-
1
-
-
0016792988
-
5S-RNA secondary structure
-
Fox, G. E., and Woese, C. R. (1975) 5S-RNA secondary structure, Nature 256, 505-507.
-
(1975)
Nature
, vol.256
, pp. 505-507
-
-
Fox, G.E.1
Woese, C.R.2
-
2
-
-
0001899745
-
Probing RNA structure, function, and history by comparative analysis
-
(Gesteland, R. F., Cech, T. R., Atkins, J. F., Eds.), Cold Spring Harbor Press, New York
-
Pace, N. R., Thomas, B. C., and Woese, C. R. (1999) Probing RNA structure, function, and history by comparative analysis, in The RNA World (Gesteland, R. F., Cech, T. R., Atkins, J. F., Eds.) pp 113-141, Cold Spring Harbor Press, New York.
-
(1999)
The RNA World
, pp. 113-141
-
-
Pace, N.R.1
Thomas, B.C.2
Woese, C.R.3
-
3
-
-
0346971259
-
ITS secondary structure derived from comparative analysis: Implications for sequence alignment and phylogeny of the Asteraceae
-
Goertzen, L. R., Cannone, J. J., Gutell, R. R., and Jansen, R. K. (2003) ITS secondary structure derived from comparative analysis: Implications for sequence alignment and phylogeny of the Asteraceae, Mol. Phylogenet. Evol. 29, 216-234.
-
(2003)
Mol. Phylogenet. Evol.
, vol.29
, pp. 216-234
-
-
Goertzen, L.R.1
Cannone, J.J.2
Gutell, R.R.3
Jansen, R.K.4
-
4
-
-
2942571539
-
The Comparative RNA Web (CRW) Site: An online database of comparative sequence and structure information for ribosomal, intron, and other RNAs
-
Cannone, J. J., Subramanian, S., Schnare, M. N., Collett, J. R., D'Souza, L. M., Du, Y. S., Feng, B., Lin, N., Madabusi, L. V., Muller, K. M., Pande, N., Shang, Z. D., Yu, N., and Gutell, R. R. (2002) The Comparative RNA Web (CRW) Site: An online database of comparative sequence and structure information for ribosomal, intron, and other RNAs, BMC Bioinf. 3.
-
(2002)
BMC Bioinf.
, vol.3
-
-
Cannone, J.J.1
Subramanian, S.2
Schnare, M.N.3
Collett, J.R.4
D'Souza, L.M.5
Du, Y.S.6
Feng, B.7
Lin, N.8
Madabusi, L.V.9
Muller, K.M.10
Pande, N.11
Shang, Z.D.12
Yu, N.13
Gutell, R.R.14
-
5
-
-
0035890840
-
RNAMotif, an RNA secondary structure definition and search algorithm
-
Macke, T. J., Ecker, D. J., Gutell, R. R., Gautheret, D., Case, D. A., and Sampath, R. (2001) RNAMotif, an RNA secondary structure definition and search algorithm, Nucleic Acids Res. 29, 4724-4735.
-
(2001)
Nucleic Acids Res.
, vol.29
, pp. 4724-4735
-
-
Macke, T.J.1
Ecker, D.J.2
Gutell, R.R.3
Gautheret, D.4
Case, D.A.5
Sampath, R.6
-
6
-
-
0024477261
-
On finding all suboptimal foldings of an RNA molecule
-
Zuker, M. (1989) On finding all suboptimal foldings of an RNA molecule, Science 244, 48-52.
-
(1989)
Science
, vol.244
, pp. 48-52
-
-
Zuker, M.1
-
7
-
-
0033591465
-
Expanded sequence dependence of thermodynamic parameters improves prediction of RNA secondary structure
-
Mathews, D. H., Sabina, J., Zuker, M., and Turner, D. H. (1999) Expanded sequence dependence of thermodynamic parameters improves prediction of RNA secondary structure, J. Mol. Biol. 288, 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
-
8
-
-
0005822936
-
Improved estimation of secondary structure in ribonucleic acids
-
Tinoco, I., Borer, P. N., Dengler, B., Levine, M. D., Uhlenbeck, O. C., Crothers, D. M., and Gralla, J. (1973) Improved estimation of secondary structure in ribonucleic acids, Nature, New Biol. 246, 40-41.
-
(1973)
Nature, New Biol.
, vol.246
, pp. 40-41
-
-
Tinoco, I.1
Borer, P.N.2
Dengler, B.3
Levine, M.D.4
Uhlenbeck, O.C.5
Crothers, D.M.6
Gralla, J.7
-
9
-
-
0032552882
-
Thermodynamic parameters for an expanded nearest-neighbor model for formation of RNA duplexes with Watson-Crick base pairs
-
Xia, T. B., SantaLucia, J., Burkard, M. E., Kierzek, R., Schroeder, S. J., Jiao, X. Q., Cox, C., and Turner, D. H. (1998) Thermodynamic parameters for an expanded nearest-neighbor model for formation of RNA duplexes with Watson-Crick base pairs, Biochemistry 37, 14719-14735.
