메뉴 건너뛰기




Volumn 52, Issue 24, 2013, Pages 4138-4148

DNA A-tracts are not curved in solutions containing high concentrations of monovalent cations

Author keywords

[No Author keywords available]

Indexed keywords

BACKBONE STRUCTURES; CATION CONCENTRATIONS; INCREASING TEMPERATURES; INTRINSIC CURVATURE; MONOVALENT CATIONS; PHYSIOLOGICAL CONDITION; POLYACRYLAMIDE GELS; TETRABUTYLAMMONIUM;

EID: 84879212980     PISSN: 00062960     EISSN: 15204995     Source Type: Journal    
DOI: 10.1021/bi400118m     Document Type: Article
Times cited : (19)

References (114)
  • 1
    • 0025312950 scopus 로고
    • Sequence-directed curvature of DNA
    • Hagerman, P. J. (1990) Sequence-directed curvature of DNA Annu. Rev. Biochem. 59, 755-781
    • (1990) Annu. Rev. Biochem. , vol.59 , pp. 755-781
    • Hagerman, P.J.1
  • 2
    • 0000541574 scopus 로고    scopus 로고
    • Twenty years of DNA bending
    • (Sarma, R. H. and Sarma, M. H. Eds.) Adenine Press, Schenectady, NY
    • Olson, W. K. and Zhurkin, V. B. (1996) Twenty years of DNA bending. In Biological Structure and Dynamics (Sarma, R. H., and Sarma, M. H., Eds.) pp 341-370, Adenine Press, Schenectady, NY.
    • (1996) Biological Structure and Dynamics , pp. 341-370
    • Olson, W.K.1    Zhurkin, V.B.2
  • 3
    • 0038713237 scopus 로고    scopus 로고
    • A unified model for the origin of DNA sequence-directed curvature
    • Hud, N. V. and Plavec, J. (2003) A unified model for the origin of DNA sequence-directed curvature Biopolymers 69, 144-159
    • (2003) Biopolymers , vol.69 , pp. 144-159
    • Hud, N.V.1    Plavec, J.2
  • 4
    • 67649710352 scopus 로고    scopus 로고
    • The unique structure of A-tracts and intrinsic DNA bending
    • Haran, T. E. and Mohanty, U. (2009) The unique structure of A-tracts and intrinsic DNA bending Q. Rev. Biophys. 42, 41-81
    • (2009) Q. Rev. Biophys. , vol.42 , pp. 41-81
    • Haran, T.E.1    Mohanty, U.2
  • 5
    • 0021268779 scopus 로고
    • The locus of sequence-directed and protein-induced DNA bending
    • Wu, H.-M. and Crothers, D. M. (1984) The locus of sequence-directed and protein-induced DNA bending Nature 308, 509-513
    • (1984) Nature , vol.308 , pp. 509-513
    • Wu, H.-M.1    Crothers, D.M.2
  • 6
    • 0022477409 scopus 로고
    • DNA bending at adenine·thymine tracts
    • Koo, H.-S., Wu, H.-M., and Crothers, D. M. (1986) DNA bending at adenine·thymine tracts Nature 320, 501-506
    • (1986) Nature , vol.320 , pp. 501-506
    • Koo, H.-S.1    Wu, H.-M.2    Crothers, D.M.3
  • 7
    • 0022527052 scopus 로고
    • Sequence-directed curvature of DNA
    • Hagerman, P. J. (1986) Sequence-directed curvature of DNA Nature 321, 449-450
    • (1986) Nature , vol.321 , pp. 449-450
    • Hagerman, P.J.1
  • 8
    • 0022359711 scopus 로고
    • On the sequence determinants and flexibility of the kinetoplast DNA fragment with abnormal gel electrophoretic mobilities
    • Diekmann, S. and Wang, J. C. (1985) On the sequence determinants and flexibility of the kinetoplast DNA fragment with abnormal gel electrophoretic mobilities J. Mol. Biol. 186, 1-11
    • (1985) J. Mol. Biol. , vol.186 , pp. 1-11
    • Diekmann, S.1    Wang, J.C.2
  • 9
    • 0023651638 scopus 로고
    • Temperature and salt dependence of the gel migration anomaly of curved DNA fragments
    • Diekmann, S. (1987) Temperature and salt dependence of the gel migration anomaly of curved DNA fragments Nucleic Acids Res. 15, 247-265
    • (1987) Nucleic Acids Res. , vol.15 , pp. 247-265
    • Diekmann, S.1
  • 10
    • 23344434829 scopus 로고    scopus 로고
    • Curved DNA molecules migrate anomalously slowly in free solution
    • Stellwagen, E., Lu, Y. J., and Stellwagen, N. C. (2005) Curved DNA molecules migrate anomalously slowly in free solution Nucleic Acids Res. 33, 4425-4432
    • (2005) Nucleic Acids Res. , vol.33 , pp. 4425-4432
    • Stellwagen, E.1    Lu, Y.J.2    Stellwagen, N.C.3
  • 11
    • 61449092920 scopus 로고    scopus 로고
    • Monovalent cation binding in the minor groove of DNA A-tracts
    • Dong, Q., Stellwagen, E., and Stellwagen, N. C. (2009) Monovalent cation binding in the minor groove of DNA A-tracts Biochemistry 48, 1047-1055
    • (2009) Biochemistry , vol.48 , pp. 1047-1055
    • Dong, Q.1    Stellwagen, E.2    Stellwagen, N.C.3
  • 12
    • 41449101436 scopus 로고    scopus 로고
    • Monovalent cation binding by curved DNA molecules containing variable numbers of A-tracts
