucl. Acids Res.
, vol.26
, pp. 148-153
-
-
Sprinzl, M.1
Horn, C.2
Brown, M.3
Ioudovitch, A.4
Steinberg, S.5
-
79
-
-
0023055766
-
Energetics of internal GU mismatches in ribooligonucleotide helixes
-
Sugimoto N., Kierzek R., Freier S. M., Turner D. H. Energetics of internal GU mismatches in ribooligonucleotide helixes. Biochemistry. 25:1986;5755-5759.
-
(1986)
Biochemistry
, vol.25
, pp. 5755-5759
-
-
Sugimoto, N.1
Kierzek, R.2
Freier, S.M.3
Turner, D.H.4
-
80
-
-
0031866152
-
5S rRNA data bank
-
Szymanski M., Specht T., Barciszewska M. Z., Barciszewski J., Erdmann V. A. 5S rRNA data bank. Nucl. Acids Res. 26:1998;156-159.
-
(1998)
Nucl. Acids Res.
, vol.26
, pp. 156-159
-
-
Szymanski, M.1
Specht, T.2
Barciszewska, M.Z.3
Barciszewski, J.4
Erdmann, V.A.5
-
81
-
-
0027295076
-
Comparative structural-analysis of nuclear RNase-P RNAs from yeast
-
Tranguch A. J., Engelke D. R. Comparative structural-analysis of nuclear RNase-P RNAs from yeast. J. Biol. Chem. 268:1993;14045-14055.
-
(1993)
J. Biol. Chem.
, vol.268
, pp. 14045-14055
-
-
Tranguch, A.J.1
Engelke, D.R.2
-
82
-
-
0028223292
-
Structure-sensitive RNA footprinting of yeast nuclear ribonuclease P
-
Tranguch A. J., Kinderberger D. W., Rohlman C. E., Lee J., Engelke D. R. Structure-sensitive RNA footprinting of yeast nuclear ribonuclease P. Biochemistry. 33:1994;1778-1787.
-
(1994)
Biochemistry
, vol.33
, pp. 1778-1787
-
-
Tranguch, A.J.1
Kinderberger, D.W.2
Rohlman, C.E.3
Lee, J.4
Engelke, D.R.5
-
83
-
-
0023973247
-
CUUCGG hairpins: Extraordinarily stable RNA secondary structures associated with various biochemical processes
-
Tuerk C., Gauss P., Thermes C., Groebe D. R., Gayle M., Guild N., Stormo G., D'Auberton-Carafa Y., Uhlenbeck O. C., Tinoco I. Jr, Brody E. N., Gold L. CUUCGG hairpins: extraordinarily stable RNA secondary structures associated with various biochemical processes. Proc. Natl Acad. Sci. USA. 85:1988;1364-1368.
-
(1988)
Proc. Natl Acad. Sci. USA
, vol.85
, pp. 1364-1368
-
-
Tuerk, C.1
Gauss, P.2
Thermes, C.3
Groebe, D.R.4
Gayle, M.5
Guild, N.6
Stormo, G.7
D'Auberton-Carafa, Y.8
Uhlenbeck, O.C.9
Tinoco I., Jr.10
Brody, E.N.11
Gold, L.12
-
84
-
-
0029025720
-
An APL-programmed genetic algorithm for the prediction of RNA secondary structure
-
Van Batenburg F. H. D., Gultyaev A. P., Pleij C. W. A. An APL-programmed genetic algorithm for the prediction of RNA secondary structure. J. Theor. Biol. 174:1995;269-280.
-
(1995)
J. Theor. Biol.
, vol.174
, pp. 269-280
-
-
Van Batenburg, F.H.D.1
Gultyaev, A.P.2
Pleij, C.W.A.3
-
85
-
-
0025811124
-
Structure of an unusually stable RNA hairpin
-
Varani G., Cheong C., Tinoco I. Jr. Structure of an unusually stable RNA hairpin. Biochemistry. 30:1991;3280-3289.
