-
1
-
-
0022612581
-
Detection of differences in higher order structure between highly homologous single-stranded DNAs by low-temperature denaturant gradient gel electrophoresis
-
Nishigaki, K., Husimi, Y., and Tsubota, M. (1986) Detection of differences in higher order structure between highly homologous single-stranded DNAs by low-temperature denaturant gradient gel electrophoresis. J. Biochem. 99, 663-671
-
(1986)
J. Biochem.
, vol.99
, pp. 663-671
-
-
Nishigaki, K.1
Husimi, Y.2
Tsubota, M.3
-
2
-
-
0024595101
-
Detection of polymorphism of human DNA by gel electrophoresis as single strand conformation polymorphism
-
Orita, M., Iwahana, H., Kanazawa, H., Hayashi, K., and Sekiya, T. (1989) Detection of polymorphism of human DNA by gel electrophoresis as single strand conformation polymorphism. Proc. Natl. Acad. Sci. USA 86, 2766-2770
-
(1989)
Proc. Natl. Acad. Sci. USA
, vol.86
, pp. 2766-2770
-
-
Orita, M.1
Iwahana, H.2
Kanazawa, H.3
Hayashi, K.4
Sekiya, T.5
-
3
-
-
0029684436
-
Single-strand conformation polymorphism (SSCP) can be explained by semistable conformation dynamics of single-stranded DNA
-
Nakabayashi, Y. and Nishigaki, K. (1996) Single-strand conformation polymorphism (SSCP) can be explained by semistable conformation dynamics of single-stranded DNA. J. Biochem. 120, 320-325
-
(1996)
J. Biochem.
, vol.120
, pp. 320-325
-
-
Nakabayashi, Y.1
Nishigaki, K.2
-
4
-
-
0026526709
-
Structural analysis of nucleic acids by precise denaturing gradient gel electrophoresis: II. Applications to the analysis of subtle and drastic mobility changes of oligo- and polynucleotides
-
Nishigaki, K., Miura, T., Tsubota, M., Sutoh, A., Amano, N., and Husimi, Y. (1992) Structural analysis of nucleic acids by precise denaturing gradient gel electrophoresis: II. Applications to the analysis of subtle and drastic mobility changes of oligo- and polynucleotides. J. Biochem. 111, 151-156
-
(1992)
J. Biochem.
, vol.111
, pp. 151-156
-
-
Nishigaki, K.1
Miura, T.2
Tsubota, M.3
Sutoh, A.4
Amano, N.5
Husimi, Y.6
-
5
-
-
0034901419
-
Stretching single-stranded DNA: Interplay of electrostatic, base-pairing, and base-pair stacking interactions
-
Zhang, Y., Zhou, H., and Ou-Yang, Z.C. (2001) Stretching single-stranded DNA: interplay of electrostatic, base-pairing, and base-pair stacking interactions. Biophys. J. 81, 133-143
-
(2001)
Biophys. J.
, vol.81
, pp. 133-143
-
-
Zhang, Y.1
Zhou, H.2
Ou-Yang, Z.C.3
-
6
-
-
18744407040
-
Stretching single stranded DNA, a model polyelectrolyte
-
Dessinges, M.N., Maier, B., Zhang, Y., Peliti, M., Bensimon, D., and Croquette, V. (2002) Stretching single stranded DNA, a model polyelectrolyte. Phys. Rev. Lett. 89, 248102
-
(2002)
Phys. Rev. Lett.
, vol.89
, pp. 248102
-
-
Dessinges, M.N.1
Maier, B.2
Zhang, Y.3
Peliti, M.4
Bensimon, D.5
Croquette, V.6
-
7
-
-
0034335665
-
Electrophoresis of DNA and other polyelectrolytes: Physical mechanisms
-
Viovy, J.L. (2000) Electrophoresis of DNA and other polyelectrolytes: Physical mechanisms. Rev. Modern Phys. 72, 813-872
-
(2000)
Rev. Modern Phys.
, vol.72
, pp. 813-872
-
-
Viovy, J.L.1
-
8
-
-
0029872258
-
A useful role for "static" models in elucidating the behaviour of DNA in solution
-
Calladine, C.R. and Drew, H.R. (1996) A useful role for "static" models in elucidating the behaviour of DNA in solution. J. Mol. Biol. 257, 479-485
-
(1996)
J. Mol. Biol.
, vol.257
, pp. 479-485
-
-
Calladine, C.R.1
Drew, H.R.2
-
9
-
-
0002099878
-
Reptation, entropic trapping, percolation, and rouse dynamics of polymers in "random" environments
-
Slater, G.W. and Song-Yan, Wu. (1995) Reptation, entropic trapping, percolation, and rouse dynamics of polymers in "random" environments. Phys. Rev. Lett. 75, 164-167
-
(1995)
Phys. Rev. Lett.
