-
1
-
-
0004052742
-
Algorithms and thermodynamics for RNA secondary structure prediction: A practical guide
-
J. Barciszewski B.F.C. Clark RNA Biochemistry and Biotechnology Kluwer Academic Publishers Dodretch
-
M. Zuker, D.H. Mathews, and D.H. Turner Algorithms and thermodynamics for RNA secondary structure prediction: a practical guide J. Barciszewski B.F.C. Clark RNA Biochemistry and Biotechnology NATO ASI Series 1999 Kluwer Academic Publishers Dodretch
-
(1999)
NATO ASI Series
-
-
Zuker, M.1
Mathews, D.H.2
Turner, D.H.3
-
2
-
-
0036301332
-
Secondary structure prediction for aligned RNA sequences
-
I.L. Hofacker, M. Fekete, and P.F. Stadler Secondary structure prediction for aligned RNA sequences J. Mol. Biol. 319 2002 1059 1066
-
(2002)
J. Mol. Biol.
, vol.319
, pp. 1059-1066
-
-
Hofacker, I.L.1
Fekete, M.2
Stadler, P.F.3
-
3
-
-
0344012459
-
Thermodynamic criteria for high hit rate antisense oligonucleotide design
-
O.V. Matveeva, D.H. Mathews, A.D. Tsodikov, S.A. Shabalina, R.F. Gesteland, J.F. Atkins, and S.M. Freier Thermodynamic criteria for high hit rate antisense oligonucleotide design Nucl. Acids Res. 31 2003 4989 4994
-
(2003)
Nucl. Acids Res.
, vol.31
, pp. 4989-4994
-
-
Matveeva, O.V.1
Mathews, D.H.2
Tsodikov, A.D.3
Shabalina, S.A.4
Gesteland, R.F.5
Atkins, J.F.6
Freier, S.M.7
-
4
-
-
0037401145
-
Modelling hybridization kinetics
-
J.-Y. Wang, and K. Drlica Modelling hybridization kinetics Math. Biosci. 183 2003 37 47
-
(2003)
Math. Biosci.
, vol.183
, pp. 37-47
-
-
Wang, J.-Y.1
Drlica, K.2
-
5
-
-
0032483347
-
Cleavage of highly structured viral RNA molecules by combinatorial libraries of hairpin ribozymes
-
Q. Yu, D.B. Pecchia, S.L. Kigsley, J.E. Heckman, and H.M. Burke Cleavage of highly structured viral RNA molecules by combinatorial libraries of hairpin ribozymes J. Biol. Chem. 273 1998 23524 23533
-
(1998)
J. Biol. Chem.
, vol.273
, pp. 23524-23533
-
-
Yu, Q.1
Pecchia, D.B.2
Kigsley, S.L.3
Heckman, J.E.4
Burke, H.M.5
-
6
-
-
0042121256
-
Mfold web server for nucleic acid folding and hybridization prediction
-
M. Zuker Mfold web server for nucleic acid folding and hybridization prediction Nucl. Acids Res. 31 2003 3406 3415
-
(2003)
Nucl. Acids Res.
, vol.31
, pp. 3406-3415
-
-
Zuker, M.1
-
7
-
-
34249772381
-
Fast folding and comparison of RNA secondary structures
-
I.L. Hofacker, W. Fontana, P.F. Stadler, L.S. Bonhoeffer, M. Tacker, and P. Schuster Fast folding and comparison of RNA secondary structures Chem. Monthly 125 1994 167 188
-
(1994)
Chem. Monthly
, 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
-
8
-
-
0032729689
-
Predicting oligonucleotide affinity to nucleic acid targets
-
D.H. Mathews, M.E. Burkard, S.M. Freier, J.R. Wyatt, and D.H. Turner Predicting oligonucleotide affinity to nucleic acid targets RNA 5 1999 1458 1469
-
(1999)
RNA
, vol.5
, pp. 1458-1469
-
-
Mathews, D.H.1
Burkard, M.E.2
Freier, S.M.3
Wyatt, J.R.4
Turner, D.H.5
-
9
-
-
0035687548
-
Selection of targets and the most efficient hairpin ribozymes for inactivation of mRNAs using a self-cleaving RNA library
-
A. Barroso-delJesus, and A. Berzal-Herranz Selection of targets and the most efficient hairpin ribozymes for inactivation of mRNAs using a self-cleaving RNA library EMBO Rep. 2 2001 1112 1118
-
(2001)
EMBO Rep.