-
(1998)
Biochemistry
, vol.37
, pp. 14719-14735
-
-
Xia, T.B.1
Santalucia, J.2
Burkard, M.E.3
Kierzek, R.4
Schroeder, S.J.5
Jiao, X.Q.6
Cox, C.7
Turner, D.H.8
-
10
-
-
0002549050
-
Thermodynamics of RNA secondary structure formation, in Prebiotic Chemistry
-
(Soll, D. G., Nishimura, S., and Moore, P. B., Eds.), Elsevier, New York
-
Xia, T. B., Mathews, D. H., and Turner, D. H. (1999) Thermodynamics of RNA secondary structure formation, in Prebiotic Chemistry, Molecular Fossils, Nucleosides, and RNA (Soll, D. G., Nishimura, S., and Moore, P. B., Eds.) pp 21-48, Elsevier, New York.
-
(1999)
Molecular Fossils, Nucleosides, and RNA
, pp. 21-48
-
-
Xia, T.B.1
Mathews, D.H.2
Turner, D.H.3
-
11
-
-
0002635816
-
Conformational changes
-
(Bloomfield, V. A., Crothers, D. M., and Tinoco, I., Eds.), University Science Book, Sausalito, CA
-
Turner, D. H. (2000) Conformational changes, in Nucleic Acids (Bloomfield, V. A., Crothers, D. M., and Tinoco, I., Eds.) pp 259-334, University Science Book, Sausalito, CA.
-
(2000)
Nucleic Acids
, pp. 259-334
-
-
Turner, D.H.1
-
12
-
-
0019876473
-
Optimal computer folding of large RNA sequences using thermodynamics and auxiliary information
-
Zuker, M., and Stiegler, P. (1981) Optimal computer folding of large RNA sequences using thermodynamics and auxiliary information, Nucleic Acids Res. 9, 133-148.
-
(1981)
Nucleic Acids Res.
, vol.9
, pp. 133-148
-
-
Zuker, M.1
Stiegler, P.2
-
13
-
-
2442626706
-
Incorporating chemical modification constraints into a dynamic programming algorithm for prediction of RNA secondary structure
-
Mathews, D. H., Disney, M. D., Childs, J. L., Schroeder, S. J., Zuker, M., and Turner, D. H. (2004) Incorporating chemical modification constraints into a dynamic programming algorithm for prediction of RNA secondary structure, Proc. Natl. Acad. Sci. U.S.A. 101, 7287-7292.
-
(2004)
Proc. Natl. Acad. Sci. U.S.A.
, vol.101
, pp. 7287-7292
-
-
Mathews, D.H.1
Disney, M.D.2
Childs, J.L.3
Schroeder, S.J.4
Zuker, M.5
Turner, D.H.6
-
14
-
-
0014935515
-
Complementary oligonucleotide binding to the anticodon loop of fMet transfer RNA
-
Uhlenbeck, O. C., Baller, J., and Doty, P. (1970) Complementary oligonucleotide binding to the anticodon loop of fMet transfer RNA, Nature 225, 508-510.
-
(1970)
Nature
, vol.225
, pp. 508-510
-
-
Uhlenbeck, O.C.1
Baller, J.2
Doty, P.3
-
15
-
-
0015505497
-
Complementary oligonucleotide binding to transfer RNA
-
Uhlenbeck, O. C. (1972) Complementary oligonucleotide binding to transfer RNA, J. Mol. Biol. 65, 25-41.
-
(1972)
J. Mol. Biol.
, vol.65
, pp. 25-41
-
-
Uhlenbeck, O.C.1
-
16
-
-
0014935509
-
Derivation of the secondary structure of 5S RNA from its binding of complementary oligonucleotides
-
Lewis, J. B., and Doty, P. (1970) Derivation of the secondary structure of 5S RNA from its binding of complementary oligonucleotides, Nature 225, 510-512.
-
(1970)
Nature
, vol.225
, pp. 510-512
-
-
Lewis, J.B.1
Doty, P.2
-
17
-
-
0030902471
-
Selecting effective antisense reagents on combinatorial oligonucleotide arrays
-
Milner, N., Mir, K. U., and Southern, E. M. (1997) Selecting effective antisense reagents on combinatorial oligonucleotide arrays, Nat. Biotechnol. 15, 537-541.
-
(1997)
Nat. Biotechnol.
, vol.15
, pp. 537-541
-
-
Milner, N.1
Mir, K.U.2
Southern, E.M.3
-
18
-
-
0032890879
-
The folding of large RNAs studied by hybridization to arrays of complementary oligonucleotides
-
Sohail, M., Akhtar, S., and Southern, E. M. (1999) The folding of large RNAs studied by hybridization to arrays of complementary oligonucleotides, RNA 5, 646-655.
-
(1999)
RNA
, vol.5
, pp. 646-655
-
-
Sohail, M.1
Akhtar, S.2
Southern, E.M.3
-
19
-
-
0035873670
-
Antisense oligonucleotides selected by hybridization to scanning arrays are effective reagents in vivo
-
Sohail, M., Hochegger, H., Klotzbucher, A., Le Guellec, R., Hunt, T., and Southern, E. M. (2001) Antisense oligonucleotides selected by hybridization to scanning arrays are effective reagents in vivo, Nucleic Acids Res. 29, 2041-2051.
-
(2001)
Nucleic Acids Res.