, vol.75
, pp. 164-167
-
-
Slater, G.W.1
Song-Yan, W.2
-
10
-
-
0034214951
-
Elastic property of single double-stranded DNA molecules: Theoretical study and comparison with experiments
-
Zhou, H., Zhang, Y., and Ou-Yang, Z. (2000) Elastic property of single double-stranded DNA molecules: theoretical study and comparison with experiments. Phys. Rev. E 62, 1045-1058
-
(2000)
Phys. Rev. E
, vol.62
, pp. 1045-1058
-
-
Zhou, H.1
Zhang, Y.2
Ou-Yang, Z.3
-
11
-
-
0022432940
-
Type II restriction endonucleases cleave single-stranded DNAs in general
-
Nishigaki, K., Kaneko, Y., Wakuda, H., Husimi, Y., and Tanaka, T. (1985) Type II restriction endonucleases cleave single-stranded DNAs in general. Nucleic Acids Res. 13, 5747-5760
-
(1985)
Nucleic Acids Res.
, vol.13
, pp. 5747-5760
-
-
Nishigaki, K.1
Kaneko, Y.2
Wakuda, H.3
Husimi, Y.4
Tanaka, T.5
-
12
-
-
0038299558
-
Role of microRNAs in plant and animal development
-
Carrington, J.C. and Ambros, V. (2003) Role of microRNAs in plant and animal development. Science 301, 336-338
-
(2003)
Science
, vol.301
, pp. 336-338
-
-
Carrington, J.C.1
Ambros, V.2
-
13
-
-
0037296036
-
Sequence-specific and non-specific mobilities of single-stranded oligonucleotides observed by changing the borate buffer concentration
-
Biyani, M. and Nishigaki, K. (2003) Sequence-specific and non-specific mobilities of single-stranded oligonucleotides observed by changing the borate buffer concentration. Electrophoresis 24, 628-633
-
(2003)
Electrophoresis
, vol.24
, pp. 628-633
-
-
Biyani, M.1
Nishigaki, K.2
-
14
-
-
84986518863
-
AMBER: Assisted model building with energy refinement. A general program for modeling molecules and their interactions
-
Weiner, P.K. and Kollman, P.A. (1981) AMBER: assisted model building with energy refinement. A general program for modeling molecules and their interactions. J. Comput. Chem. 2, 287-303
-
(1981)
J. Comput. Chem.
, vol.2
, pp. 287-303
-
-
Weiner, P.K.1
Kollman, P.A.2
-
15
-
-
28244443539
-
-
University of California, San Francisco, CA
-
Case, D.A. et al. (2002) AMBER7 Manual, University of California, San Francisco, CA
-
(2002)
AMBER7 Manual
-
-
Case, D.A.1
-
16
-
-
0029011701
-
A second generation force field for the simulation of proteins, nucleic acids, and organic molecules
-
Cornell, W.D., Cieplak, P., Bayly, C.I., Gould, I.R., Merz, K.M., Ferguson, D.M., Spellmeyer, D.C., Fox, T., Caldwell, J.W., and Kollman, P.A. (1995) A second generation force field for the simulation of proteins, nucleic acids, and organic molecules. J. Am. Chem. Soc. 117, 5179-5197
-
(1995)
J. Am. Chem. Soc.
, vol.117
, pp. 5179-5197
-
-
Cornell, W.D.1
Cieplak, P.2
Bayly, C.I.3
Gould, I.R.4
Merz, K.M.5
Ferguson, D.M.6
Spellmeyer, D.C.7
Fox, T.8
Caldwell, J.W.9
Kollman, P.A.10
-
17
-
-
0344778061
-
Semianalytical treatment of solvation for molecular mechanics and dynamics
-
Still, W.C., Tempczyk, A., Hawley, R.C., and Hendrickson, T. (1990) Semianalytical treatment of solvation for molecular mechanics and dynamics. J. Am. Chem. Soc. 112, 6127-6129
-
(1990)