-
(1991)
Biochemistry
, vol.30
, pp. 3280-3289
-
-
Varani, G.1
Cheong, C.2
Tinoco I., Jr.3
-
86
-
-
0028000994
-
Coaxial stacking of helixes enhances binding of oligoribonucleotides and improves predictions of RNA folding
-
Walter A. E., Turner D. H., Kim J., Lyttle M. H., Müller P., Mathews D. H., Zuker M. Coaxial stacking of helixes enhances binding of oligoribonucleotides and improves predictions of RNA folding. Proc. Natl Acad. Sci. USA. 91:1994a;9218-9222.
-
(1994)
Proc. Natl Acad. Sci. USA
, vol.91
, pp. 9218-9222
-
-
Walter, A.E.1
Turner, D.H.2
Kim, J.3
Lyttle, M.H.4
Müller, P.5
Mathews, D.H.6
Zuker, M.7
-
87
-
-
0028143014
-
Sequence dependence of stability for coaxial stacking of RNA helixes with Watson-Crick base paired interfaces
-
Walter A. E., Turner D. H. Sequence dependence of stability for coaxial stacking of RNA helixes with Watson-Crick base paired interfaces. Biochemistry. 33:1994b;12715-12719.
-
(1994)
Biochemistry
, vol.33
, pp. 12715-12719
-
-
Walter, A.E.1
Turner, D.H.2
-
88
-
-
0028085964
-
The stability and structure of tandem GA mismatches in RNA depend on closing base-pairs
-
Walter A. E., Wu M., Turner D. H. The stability and structure of tandem GA mismatches in RNA depend on closing base-pairs. Biochemistry. 33:1994c;11349-11354.
-
(1994)
Biochemistry
, vol.33
, pp. 11349-11354
-
-
Walter, A.E.1
Wu, M.2
Turner, D.H.3
-
89
-
-
0021256581
-
Assessment of a model for intron RNA secondary structure relevant to RNA self-splicing - A review
-
Waring R. B., Davies R. W. Assessment of a model for intron RNA secondary structure relevant to RNA self-splicing - a review. Gene. 28:1984;277-291.
-
(1984)
Gene.
, vol.28
, pp. 277-291
-
-
Waring, R.B.1
Davies, R.W.2
-
90
-
-
0027370486
-
Major groove accessibility of RNA
-
Weeks K. M., Crothers D. M. Major groove accessibility of RNA. Science. 261:1993;1574-1577.
-
(1993)
Science
, vol.261
, pp. 1574-1577
-
-
Weeks, K.M.1
Crothers, D.M.2
-
91
-
-
0029907105
-
Phylogenetic analysis of tmRNA secondary structure
-
Williams K. P., Bartel D. P. Phylogenetic analysis of tmRNA secondary structure. RNA. 2:1996;1306-1310.
-
(1996)
RNA
, vol.2
, pp. 1306-1310
-
-
Williams, K.P.1
Bartel, D.P.2
-
92
-
-
0021012648
-
Detailed analysis of the higher order structure of 16S-like ribosomal ribonucleic acids
-
Woese C. R., Gutell R. R., Gupta R., Noller H. F. Detailed analysis of the higher order structure of 16S-like ribosomal ribonucleic acids. Microbiol. Rev. 47:1983;621-669.
-
(1983)
Microbiol. Rev.
, vol.47
, pp. 621-669
-
-
Woese, C.R.1
Gutell, R.R.2
Gupta, R.3
Noller, H.F.4
-
93
-
-
0025047647
-
Architecture of ribosomal RNA: Constraints on the sequence of "tetra-loops."
-
Woese C. R., Winker S., Gutell R. R. Architecture of ribosomal RNA: constraints on the sequence of "tetra-loops." Proc. Natl Acad. Sci. USA. 87:1990;8467-8471.