, vol.29
, pp. 2041-2051
-
-
Sohail, M.1
Hochegger, H.2
Klotzbucher, A.3
Le Guellec, R.4
Hunt, T.5
Southern, E.M.6
-
20
-
-
0033796357
-
Sequencing by hybridization with the generic 6-mer oligonucleotide microarray: An advanced scheme for data processing
-
Chechetkin, V. R., Turygin, A. Y., Proudnikov, D. Y., Prokopenko, D. V., Kirillov, E. V., and Mirzabekov, A. D. (2000) Sequencing by hybridization with the generic 6-mer oligonucleotide microarray: An advanced scheme for data processing, J. Biomol. Struct. Dyn. 18, 83-101.
-
(2000)
J. Biomol. Struct. Dyn.
, vol.18
, pp. 83-101
-
-
Chechetkin, V.R.1
Turygin, A.Y.2
Proudnikov, D.Y.3
Prokopenko, D.V.4
Kirillov, E.V.5
Mirzabekov, A.D.6
-
21
-
-
0031866152
-
5S rRNA data bank
-
Szymanski, M., Specht, T., Barciszewska, M. Z., Barciszewski, J., and Erdmann, V. A. (1998) 5S rRNA data bank, Nucleic Acids Res. 26, 156-159.
-
(1998)
Nucleic Acids Res.
, vol.26
, pp. 156-159
-
-
Szymanski, M.1
Specht, T.2
Barciszewska, M.Z.3
Barciszewski, J.4
Erdmann, V.A.5
-
22
-
-
0031574326
-
The loop e loop D region of Escherichia coll 5S rRNA: The solution structure reveals an unusual loop that may be important for binding ribosomal proteins
-
Dallas, A., and Moore, P. B. (1997) The loop E loop D region of Escherichia coll 5S rRNA: The solution structure reveals an unusual loop that may be important for binding ribosomal proteins, Structure 5, 1639-1653.
-
(1997)
Structure
, vol.5
, pp. 1639-1653
-
-
Dallas, A.1
Moore, P.B.2
-
23
-
-
0030856333
-
Metals, motifs, and recognition in the crystal structure of a 5S rRNA domain
-
Correll, C. C., Freeborn, B., Moore, P. B., and Steitz, T. A. (1997) Metals, motifs, and recognition in the crystal structure of a 5S rRNA domain, Cell 91, 705-712.
-
(1997)
Cell
, vol.91
, pp. 705-712
-
-
Correll, C.C.1
Freeborn, B.2
Moore, P.B.3
Steitz, T.A.4
-
24
-
-
0034637111
-
The complete atomic structure of the large ribosomal subunit at 2.4 Å resolution
-
Ban, N., Nissen, P., Hansen, J., Moore, P. B., and Steitz, T. A. (2000) The complete atomic structure of the large ribosomal subunit at 2.4 Å resolution, Science 289, 905-920.
-
(2000)
Science
, vol.289
, pp. 905-920
-
-
Ban, N.1
Nissen, P.2
Hansen, J.3
Moore, P.B.4
Steitz, T.A.5
-
26
-
-
0024263088
-
5S RNA structure and function
-
Geringer, H. U., and Wagner, R. (1988) 5S RNA structure and function, Method Enzymol. 164, 721-747.
-
(1988)
Method Enzymol.
, vol.164
, pp. 721-747
-
-
Geringer, H.U.1
Wagner, R.2
-
27
-
-
0022430997
-
Alternative conformers of 5S ribosomal-RNA and their biological relevance
-
Christensen, A., Mathiesen, M., Peattie, D., and Garrett, R. A. (1985) Alternative conformers of 5S ribosomal-RNA and their biological relevance, Biochemistry 24, 2284-2291.
-
(1985)
Biochemistry
, vol.24
, pp. 2284-2291
-
-
Christensen, A.1
Mathiesen, M.2
Peattie, D.3
Garrett, R.A.4
-
28
-
-
0017604507
-
Does 5S RNA function by a switch between two secondary structures?
-
Weidner, H., Yuan, R., and Crothers, D. M. (1977) Does 5S RNA function by a switch between two secondary structures? Nature 266, 193-194.
-
(1977)
Nature
, vol.266
, pp. 193-194
-
-
Weidner, H.1
Yuan, R.2
Crothers, D.M.3
-
29
-
-
0026722435
-
Chemical synthesis of deoxyoligonucleotides and deoxyoligo-nucleotide analogs
-
Caruthers, M. H., Beaton, G., Wu, J. V., and Wiesler, W. (1992) Chemical synthesis of deoxyoligonucleotides and deoxyoligo-nucleotide analogs, Methods Enzymol. 211, 3-20.
-
(1992)
Methods Enzymol.
, vol.211
, pp. 3-20
-
-
Caruthers, M.H.1
Beaton, G.2
Wu, J.V.3
Wiesler, W.4
-
30
-
-
0001009950
-
Nucleotide chemistry. 1. Synthesis of oligodeoxypyrimidines on a polymer support
-
Matteucci, M. D., and Caruthers, M. H. (1980) Nucleotide chemistry. 1. Synthesis of oligodeoxypyrimidines on a polymer support, Tetrahedron Lett. 21, 719-722.
-
(1980)
Tetrahedron Lett.