J. Am. Chem. Soc.
, vol.112
, pp. 6127-6129
-
-
Still, W.C.1
Tempczyk, A.2
Hawley, R.C.3
Hendrickson, T.4
-
18
-
-
0034701222
-
Molecular dynamics simulations of nucleic acids with a generalized Born solvation model
-
Tsui, V. and Case, D.A. (2000) Molecular dynamics simulations of nucleic acids with a generalized Born solvation model. J. Am. Chem. Soc. 122, 2489-2498
-
(2000)
J. Am. Chem. Soc.
, vol.122
, pp. 2489-2498
-
-
Tsui, V.1
Case, D.A.2
-
19
-
-
84961985307
-
Development of a generalized Born model parameterization for proteins and nucleic acids
-
Dominy, B. and Brooks, C. III (1999) Development of a generalized Born model parameterization for proteins and nucleic acids. J. Phys. Chem. B 103, 3765-3773
-
(1999)
J. Phys. Chem. B
, vol.103
, pp. 3765-3773
-
-
Dominy, B.1
Brooks III, C.2
-
20
-
-
0035501755
-
Protein molecular dynamics with the generalized Born/ACE solvent model
-
Calimat, N., Schaefer, M., and Simonson, T. (2001) Protein molecular dynamics with the generalized Born/ACE solvent model. Proteins 45, 144-158
-
(2001)
Proteins
, vol.45
, pp. 144-158
-
-
Calimat, N.1
Schaefer, M.2
Simonson, T.3
-
21
-
-
0036234027
-
Comparison of protein solution structures refined by molecular dynamics simulation in vacuum, with a generalized Born model, and with explicit water
-
Xia, B., Tsui, V., Case, D.A., Dyson, H.J., and Wright, P.E. (2002) Comparison of protein solution structures refined by molecular dynamics simulation in vacuum, with a generalized Born model, and with explicit water. J. Biomol. NMR 22, 317-331
-
(2002)
J. Biomol. NMR
, vol.22
, pp. 317-331
-
-
Xia, B.1
Tsui, V.2
Case, D.A.3
Dyson, H.J.4
Wright, P.E.5
-
22
-
-
33646940952
-
Numerical integration of the Cartesian equations of motion of a system with constraints: Molecular dynamics of n-alkanes
-
Ryckaert, J.P., Ciccotti, G., and Bereendsen, H.J.C. (1977) Numerical integration of the Cartesian equations of motion of a system with constraints: molecular dynamics of n-alkanes. J. Comput. Phys. 23, 327-341
-
(1977)
J. Comput. Phys.
, vol.23
, pp. 327-341
-
-
Ryckaert, J.P.1
Ciccotti, G.2
Bereendsen, H.J.C.3
-
23
-
-
14244273182
-
Theory and applications of the Generalized Born solvation model in macromolecular simulations
-
Tsui, V. and Case, D.A. (2001) Theory and applications of the Generalized Born solvation model in macromolecular simulations. Biopolymers 56, 275-291
-
(2001)
Biopolymers
, vol.56
, pp. 275-291
-
-
Tsui, V.1
Case, D.A.2
-
24
-
-
0029878720
-
VMD: Visual molecular dynamics
-
Humphrey, W., Dalke, A., and Schulten, K. (1996) VMD: Visual molecular dynamics. J. Mol. Graphics 14, 33-38
-
(1996)
J. Mol. Graphics
, vol.14
, pp. 33-38
-
-
Humphrey, W.1
Dalke, A.2
Schulten, K.3
-
26
-
-
0024524479
-
Extraordinary stable structure of short single-stranded DNA fragments containing a specific base sequence: D(GCGAAAGC)
-
Hirao, I., Nishimura, Y., Naraoka, T., Watanabe, K., Arata, Y., and Miura, K. (1989) Extraordinary stable structure of short single-stranded DNA fragments containing a specific base sequence: d(GCGAAAGC). Nucleic Acids Res. 17, 2223-2231
-
(1989)
Nucleic Acids Res.
, vol.17
, pp. 2223-2231
-
-
Hirao, I.1
Nishimura, Y.2
Naraoka, T.3
Watanabe, K.4
Arata, Y.5
Miura, K.6
-
27
-
-
0025855936
-
Neighboring nucleotide interactions during DNA sequencing gel electrophoresis
-
Bowling, J.M., Bruner, K.L., Cmarik, J.L., and Tibbetts, C. (1991) Neighboring nucleotide interactions during DNA sequencing gel electrophoresis. Nucleic Acids Res. 19, 3089-3097
-
(1991)
Nucleic Acids Res.