, vol.2
, pp. 1112-1118
-
-
Barroso-Deljesus, A.1
Berzal-Herranz, A.2
-
10
-
-
2642555548
-
An autonomous molecular computer for logical control of gene expression
-
Y. Benenson, B. Gil, U. Ben-Dor, R. Adar, and E. Shapiro An autonomous molecular computer for logical control of gene expression Nature 429 2004 423 429
-
(2004)
Nature
, vol.429
, pp. 423-429
-
-
Benenson, Y.1
Gil, B.2
Ben-Dor, U.3
Adar, R.4
Shapiro, E.5
-
12
-
-
0033591465
-
Expanded sequence dependence of thermodynamic parameters improves prediction of RNA secondary structure
-
D.H. Mathews, J. Sabina, M. Zuker, and D.H. Turner Expanded sequence dependence of thermodynamic parameters improves prediction of RNA secondary structure J. Mol. Biol. 288 1999 911 940
-
(1999)
J. Mol. Biol.
, vol.288
, pp. 911-940
-
-
Mathews, D.H.1
Sabina, J.2
Zuker, M.3
Turner, D.H.4
-
13
-
-
0032539693
-
A unified view of polymer, dumbbell, and oligonucleotide DNA nearest neighbour thermodynamics
-
J. SantaLucia Jr A unified view of polymer, dumbbell, and oligonucleotide DNA nearest neighbour thermodynamics Proc. Natl Acad. Sci. USA 92 1998 1460 1465
-
(1998)
Proc. Natl Acad. Sci. USA
, vol.92
, pp. 1460-1465
-
-
Santalucia, J.1
Jr2
-
14
-
-
0019876473
-
Optimal computer folding of large RNA sequences using thermodynamics and auxiliary information
-
M. Zuker, and P. Stiegler 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
-
15
-
-
0025944267
-
DNA probes: Applications of the principles of nucleic acid hybridization
-
J.G. Wetmur DNA probes: applications of the principles of nucleic acid hybridization Crit. Rev. Biochem. Mol. Biol. 26 1991 227 259
-
(1991)
Crit. Rev. Biochem. Mol. Biol.
, vol.26
, pp. 227-259
-
-
Wetmur, J.G.1
-
16
-
-
0033080745
-
Complete sub-optimal folding of RNA and the stability of secondary structures
-
S. Wuchty, W. Fontana, I.L. Hofacker, and P. Schuster Complete sub-optimal folding of RNA and the stability of secondary structures Biopolymers 49 1999 145 165
-
(1999)
Biopolymers
, vol.49
, pp. 145-165
-
-
Wuchty, S.1
Fontana, W.2
Hofacker, I.L.3
Schuster, P.4
-
17
-
-
0036606177
-
Measurements of weak interactions between truncated substrates and a hammerhead ribozyme by competitive kinetic analyses: Implications for the design of new and efficient ribozymes with high sequence specificity
-
Y. Kasai, H. Shizuku, Y. Takagi, M. Warashina, and K. Taira Measurements of weak interactions between truncated substrates and a hammerhead ribozyme by competitive kinetic analyses: implications for the design of new and efficient ribozymes with high sequence specificity Nucl. Acids Res. 30 2002 2383 2389
-
(2002)
Nucl. Acids Res.
, vol.30
, pp. 2383-2389
-
-
Kasai, Y.1
Shizuku, H.2
Takagi, Y.3
Warashina, M.4
Taira, K.5
-
18
-
-
0032403146
-
Recent developments in the hammerhead ribozyme field
-
N.K. Vaish, A.R. Kore, and F. Eckstein Recent developments in the hammerhead ribozyme field Nucl. Acids Res. 26 1998 5237 5242
-
(1998)
Nucl. Acids Res.