, vol.21
, pp. 719-722
-
-
Matteucci, M.D.1
Caruthers, M.H.2
-
31
-
-
0024804759
-
Absorbency melting curves of RNA
-
Puglisi, J. D., and Tinoco, I. (1989) Absorbency melting curves of RNA, Methods Enzymol. 180, 304-325.
-
(1989)
Methods Enzymol.
, vol.180
, pp. 304-325
-
-
Puglisi, J.D.1
Tinoco, I.2
-
32
-
-
0024195411
-
Preparation of 5S RNA-related materials for nuclear magnetic resonance and crystallography studies
-
Moore, P. B., Abo, S., Freeborn, B., Gewinn, D. T., Leontis, N. B., and Sun, G. (1988) Preparation of 5S RNA-related materials for nuclear magnetic resonance and crystallography studies, Methods Enzymol. 164, 158-174.
-
(1988)
Methods Enzymol.
, vol.164
, pp. 158-174
-
-
Moore, P.B.1
Abo, S.2
Freeborn, B.3
Gewinn, D.T.4
Leontis, N.B.5
Sun, G.6
-
33
-
-
16244412610
-
RNA structure analysis at single nucleotide resolution by selective 2′-hydroxyl acylation and primer extension (SHAPE)
-
Merino, E. J., Wilkinson, K. A., Coughlan, J. L., and Weeks, K. M. (2005) RNA structure analysis at single nucleotide resolution by selective 2′-hydroxyl acylation and primer extension (SHAPE), J. Am. Chem. Soc. 127, 4223-4231.
-
(2005)
J. Am. Chem. Soc.
, vol.127
, pp. 4223-4231
-
-
Merino, E.J.1
Wilkinson, K.A.2
Coughlan, J.L.3
Weeks, K.M.4
-
35
-
-
16344370497
-
RNA SHAPE chemistry reveals nonhierarchical interactions dominate equilibrium structural transitions in tRNA(Asp) transcripts
-
Wilkinson, K. A., Merino, E. J., and Weeks, K. M. (2005) RNA SHAPE chemistry reveals nonhierarchical interactions dominate equilibrium structural transitions in tRNA(Asp) transcripts, J. Am. Chem. Soc. 127, 4659-4667.
-
(2005)
J. Am. Chem. Soc.
, vol.127
, pp. 4659-4667
-
-
Wilkinson, K.A.1
Merino, E.J.2
Weeks, K.M.3
-
36
-
-
0034658890
-
Preparation of DNA and protein micro arrays on glass slides coated with an agarose film
-
Afanassiev, V. H., V., and Wölfl, S. (2000) Preparation of DNA and protein micro arrays on glass slides coated with an agarose film, Nucleic Acids Res. 28, e66.
-
(2000)
Nucleic Acids Res.
, vol.28
-
-
Afanassiev, V.H.V.1
Wölfl, S.2
-
37
-
-
0029805937
-
2 by two-dimensional NMR and simulated annealing
-
2 by two-dimensional NMR and simulated annealing, Biochemistry 35, 14077-14089.
-
(1996)
Biochemistry
, vol.35
, pp. 14077-14089
-
-
McDowell, J.A.1
Turner, D.H.2
-
38
-
-
0023665268
-
Probing the structure of RNAs in solution
-
Ehresmann, C., Baudin, F., Mougel, M., Romby, P., Ebel, J. P., and Ehresmann, B. (1987) Probing the structure of RNAs in solution, Nucleic Acids Res. 15, 9109-9128.
-
(1987)
Nucleic Acids Res.
, vol.15
, pp. 9109-9128
-
-
Ehresmann, C.1
Baudin, F.2
Mougel, M.3
Romby, P.4
Ebel, J.P.5
Ehresmann, B.6
-
39
-
-
0022470564
-
Rapid chemical probing of conformation in 16-S ribosomal-RNA and 30-S ribosomal-subunits using primer extension
-
Moazed, D., Stern, S., and Noller, H. F. (1986) Rapid chemical probing of conformation in 16-S ribosomal-RNA and 30-S ribosomal-subunits using primer extension, J. Mol. Biol. 187, 399-416.
-
(1986)
J. Mol. Biol.
, vol.187
, pp. 399-416
-
-
Moazed, D.1
Stern, S.2
Noller, H.F.3
-
40
-
-
0019875767
-
Secondary structure of prokaryotic 5S ribosomal ribonucleic-acids-A study with ribonucleases
-
Douthwaite, S., and Garrett, R. A. (1981) Secondary structure of prokaryotic 5S ribosomal ribonucleic-acids-A study with ribonucleases, Biochemistry 20, 7301-7307.
-
(1981)
Biochemistry
, vol.20
, pp. 7301-7307
-
-
Douthwaite, S.1
Garrett, R.A.2
-
41
-
-
0025771080
-
3-Dimensional model of Escherichia coli ribosomal 5-S RNA as deduced from structure probing in solution and computer modeling
-
Brunel, C., Romby, P., Westhof, E., Ehresmann, C., and Ehresmann, B. (1991) 3-Dimensional model of Escherichia coli ribosomal 5-S RNA as deduced from structure probing in solution and computer modeling, J. Mol. Biol. 221, 293-308.
