메뉴 건너뛰기




Volumn 138, Issue 4, 2005, Pages 363-373

Single-strand conformation polymorphism (SSCP) of oligodeoxyribonucleotides: An insight into solution structural dynamics of DNAs provided by gel electrophoresis and molecular dynamics simulations

Author keywords

Gel electrophoresis; Molecular dynamics; Oligonucleotides; Single strand conformation polymorphism; Solution structure dynamics

Indexed keywords

ADENINE; CYTOSINE; DNA BASE; GUANINE; NUCLEOTIDE DERIVATIVE; OLIGODEOXYRIBONUCLEOTIDE; SINGLE STRANDED DNA; SINGLE STRANDED DODECANUCLEOTIDE; UNCLASSIFIED DRUG;

EID: 28244451936     PISSN: 0021924X     EISSN: None     Source Type: Journal    
DOI: 10.1093/jb/mvi149     Document Type: Article
Times cited : (19)

References (46)
  • 1
    • 0022612581 scopus 로고
    • 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 scopus 로고
    • 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 scopus 로고    scopus 로고
    • 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 scopus 로고
    • 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 scopus 로고    scopus 로고
    • 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
  • 7
    • 0034335665 scopus 로고    scopus 로고
    • 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 scopus 로고    scopus 로고
    • 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 scopus 로고
    • 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 scopus 로고    scopus 로고
    • 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 scopus 로고
    • 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 scopus 로고    scopus 로고
    • 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 scopus 로고    scopus 로고
    • 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 scopus 로고
    • 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 scopus 로고    scopus 로고
    • 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
  • 17
    • 0344778061 scopus 로고
    • 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 scopus 로고    scopus 로고
    • 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 scopus 로고    scopus 로고
    • 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 scopus 로고    scopus 로고
    • 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 scopus 로고    scopus 로고
    • 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 scopus 로고
    • 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 scopus 로고    scopus 로고
    • 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
  • 26
    • 0024524479 scopus 로고
    • 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 scopus 로고
    • 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 scopus 로고
    • 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 scopus 로고
    • 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 scopus 로고    scopus 로고
    • 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 scopus 로고    scopus 로고
    • 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 scopus 로고
    • 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 scopus 로고
    • 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 scopus 로고    scopus 로고
    • 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 scopus 로고    scopus 로고
    • 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 scopus 로고
    • 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 scopus 로고
    • 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 scopus 로고
    • 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 scopus 로고
    • 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 scopus 로고
    • 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 scopus 로고
    • 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 scopus 로고    scopus 로고
    • 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 scopus 로고    scopus 로고
    • 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 scopus 로고    scopus 로고
    • 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 scopus 로고
    • 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 scopus 로고    scopus 로고
    • 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


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.