, vol.26
, pp. 5237-5242
-
-
Vaish, N.K.1
Kore, A.R.2
Eckstein, F.3
-
19
-
-
0030813878
-
The subcellular localization and length of hammerhead ribozymes determine efficacy in human cells
-
R. Hormes, M. Homann, I. Oelze, P. Marschall, M. Tabler, F. Eckstein, and G. Sczakiel The subcellular localization and length of hammerhead ribozymes determine efficacy in human cells Nucl. Acids Res. 25 1997 769 775
-
(1997)
Nucl. Acids Res.
, vol.25
, pp. 769-775
-
-
Hormes, R.1
Homann, M.2
Oelze, I.3
Marschall, P.4
Tabler, M.5
Eckstein, F.6
Sczakiel, G.7
-
20
-
-
0034651754
-
RNA double cleavage by a hairpin-derived twin ribozyme
-
C. Schmidt, R. Welz, and S. Miller RNA double cleavage by a hairpin-derived twin ribozyme Nucl. Acids Res. 28 2000 886 894
-
(2000)
Nucl. Acids Res.
, vol.28
, pp. 886-894
-
-
Schmidt, C.1
Welz, R.2
Miller, S.3
-
21
-
-
0035848837
-
Crystal structure of a hairpin ribozyme-inhibitor complex with implications for catalysis
-
P.B. Rupert, and A.R. Ferre-d'Amare Crystal structure of a hairpin ribozyme-inhibitor complex with implications for catalysis Nature 410 2001 780 786
-
(2001)
Nature
, vol.410
, pp. 780-786
-
-
Rupert, P.B.1
Ferre-D'Amare, A.R.2
-
22
-
-
0034004464
-
Intracellular ribozyme-catalyzed trans-cleavage of RNA monitored by fluorescence resonance energy transfer
-
D. Vitiello, D.B. Pecchia, and J.M. Burke Intracellular ribozyme-catalyzed trans-cleavage of RNA monitored by fluorescence resonance energy transfer RNA 6 2000 628 637
-
(2000)
RNA
, vol.6
, pp. 628-637
-
-
Vitiello, D.1
Pecchia, D.B.2
Burke, J.M.3
-
23
-
-
0035957257
-
A conformational change in the "loop E-like" motif of the hairpin ribozyme is coincidental with domain docking and is essential for catalysis
-
K.J. Hampel, and J.M. Burke A conformational change in the "loop E-like" motif of the hairpin ribozyme is coincidental with domain docking and is essential for catalysis Biochemistry 40 2001 3723 3729
-
(2001)
Biochemistry
, vol.40
, pp. 3723-3729
-
-
Hampel, K.J.1
Burke, J.M.2
-
24
-
-
0038475923
-
Substrate specificity and reaction kinetics of an X-motif ribozyme
-
D. Lazarev, I. Puskarz, and R.R. Breaker Substrate specificity and reaction kinetics of an X-motif ribozyme RNA 9 2003 688 697
-
(2003)
RNA
, vol.9
, pp. 688-697
-
-
Lazarev, D.1
Puskarz, I.2
Breaker, R.R.3
-
25
-
-
0032530868
-
Mechanism for allosteric inhibition of an ATP-sensitive ribozyme
-
J. Tang, and R.R. Breaker Mechanism for allosteric inhibition of an ATP-sensitive ribozyme Nucl. Acids Res. 26 1998 4214 4221
-
(1998)
Nucl. Acids Res.