-
(1991)
J. Mol. Biol.
, vol.221
, pp. 293-308
-
-
Brunel, C.1
Romby, P.2
Westhof, E.3
Ehresmann, C.4
Ehresmann, B.5
-
42
-
-
0023056963
-
Does 5S RNA from Escherichia coli have a pseudoknotted structure?
-
Goringer, H. U., and Wagner, R. (1986) Does 5S RNA from Escherichia coli have a pseudoknotted structure? Nucleic Acids Res. 14, 7473-7485.
-
(1986)
Nucleic Acids Res.
, vol.14
, pp. 7473-7485
-
-
Goringer, H.U.1
Wagner, R.2
-
43
-
-
0017895903
-
Molecular theory of polyelectrolyte solutions with applications to electrostatic properties of polynucleotides
-
Manning, G. S. (1978) Molecular theory of polyelectrolyte solutions with applications to electrostatic properties of polynucleotides, Q. Rev. Biophys. 11, 179-246.
-
(1978)
Q. Rev. Biophys.
, vol.11
, pp. 179-246
-
-
Manning, G.S.1
-
44
-
-
0016682305
-
Application of poly-electrolyte limiting laws to helix-coil transition of DNA. 3. Dependence of helix stability on excess univalent salt and on polynucleotide phosphate concentration for variable equivalent ratios of divalent metal-ion to phosphate
-
Demarky, N., and Manning, G. S. (1975) Application of poly-electrolyte limiting laws to helix-coil transition of DNA. 3. Dependence of helix stability on excess univalent salt and on polynucleotide phosphate concentration for variable equivalent ratios of divalent metal-ion to phosphate, Biopolymers 14, 1407-1422.
-
(1975)
Biopolymers
, vol.14
, pp. 1407-1422
-
-
Demarky, N.1
Manning, G.S.2
-
45
-
-
0029619816
-
Kinetic characteristics of Escherichia coli RNase HI-Cleavage of various antisense oligonucleotide-RNA duplexes
-
Crooke, S. T., Lemonidis, K. M., Neilson, L., Griffey, R., Lesnik, E. A., and Monia, B. P. (1995) Kinetic characteristics of Escherichia coli RNase HI-Cleavage of various antisense oligonucleotide-RNA duplexes, Biochem. J. 312, 599-608.
-
(1995)
Biochem. J.
, vol.312
, pp. 599-608
-
-
Crooke, S.T.1
Lemonidis, K.M.2
Neilson, L.3
Griffey, R.4
Lesnik, E.A.5
Monia, B.P.6
-
46
-
-
0027168725
-
Evaluation of 2′-modified oligonucleotides containing 2′-deoxy gaps as antisense inhibitors of gene expression
-
Monia, B. P., Lesnik, E. A., Gonzalez, C., Lima, W. F., McGee, D., Guinosso, C. J., Kawasaki, A. M., Cook, P. D., and Freier, S. M. (1993) Evaluation of 2′-modified oligonucleotides containing 2′-deoxy gaps as antisense inhibitors of gene expression, J. Biol. Chem. 268, 14514-14522.
-
(1993)
J. Biol. Chem.
, vol.268
, pp. 14514-14522
-
-
Monia, B.P.1
Lesnik, E.A.2
Gonzalez, C.3
Lima, W.F.4
McGee, D.5
Guinosso, C.J.6
Kawasaki, A.M.7
Cook, P.D.8
Freier, S.M.9
-
48
-
-
0025269255
-
A sodium-potassium switch in the formation of 4-stranded G4-DNA
-
Sen, D., and Gilbert, W. (1990) A sodium-potassium switch in the formation of 4-stranded G4-DNA, Nature 344, 410-414.
-
(1990)
Nature
, vol.344
, pp. 410-414
-
-
Sen, D.1
Gilbert, W.2
-
49
-
-
0023788886
-
Formation of parallel 4-stranded complexes by guanine-rich motifs in DNA and its implications for meiosis
-
Sen, D., and Gilbert, W. (1988) Formation of parallel 4-stranded complexes by guanine-rich motifs in DNA and its implications for meiosis, Nature 334, 364-366.
-
(1988)
Nature
, vol.334
, pp. 364-366
-
-
Sen, D.1
Gilbert, W.2
-
50
-
-
0032729689
-
Predicting oligonucleotide affinity to nucleic acid targets
-
Mathews, D. H., Burkard, M. E., Freier, S. M., Wyatt, J. R., and Turner, D. H. (1999) Predicting oligonucleotide affinity to nucleic acid targets, RNA 5, 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
-
51
-
-
25144497136
-
The influence of locked nucleic acid residues on the thermodynamic properties of 2′-O-methyl RNA/RNA heteroduplexes
-
Kierzek, E., Ciesielska, A., Pasternak, K., Mathews, D. H., Turner, D. H., and Kierzek, R. (2005) The influence of locked nucleic acid residues on the thermodynamic properties of 2′-O-methyl RNA/RNA heteroduplexes, Nucleic Acids Res. 33, 5082-5093.
-
(2005)
Nucleic Acids Res.
, vol.33
, pp. 5082-5093
-
-
Kierzek, E.1
Ciesielska, A.2
Pasternak, K.3
Mathews, D.H.4
Turner, D.H.5
Kierzek, R.6
-
52
-
-
0028143014
-
Sequence dependence of stability for coaxial stacking of RNA helixes with Watson-Crick base paired interfaces
-
Walter, A. E., and Turner, D. H. (1994) Sequence dependence of stability for coaxial stacking of RNA helixes with Watson-Crick base paired interfaces, Biochemistry 33, 12715-12719.