-
(1990)
Proc. Natl Acad. Sci. USA
, vol.87
, pp. 8467-8471
-
-
Woese, C.R.1
Winker, S.2
Gutell, R.R.3
-
94
-
-
0028917227
-
A periodic table of symmetric tandem mismatches in RNA
-
Wu M., McDowell J. A., Turner D. H. A periodic table of symmetric tandem mismatches in RNA. Biochemistry. 34:1995;3204-3211.
-
(1995)
Biochemistry
, vol.34
, pp. 3204-3211
-
-
Wu, M.1
McDowell, J.A.2
Turner, D.H.3
-
95
-
-
0030815643
-
Thermodynamics of nonsymmetric tandem mismatches adjacent to G·C base pairs in RNA
-
Xia T., McDowell J. A., Turner D. H. Thermodynamics of nonsymmetric tandem mismatches adjacent to G·C base pairs in RNA. Biochemistry. 36:1997;12486-12487.
-
(1997)
Biochemistry
, vol.36
, pp. 12486-12487
-
-
Xia, T.1
McDowell, J.A.2
Turner, D.H.3
-
96
-
-
0032552882
-
Parameters for an expanded nearest-neighbor model for formation of RNA duplexes with Watson-Crick pairs
-
Xia T., SantaLucia J. Jr, Burkard M. E., Kierzek R., Schroeder S. J., Jiao X., Cox C., Turner D. H. Parameters for an expanded nearest-neighbor model for formation of RNA duplexes with Watson-Crick pairs. Biochemistry. 37:1998;14719-14735.
-
(1998)
Biochemistry
, vol.37
, pp. 14719-14735
-
-
Xia, T.1
Santalucia J., Jr.2
Burkard, M.E.3
Kierzek, R.4
Schroeder, S.J.5
Jiao, X.6
Cox, C.7
Turner, D.H.8
-
97
-
-
0030700595
-
The relative stabilities of base-pair stacking interactions and single mismatches in long RNA measured by temperature gradient gel electrophoresis
-
Zhu J., Wartell R. M. The relative stabilities of base-pair stacking interactions and single mismatches in long RNA measured by temperature gradient gel electrophoresis. Biochemistry. 36:1997;15326-15335.
-
(1997)
Biochemistry
, vol.36
, pp. 15326-15335
-
-
Zhu, J.1
Wartell, R.M.2
-
98
-
-
0024477261
-
On finding all suboptimal foldings of an RNA molecule
-
Zuker M. On finding all suboptimal foldings of an RNA molecule. Science. 244:1989;48-52.
-
(1989)
Science
, vol.244
, pp. 48-52
-
-
Zuker, M.1
-
99
-
-
0029131459
-
"well-determined" regions in RNA secondary structure predictions. Applications to small and large subunit rRNA
-
Zuker M., Jacobson A. B. "Well-determined" regions in RNA secondary structure predictions. Applications to small and large subunit rRNA. Nucl. Acids Res. 23:1995;2791-2798.
-
(1995)
Nucl. Acids Res.
, vol.23
, pp. 2791-2798
-
-
Zuker, M.1
Jacobson, A.B.2
-
100
-
-
0031745782
-
Using reliability information to annotate RNA secondary structures
-
Zuker M., Jacobson A. B. Using reliability information to annotate RNA secondary structures. RNA. 4:1998;669-679.
-
(1998)
RNA
, vol.4
, pp. 669-679
-
-
Zuker, M.1
Jacobson, A.B.2
-
101
-
-
0019876473
-
Optimal computer folding of large RNA sequences using thermodynamics and auxiliary information
-
Zuker M., Stiegler P. Optimal computer folding of large RNA sequences using thermodynamics and auxiliary information. Nucl. Acids Res. 9:1981;133-148.
-
(1981)
Nucl. Acids Res.
, vol.9
, pp. 133-148
-
-
Zuker, M.1
Stiegler, P.2
|