, vol.19
, pp. 3089-3097
-
-
Bowling, J.M.1
Bruner, K.L.2
Cmarik, J.L.3
Tibbetts, C.4
-
28
-
-
0019769456
-
Determination of nucleotide sequences in DNA
-
Sanger, F. (1981) Determination of nucleotide sequences in DNA. Science 214, 1205-1210
-
(1981)
Science
, vol.214
, pp. 1205-1210
-
-
Sanger, F.1
-
29
-
-
0027452299
-
Effect of urea concentration on the base-specific separation of oligodeoxynucleotides in capillary affinity gel electrophoresis
-
Baba, Y., Tsuhako, M., Sawa, T., and Akashi, M. (1993) Effect of urea concentration on the base-specific separation of oligodeoxynucleotides in capillary affinity gel electrophoresis. J. Chromatogr. A 652, 93-99
-
(1993)
J. Chromatogr. A
, vol.652
, pp. 93-99
-
-
Baba, Y.1
Tsuhako, M.2
Sawa, T.3
Akashi, M.4
-
30
-
-
0034820744
-
MD simulations of homomorphous PNA, DNA, and RNA single strands: Characterization and comparison of conformations and dynamics
-
Sen, S. and Nilsson, L. (2001) MD simulations of homomorphous PNA, DNA, and RNA single strands: characterization and comparison of conformations and dynamics. J. Am. Chem. Soc. 123, 7414-7422
-
(2001)
J. Am. Chem. Soc.
, vol.123
, pp. 7414-7422
-
-
Sen, S.1
Nilsson, L.2
-
31
-
-
0035852130
-
Influence of sodium ions on the dynamics and structure of single-stranded DNA oligomers: A molecular dynamics study
-
Martinez, J.M., Elmroth, S.K., and Kloo, L. (2001) Influence of sodium ions on the dynamics and structure of single-stranded DNA oligomers: a molecular dynamics study. J. Am. Chem. Soc. 123, 12279-12289
-
(2001)
J. Am. Chem. Soc.
, vol.123
, pp. 12279-12289
-
-
Martinez, J.M.1
Elmroth, S.K.2
Kloo, L.3
-
32
-
-
0028233393
-
Matrix effects suggest an important influence of DNA-polyacrylamide interactions on the electrophoretic mobility of DNA
-
Niederweis, M., Lederer, T., and Hillen, W. (1994) Matrix effects suggest an important influence of DNA-polyacrylamide interactions on the electrophoretic mobility of DNA. J. Biol. Chem. 269, 10156-10162
-
(1994)
J. Biol. Chem.
, vol.269
, pp. 10156-10162
-
-
Niederweis, M.1
Lederer, T.2
Hillen, W.3
-
33
-
-
0028138809
-
Computer prediction of general PCR products based on dynamical solution structures of DNA
-
Sakuma, Y. and Nishigaki, K. (1994) Computer prediction of general PCR products based on dynamical solution structures of DNA. J. Biochem. 116, 736-741
-
(1994)
J. Biochem.
, vol.116
, pp. 736-741
-
-
Sakuma, Y.1
Nishigaki, K.2
-
34
-
-
0034194134
-
Whole genome sequence-enabled prediction of sequences performed for random PCR products of Escherichia coli
-
Nishigaki, K., Saito, A., Hasegawa, T., and Naimuddin, M. (2000) Whole genome sequence-enabled prediction of sequences performed for random PCR products of Escherichia coli. Nucleic Acids Res. 28, 1879-1884
-
(2000)
Nucleic Acids Res.