-
(1994)
Biochemistry
, vol.33
, pp. 12715-12719
-
-
Walter, A.E.1
Turner, D.H.2
-
53
-
-
0026335264
-
Nearest-neighbor parameters for GU mismatches-5′GU3′/ 3′UG5′ is destabilizing in the contexts CGUG/GUGC, UGUA/AUGU, and AGUU/UUGU but stabilizing in GGUC/ CUGG
-
He, L., Kierzek, R., SantaLucia, J., Walter, A. E., and Turner, D. H. (1991) Nearest-neighbor parameters for GU mismatches-5′GU3′/ 3′UG5′ is destabilizing in the contexts CGUG/GUGC, UGUA/AUGU, and AGUU/UUGU but stabilizing in GGUC/ CUGG, Biochemistry 30, 11124-11132.
-
(1991)
Biochemistry
, vol.30
, pp. 11124-11132
-
-
He, L.1
Kierzek, R.2
Santalucia, J.3
Walter, A.E.4
Turner, D.H.5
-
54
-
-
0000635454
-
Thiolation of uridine carbon-2 restricts the motional dynamics of the transfer-RNA wobble position nucleoside
-
Agris, P. F., Sierzputowska-Gracz, H., Smith, W., Malkiewicz, A., Sochacka, E., and Nawrot, B. (1992) Thiolation of uridine carbon-2 restricts the motional dynamics of the transfer-RNA wobble position nucleoside, J. Am. Chem. Soc. 114, 2652-2656.
-
(1992)
J. Am. Chem. Soc.
, vol.114
, pp. 2652-2656
-
-
Agris, P.F.1
Sierzputowska-Gracz, H.2
Smith, W.3
Malkiewicz, A.4
Sochacka, E.5
Nawrot, B.6
-
55
-
-
0001681749
-
Chemistry and structure of modified uridine dinucleosides are determined by thiolation
-
Smith, W. S., Sierzputowska-Gracz, H., Sochacka, E., Malkiewicz, A., and Agris, P. F. (1992) Chemistry and structure of modified uridine dinucleosides are determined by thiolation, J. Am. Chem. Soc. 114, 7989-7997.
-
(1992)
J. Am. Chem. Soc.
, vol.114
, pp. 7989-7997
-
-
Smith, W.S.1
Sierzputowska-Gracz, H.2
Sochacka, E.3
Malkiewicz, A.4
Agris, P.F.5
-
56
-
-
0030839446
-
Synthesis and studies on the effect of 2-thiouridine and 4-thiouridine on sugar conformation and RNA duplex stability
-
Kumar, R. K., and Davis, D. R. (1997) Synthesis and studies on the effect of 2-thiouridine and 4-thiouridine on sugar conformation and RNA duplex stability, Nucleic Acids Res. 25, 1272-1280.
-
(1997)
Nucleic Acids Res.
, vol.25
, pp. 1272-1280
-
-
Kumar, R.K.1
Davis, D.R.2
-
57
-
-
0033554848
-
Thermodynamics of RNA-RNA duplexes with 2- Or 4-thiouridines: Implications for antisense design and targeting a group I intron
-
Testa, S. M., Disney, M. D., Turner, D. H., and Kierzek, R. (1999) Thermodynamics of RNA-RNA duplexes with 2- or 4-thiouridines: Implications for antisense design and targeting a group I intron, Biochemistry 38, 16655-16662.
-
(1999)
Biochemistry
, vol.38
, pp. 16655-16662
-
-
Testa, S.M.1
Disney, M.D.2
Turner, D.H.3
Kierzek, R.4
-
58
-
-
0345732095
-
A new route to 2′-O-alkyl-2-thiouridine derivatives via 4-O-protection of the uracil base and hybridization properties of oligonucleotides incorporating these modified nucleoside derivatives
-
Okamoto, I., Shohda, K., Seio, K., and Sekine, M. (2003) A new route to 2′-O-alkyl-2-thiouridine derivatives via 4-O-protection of the uracil base and hybridization properties of oligonucleotides incorporating these modified nucleoside derivatives, J. Org. Chem. 68, 9971-9982.
-
(2003)
J. Org. Chem.
, vol.68
, pp. 9971-9982
-
-
Okamoto, I.1
Shohda, K.2
Seio, K.3
Sekine, M.4
-
59
-
-
0024841809
-
Enzymatic approaches to probing of RNA secondary and tertiary structure
-
Knapp, G. (1989) Enzymatic approaches to probing of RNA secondary and tertiary structure, Methods Enzymol. 180, 192-212.
-
(1989)
Methods Enzymol.
, vol.180
, pp. 192-212
-
-
Knapp, G.1
-
60
-
-
0032857575
-
Determining the influence of structure on hybridization using oligonucleotide arrays
-
Mir, K. U., and Southern, E. M. (1999) Determining the influence of structure on hybridization using oligonucleotide arrays, Nat. Biotechnol. 17, 788-792.
-
(1999)
Nat. Biotechnol.