, vol.26
, pp. 4214-4221
-
-
Tang, J.1
Breaker, R.R.2
-
26
-
-
0035671634
-
Interactions of mRNAs and gRNAs involved in trypanosome mitochondrial RNA editing: Structure probing of an mRNA bound to its cognate gRNA
-
S.S. Leung, and D.J. Koslowsky Interactions of mRNAs and gRNAs involved in trypanosome mitochondrial RNA editing: structure probing of an mRNA bound to its cognate gRNA RNA 7 2001 1803 1816
-
(2001)
RNA
, vol.7
, pp. 1803-1816
-
-
Leung, S.S.1
Koslowsky, D.J.2
-
27
-
-
0032832044
-
Ribozyme cleavage of a 2′,5′-phosphodiester linkage: Mechanism and a restricted divalent metal-ion requirement
-
I.-H. Shih, and M.D. Been Ribozyme cleavage of a 2′,5′- phosphodiester linkage: mechanism and a restricted divalent metal-ion requirement RNA 5 1999 1140 1148
-
(1999)
RNA
, vol.5
, pp. 1140-1148
-
-
Shih, I.-H.1
Been, M.D.2
-
28
-
-
0035504748
-
Catalytic cleavage of cis- and trans-acting antigenomic delta ribozymes in the presence of various divalent metal ions
-
J. Wrzesinski, M. Legiewicz, B. Smólska, and J. Ciesiolka Catalytic cleavage of cis- and trans-acting antigenomic delta ribozymes in the presence of various divalent metal ions Nucl. Acids Res. 29 2001 4482 4492
-
(2001)
Nucl. Acids Res.
, vol.29
, pp. 4482-4492
-
-
Wrzesinski, J.1
Legiewicz, M.2
Smólska, B.3
Ciesiolka, J.4
-
29
-
-
0031591383
-
The structure of an RNA "kissing" hairpin complex of the HIV TAR hairpin loop and its complement
-
K.-Y. Chang, and I. Tinoco 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
-
-
Chang, K.-Y.1
Tinoco Jr., I.2
-
30
-
-
0344474519
-
A role for U2/U6 helix lb in 5′ splice site selection
-
B.G.M. Luukkonen, and B. Séraphin A role for U2/U6 helix lb in 5′ splice site selection RNA 4 1998 915 927
-
(1998)
RNA
, vol.4
, pp. 915-927
-
-
Luukkonen, B.G.M.1
Séraphin, B.2
-
31
-
-
0036297657
-
Direct probing of RNA structure and RNA-protein interactions in purified HeLa cells and yeast spliceosomal U4/U6.U5 tri-snRNP particles
-
A. Mougin, A. Gottschalk, P. Fabrizio, R. Lührmann, and C. Branlant Direct probing of RNA structure and RNA-protein interactions in purified HeLa cells and yeast spliceosomal U4/U6.U5 tri-snRNP particles J. Mol. Biol. 317 2002 631 649
-
(2002)
J. Mol. Biol.
, vol.317
, pp. 631-649
-
-
Mougin, A.1
Gottschalk, A.2
Fabrizio, P.3
Lührmann, R.4
Branlant, C.5
-
32
-
-
0033596964
-
Nearest-neighbor thermodynamics and NMR of DNA sequences with internal A·A, C·C, G·G and T·T mismatches
-
N. Peyret, A.P. Seneviratne, H.T. Allawi, and J. SantaLucia Jr Nearest-neighbor thermodynamics and NMR of DNA sequences with internal A·A, C·C, G·G and T·T mismatches Biochemistry 38 1999 3468 3477
-
(1999)
Biochemistry
, vol.38
, pp. 3468-3477
-
-
Peyret, N.1
Seneviratne, A.P.2
Allawi, H.T.3
SantaLucia Jr., J.4
-
33
-
-
0032552882
-
Thermodynamic parameters for an expanded nearest-neighbor model for formation of RNA duplexes with Watson-Crick base-pairs
-
T. Xia, J. SantaLucia Jr, M.E. Burkard, R. Kierzek, S.J. Schroeder, and X. Jiao Thermodynamic parameters for an expanded nearest-neighbor model for formation of RNA duplexes with Watson-Crick base-pairs Biochemistry 37 1998 14719 14735
-
(1998)
Biochemistry
, vol.37
, pp. 14719-14735
-
-
Xia, T.1
SantaLucia Jr., J.2
Burkard, M.E.3
Kierzek, R.4
Schroeder, S.J.5
Jiao, X.6
-
34
-
-
0035890245
-
Functional involvement of G8 in the hairpin ribozyme cleavage mechanism
-
R. Pinard, K.J. Hampel, J.E. Heckman, D. Lambert, P.A. Chan, F. Major, and J.M. Burke Functional involvement of G8 in the hairpin ribozyme cleavage mechanism EMBO J. 20 2001 6434 6442
-
(2001)
EMBO J.