, vol.28
, pp. 1879-1884
-
-
Nishigaki, K.1
Saito, A.2
Hasegawa, T.3
Naimuddin, M.4
-
35
-
-
0032545933
-
Potent and specific genetic interference by double-stranded RNA in Caenorhabditis elegans
-
Fire, A., Xu, S., Montgomery, M.K., Kostas, S.A., Driver, S.E., and Mello, C.C. (1998) Potent and specific genetic interference by double-stranded RNA in Caenorhabditis elegans. Nature 391, 806-811
-
(1998)
Nature
, vol.391
, pp. 806-811
-
-
Fire, A.1
Xu, S.2
Montgomery, M.K.3
Kostas, S.A.4
Driver, S.E.5
Mello, C.C.6
-
36
-
-
0028307171
-
Split genes and RNA splicing
-
Sharp, P.A. (1994) Split genes and RNA splicing. Cell 77, 805-815
-
(1994)
Cell
, vol.77
, pp. 805-815
-
-
Sharp, P.A.1
-
37
-
-
0003017978
-
Structure and mechanism of the large catalytic RNAs: Group I and Group II introns and ribonuclease P
-
(Gesteland, R.F. and Atkins, J.F., eds.), Cold Spring Harbor Press
-
Cech, T.R. (1993) Structure and mechanism of the large catalytic RNAs: Group I and Group II introns and ribonuclease P in The RNA World (Gesteland, R.F. and Atkins, J.F., eds.) pp. 239-269, Cold Spring Harbor Press
-
(1993)
The RNA World
, pp. 239-269
-
-
Cech, T.R.1
-
38
-
-
0027376439
-
Antisense oligonucleotides as therapeutic agents-is the bullet really magical?
-
Stein, C.A. and Cheng, Y.C. (1993) Antisense oligonucleotides as therapeutic agents-is the bullet really magical? Science 261, 1004-1012
-
(1993)
Science
, vol.261
, pp. 1004-1012
-
-
Stein, C.A.1
Cheng, Y.C.2
-
39
-
-
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
-
40
-
-
0019082587
-
Fast algorithm for predicting the secondary structure of single-stranded RNA
-
Nussinov, R. and Jacobason, A.B. (1980) Fast algorithm for predicting the secondary structure of single-stranded RNA. Proc. Natl. Acad. Sci. USA 77, 6903-6913
-
(1980)
Proc. Natl. Acad. Sci. USA
, vol.77
, pp. 6903-6913
-
-
Nussinov, R.1
Jacobason, A.B.2
-
41
-
-
0038497542
-
A structure for Deoxyribose Nucleic Acid
-
Watson, J.D. and Crick, F.H.C. (1953) A structure for Deoxyribose Nucleic Acid. Nature 171, 737-738
-
(1953)
Nature
, vol.171
, pp. 737-738
-
-
Watson, J.D.1
Crick, F.H.C.2
-
42
-
-
0035656688
-
Non-coding RNA genes and the modern RNA world
-
Eddy, S.R. (2001) Non-coding RNA genes and the modern RNA world. Nat. Rev. Genet. 2, 919-929
-
(2001)
Nat. Rev. Genet.
, vol.2
, pp. 919-929
-
-
Eddy, S.R.1
-
43
-
-
0035806973
-
Computational identification of noncoding RNAs in E. coli by comparative genomics
-
Rivas, E., Klein, R.J., Jones, T.A., and Eddy, S.R. (2001) Computational identification of noncoding RNAs in E. coli by comparative genomics. Curr. Biol. 11, 1369-1373
-
(2001)
Curr. Biol.
, vol.11
, pp. 1369-1373
-
-
Rivas, E.1
Klein, R.J.2
Jones, T.A.3
Eddy, S.R.4
-
44
-
-
0242317680
-
Computational identification of non-coding RNAs in Saccharomyces cerevisiae by comparative genomics
-
McCutcheon, J.P. and Eddy, S.R. (2003) Computational identification of non-coding RNAs in Saccharomyces cerevisiae by comparative genomics. Nucleic Acids Res. 31, 4119-4128
-
(2003)
Nucleic Acids Res.
, vol.31
, pp. 4119-4128
-
-
McCutcheon, J.P.1
Eddy, S.R.2
-
45
-
-
0025835296
-
Fast and sensitive silver staining of DNA in polyacrylamide gels
-
Bassam, B.J., Caetano-Anolles, G., and Gresshoff P.M. (1991) Fast and sensitive silver staining of DNA in polyacrylamide gels. Anal. Biochem. 196, 80-83
-
(1991)
Anal. Biochem.
, vol.196
, pp. 80-83
-
-
Bassam, B.J.1
Caetano-Anolles, G.2
Gresshoff, P.M.3
-
46
-
-
28244440901
-
Structural characterization of ultra-stable higher-ordered aggregates generated by novel guanine-rich DNA sequences
-
in press
-
Biyani, M. and Nishigaki, K. (2005) Structural characterization of ultra-stable higher-ordered aggregates generated by novel guanine-rich DNA sequences. Gene (in press)
-
(2005)
Gene
-
-
Biyani, M.1
Nishigaki, K.2
|