, vol.17
, pp. 788-792
-
-
Mir, K.U.1
Southern, E.M.2
-
61
-
-
0032077477
-
Advantages of 2′-O-methyl oligoribonucleotide probes for detecting RNA targets
-
Majlessi, M., Nelson, N. C., and Becker, M. M. (1998) Advantages of 2′-O-methyl oligoribonucleotide probes for detecting RNA targets, Nucleic Acids Res. 26, 2224-2229.
-
(1998)
Nucleic Acids Res.
, vol.26
, pp. 2224-2229
-
-
Majlessi, M.1
Nelson, N.C.2
Becker, M.M.3
-
62
-
-
0029134549
-
Thermodynamic parameters to predict stability of RNA/DNA hybrid duplexes
-
Sugimoto, N., Nakano, S., Katoh, M., Matsumura, A., Nakamuta, H., Ohmichi, T., Yoneyama, M., and Sasaki, M. (1995) Thermodynamic parameters to predict stability of RNA/DNA hybrid duplexes, Biochemistry 34, 11211-11216.
-
(1995)
Biochemistry
, vol.34
, pp. 11211-11216
-
-
Sugimoto, N.1
Nakano, S.2
Katoh, M.3
Matsumura, A.4
Nakamuta, H.5
Ohmichi, T.6
Yoneyama, M.7
Sasaki, M.8
-
63
-
-
0036224052
-
Effects of magnesium ions on the stabilization of RNA oligomers of defined structures
-
Serra, M. J., Baird, J. D., Dale, T., Fey, B. L., Retatagos, K., and Westhof, E. (2002) Effects of magnesium ions on the stabilization of RNA oligomers of defined structures, RNA 8, 307-323.
-
(2002)
RNA
, vol.8
, pp. 307-323
-
-
Serra, M.J.1
Baird, J.D.2
Dale, T.3
Fey, B.L.4
Retatagos, K.5
Westhof, E.6
-
64
-
-
0142147363
-
Ribosomal dynamics inferred from variations in experimental measurements
-
Gabashvili, I. S., Whirl-Carrillo, M., Bada, M., Banatao, D. R., and Altman, R. B. (2003) Ribosomal dynamics inferred from variations in experimental measurements, RNA 9, 1301-1307.
-
(2003)
RNA
, vol.9
, pp. 1301-1307
-
-
Gabashvili, I.S.1
Whirl-Carrillo, M.2
Bada, M.3
Banatao, D.R.4
Altman, R.B.5
-
65
-
-
0022368250
-
RNA structural dynamics-Pre-melting and melting transitions in Escherichia coli 5S ribosomal RNA
-
Pieler, T., Digweed, M., and Erdmann, V. A. (1985) RNA structural dynamics-Pre-melting and melting transitions in Escherichia coli 5S ribosomal RNA, J. Biomol. Struct. Dyn. 3, 495-514.
-
(1985)
J. Biomol. Struct. Dyn.
, vol.3
, pp. 495-514
-
-
Pieler, T.1
Digweed, M.2
Erdmann, V.A.3
-
66
-
-
0031664960
-
The 5S rRNA loop E: Chemical probing and phylogenetic data versus crystal structure
-
Leontis, N. B., and Westhof, E. (1998) The 5S rRNA loop E: Chemical probing and phylogenetic data versus crystal structure, RNA 4, 1134-1153.
-
(1998)
RNA
, vol.4
, pp. 1134-1153
-
-
Leontis, N.B.1
Westhof, E.2
-
67
-
-
0035849554
-
Thermodynamics of three-way multibranch loops in RNA
-
Diamond, J. M., Turner, D. H., and Mathews, D. H. (2001) Thermodynamics of three-way multibranch loops in RNA, Biochemistry 40, 6971-6981.
-
(2001)
Biochemistry
, vol.40
, pp. 6971-6981
-
-
Diamond, J.M.1
Turner, D.H.2
Mathews, D.H.3
-
68
-
-
0033080745
-
Complete suboptimal folding of RNA and the stability of secondary structures
-
Wuchty, S., Fontana, W., Hofacker, I. L., and Schuster, P. (1999) Complete suboptimal folding of RNA and the stability of secondary structures, Biopolymers 49, 145-165.
-
(1999)
Biopolymers
, vol.49
, pp. 145-165
-
-
Wuchty, S.1
Fontana, W.2
Hofacker, I.L.3
Schuster, P.4
-
69
-
-
0029061125
-
The computer-simulation of RNA folding pathways using a genetic algorithm
-
Gultyaev, A. P., Vanbatenburg, F. H. D., and Pleij, C. W. A. (1995) The computer-simulation of RNA folding pathways using a genetic algorithm, J. Mol. Biol. 250, 37-51.
-
(1995)
J. Mol. Biol.
, vol.250
, pp. 37-51
-
-
Gultyaev, A.P.1
Vanbatenburg, F.H.D.2
Pleij, C.W.A.3
-
70
-
-
0033524952
-
A dynamic programming algorithm for RNA structure prediction including pseudoknots
-
Rivas, E., and Eddy, S. R. (1999) A dynamic programming algorithm for RNA structure prediction including pseudoknots, J. Mol. Biol. 285, 2053-2068.