, vol.20
, pp. 6434-6442
-
-
Pinard, R.1
Hampel, K.J.2
Heckman, J.E.3
Lambert, D.4
Chan, P.A.5
Major, F.6
Burke, J.M.7
-
35
-
-
0029868499
-
Oligonucleotide facilitators may inhibit or activate a hammerhead ribozyme
-
E. Jankowsky, and B. Schwenzer Oligonucleotide facilitators may inhibit or activate a hammerhead ribozyme Nucl. Acids Res. 24 1996 423 429
-
(1996)
Nucl. Acids Res.
, vol.24
, pp. 423-429
-
-
Jankowsky, E.1
Schwenzer, B.2
-
36
-
-
0347724163
-
An iterated loop matching approach to the prediction of RNA secondary structures with pseudoknots
-
J. Ruan, G.D. Stormo, and W. Zhang An iterated loop matching approach to the prediction of RNA secondary structures with pseudoknots Bioinformatics 20 2004 58 66
-
(2004)
Bioinformatics
, vol.20
, pp. 58-66
-
-
Ruan, J.1
Stormo, G.D.2
Zhang, W.3
-
37
-
-
0037154101
-
Experimentally derived nearest-neighbor parameters for the stability of RNA three- and four-way multibranch loops
-
D.H. Mathews, and D.H. Turner Experimentally derived nearest-neighbor parameters for the stability of RNA three- and four-way multibranch loops Bioinformatics 41 2002 869 880
-
(2002)
Bioinformatics
, vol.41
, pp. 869-880
-
-
Mathews, D.H.1
Turner, D.H.2
-
39
-
-
35248820719
-
Algorithms for testing that sets of DNA words concatenate without secondary structure
-
M. Andronescu, D. Dees, L. Slaybaugh, Y. Zhao, B. Cohen, A. Condon, and S. Skiena Algorithms for testing that sets of DNA words concatenate without secondary structure Proc. Eighth Int. Workshop DNA Based Computers, Hokkaido, Japan, LNCS. 2568, Springer 2003 2002 182 195
-
(2002)
Proc. Eighth Int. Workshop DNA Based Computers, Hokkaido, Japan, LNCS. 2568, Springer 2003
, pp. 182-195
-
-
Andronescu, M.1
Dees, D.2
Slaybaugh, L.3
Zhao, Y.4
Cohen, B.5
Condon, A.6
Skiena, S.7
-
40
-
-
0043285072
-
A partition function algorithm for nucleic acid secondary structure including pseudoknots
-
R.M. Dirks, and N.A. Pierce A partition function algorithm for nucleic acid secondary structure including pseudoknots J. Comput. Chem. 24 2003 1664 1677
-
(2003)
J. Comput. Chem.
, vol.24
, pp. 1664-1677
-
-
Dirks, R.M.1
Pierce, N.A.2
-
41
-
-
0033524952
-
A dynamic programming algorithm for RNA structure prediction including pseudoknots
-
E. Rivas, and S.R. Eddy A dynamic programming algorithm for RNA structure prediction including pseudoknots J. Mol. Biol. 285 1999 2053 2068
-
(1999)
J. Mol. Biol.
, vol.285
, pp. 2053-2068
-
-
Rivas, E.1
Eddy, S.R.2
-
42
-
-
0025264854
-
The equilibrium partition function and base-pair binding probabilities for RNA secondary structure
-
J.S. McCaskill The equilibrium partition function and base-pair binding probabilities for RNA secondary structure Biopolymers 29 1990 1105 1119
-
(1990)
Biopolymers
, vol.29
, pp. 1105-1119
-
-
McCaskill, J.S.1
|