-
(1999)
J. Mol. Biol.
, vol.285
, pp. 2053-2068
-
-
Rivas, E.1
Eddy, S.R.2
-
71
-
-
0346888665
-
A statistical sampling algorithm for RNA secondary structure prediction
-
Ding, Y., and Lawrence, C. E. (2003) A statistical sampling algorithm for RNA secondary structure prediction, Nucleic Acids Res. 31, 7280-7301.
-
(2003)
Nucleic Acids Res.
, vol.31
, pp. 7280-7301
-
-
Ding, Y.1
Lawrence, C.E.2
-
72
-
-
0043285072
-
A partition function algorithm for nucleic acid secondary structure including pseudoknots
-
Dirks, R. M., and Pierce, N. A. (2003) A partition function algorithm for nucleic acid secondary structure including pseudoknots, J. Comput. Chem. 24, 1664-1677.
-
(2003)
J. Comput. Chem.
, vol.24
, pp. 1664-1677
-
-
Dirks, R.M.1
Pierce, N.A.2
-
73
-
-
3543046155
-
Reflective interferometric detection of label-free oligonucleotides
-
Lu, J. H., Strohsahl, C. M., Miller, B. L., and Rothberg, L. J. (2004) Reflective interferometric detection of label-free oligonucleotides, Anal. Chem. 76, 4416-4420.
-
(2004)
Anal. Chem.
, vol.76
, pp. 4416-4420
-
-
Lu, J.H.1
Strohsahl, C.M.2
Miller, B.L.3
Rothberg, L.J.4
-
74
-
-
0005772676
-
Inhibition of Rous-Sarcoma viral-RNA translation by a specific oligodeoxyribonucleotide
-
Stephenson, M. L., and Zamecnik, P. C. (1978) Inhibition of Rous-Sarcoma viral-RNA translation by a specific oligodeoxyribonucleotide, Proc. Natl. Acad. Sci. U.S.A. 75, 285-288.
-
(1978)
Proc. Natl. Acad. Sci. U.S.A.
, vol.75
, pp. 285-288
-
-
Stephenson, M.L.1
Zamecnik, P.C.2
-
75
-
-
0041582974
-
Inhibition of Rous-Sarcoma virus-replication and cell transformation by a specific oligodeoxynucleotide
-
Zamecnik, P. C., and Stephenson, M. L. (1978) Inhibition of Rous-Sarcoma virus-replication and cell transformation by a specific oligodeoxynucleotide, Proc. Natl. Acad. Sci. U.S.A. 75, 280-284.
-
(1978)
Proc. Natl. Acad. Sci. U.S.A.
, vol.75
, pp. 280-284
-
-
Zamecnik, P.C.1
Stephenson, M.L.2
-
76
-
-
0025015229
-
Site-specific excision from RNA by RNase-H and mixed-phosphate-backbone oligodeoxynucleotides
-
Agrawal, S., Mayrand, S. H., Zamecnik, P. C., and Pederson, T. (1990) Site-specific excision from RNA by RNase-H and mixed-phosphate-backbone oligodeoxynucleotides. Proc. Natl. Acad. Sci. U.S.A. 87, 1401-1405.
-
(1990)
Proc. Natl. Acad. Sci. U.S.A.
, vol.87
, pp. 1401-1405
-
-
Agrawal, S.1
Mayrand, S.H.2
Zamecnik, P.C.3
Pederson, T.4
-
77
-
-
0030909609
-
Mixed-backbone oligonucleotides as second generation antisense oligonucleotides: In vitro and in vivo studies
-
Agrawal, S., Jiang, Z. W., Zhao, Q. Y., Shaw, D., Cai, Q. Y., Roskey, A., Channavajjala, L., Saxinger, C., and Zhang, R. W. (1997) Mixed-backbone oligonucleotides as second generation antisense oligonucleotides: In vitro and in vivo studies, Proc. Natl. Acad. Sci. U.S.A. 94, 2620-2625.
-
(1997)
Proc. Natl. Acad. Sci. U.S.A.
, vol.94
, pp. 2620-2625
-
-
Agrawal, S.1
Jiang, Z.W.2
Zhao, Q.Y.3
Shaw, D.4
Cai, Q.Y.5
Roskey, A.6
Channavajjala, L.7
Saxinger, C.8
Zhang, R.W.9
-
78
-
-
10744225153
-
Asymmetry in the assembly of the RNAi enzyme complex
-
Schwarz, D. S., Hutvagner, G., Du, T., Xu, Z. S., Aronin, N., and Zamore, P. D. (2003) Asymmetry in the assembly of the RNAi enzyme complex, Cell 115, 199-208.
-
(2003)
Cell
, vol.115
, pp. 199-208
-
-
Schwarz, D.S.1
Hutvagner, G.2
Du, T.3
Xu, Z.S.4
Aronin, N.5
Zamore, P.D.6
-
79
-
-
0142165224
-
Functional siRNAs and miRNAs exhibit strand bias
-
Khvorova, A., Reynolds, A., and Jayasena, S. D. (2003) Functional siRNAs and miRNAs exhibit strand bias, Cell 115, 209-216.
-
(2003)
Cell
, vol.115
, pp. 209-216
-
-
Khvorova, A.1
Reynolds, A.2
Jayasena, S.D.3
|