    • Lu, Y. J. and Stellwagen, N. C. (2008) Monovalent cation binding by curved DNA molecules containing variable numbers of A-tracts Biophys. J. 94, 1719-1725
    • (2008) Biophys. J. , vol.94 , pp. 1719-1725
    • Lu, Y.J.1    Stellwagen, N.C.2
  • 13
    • 0000935665 scopus 로고
    • Evidence for the existence of stable curvature of DNA in solution
    • Hagerman, P. J. (1984) Evidence for the existence of stable curvature of DNA in solution Proc. Natl. Acad. Sci. U.S.A. 81, 4632-4636
    • (1984) Proc. Natl. Acad. Sci. U.S.A. , vol.81 , pp. 4632-4636
    • Hagerman, P.J.1
  • 14
    • 0022456498 scopus 로고
    • Bending and flexibility of kinetoplast DNA
    • Levene, S. D., Wu, H.-M., and Crothers, D. M. (1986) Bending and flexibility of kinetoplast DNA Biochemistry 25, 3988-3995
    • (1986) Biochemistry , vol.25 , pp. 3988-3995
    • Levene, S.D.1    Wu, H.-M.2    Crothers, D.M.3
  • 15
    • 0026253603 scopus 로고
    • Transient electric birefringence of two small DNA restriction fragments of the same molecular weight
    • Stellwagen, N. C. (1991) Transient electric birefringence of two small DNA restriction fragments of the same molecular weight Biopolymers 31, 1651-1667
    • (1991) Biopolymers , vol.31 , pp. 1651-1667
    • Stellwagen, N.C.1
  • 16
    • 0037952887 scopus 로고    scopus 로고
    • Analysis of DNA bending by transient electric birefringence
    • Lu, Y. J., Weers, B. D., and Stellwagen, N. C. (2003) Analysis of DNA bending by transient electric birefringence Biopolymers 70, 270-288
    • (2003) Biopolymers , vol.70 , pp. 270-288
    • Lu, Y.J.1    Weers, B.D.2    Stellwagen, N.C.3
  • 17
    • 21244498503 scopus 로고    scopus 로고
    • Intrinsic curvature in the VP1 gene of SV40: Comparison of solution and gel results
    • Lu, Y. J., Weers, B. D., and Stellwagen, N. C. (2005) Intrinsic curvature in the VP1 gene of SV40: Comparison of solution and gel results Biophys. J. 88, 1191-1206
    • (2005) Biophys. J. , vol.88 , pp. 1191-1206
    • Lu, Y.J.1    Weers, B.D.2    Stellwagen, N.C.3
  • 22
    • 0023513912 scopus 로고
    • The structure of an oligo(dA)·oligo(dT) tract and its biological implications
    • Nelson, H. C. M., Finch, J. T., Luisi, B. F., and Klug, A. (1987) The structure of an oligo(dA)·oligo(dT) tract and its biological implications Nature 330, 221-226
    • (1987) Nature , vol.330 , pp. 221-226
    • Nelson, H.C.M.1    Finch, J.T.2    Luisi, B.F.3    Klug, A.4
  • 23
    • 0023494886 scopus 로고
    • A bifurcated hydrogen-bonded conformation in the d(A·T) base pairs of the DNA dodecamer d(CGCAAATTTGCG) and its complex with distamycin
    • Coll, M., Frederick, C. A., Wang, A. H.-J., and Rich, A. (1987) A bifurcated hydrogen-bonded conformation in the d(A·T) base pairs of the DNA dodecamer d(CGCAAATTTGCG) and its complex with distamycin Proc. Natl. Acad. Sci. U.S.A. 84, 8385-8389
    • (1987) Proc. Natl. Acad. Sci. U.S.A. , vol.84 , pp. 8385-8389
    • Coll, M.1    Frederick, C.A.2    Wang, A.H.-J.3    Rich, A.4
  • 24
  • 26
    • 0027203669 scopus 로고
    • A DNA dodecamer containing an adenine tract crystallizes in a unique lattice and exhibits a new bend
    • DiGabriele, A. D. and Steitz, T. A. (1993) A DNA dodecamer containing an adenine tract crystallizes in a unique lattice and exhibits a new bend J. Mol. Biol. 231, 1024-1039
    • (1993) J. Mol. Biol. , vol.231 , pp. 1024-1039
    • Digabriele, A.D.1    Steitz, T.A.2
  • 27
    • 36749098380 scopus 로고    scopus 로고
    • Dynamics of B-DNA on the microsecond time scale
    • Pérez, A., Luque, F. J., and Orozco, M. (2007) Dynamics of B-DNA on the microsecond time scale J. Am. Chem. Soc. 129, 14729-14745
    • (2007) J. Am. Chem. Soc. , vol.129 , pp. 14729-14745
    • Pérez, A.1    Luque, F.J.2    Orozco, M.3
  • 28
    • 84860376513 scopus 로고    scopus 로고
    • B-DNA structure is intrinsically polymorphic: Even at the level of base pair positions
    • Maehigashi, T., Hsiao, C., Woods, K. K., Moulaei, T., Hud, N. V., and Williams, L. D. (2012) B-DNA structure is intrinsically polymorphic: Even at the level of base pair positions Nucleic Acids Res. 40, 3714-3722
    • (2012) Nucleic Acids Res. , vol.40 , pp. 3714-3722
    • Maehigashi, T.1    Hsiao, C.2    Woods, K.K.3    Moulaei, T.4    Hud, N.V.5    Williams, L.D.6
  • 29
    • 0025228644 scopus 로고
    • Determination of the extent of DNA bending by an adenine-thymine tract
    • Koo, H.-S., Drak, J., Rice, J. A., and Crothers, D. M. (1990) Determination of the extent of DNA bending by an adenine-thymine tract Biochemistry 29, 4227-4234
    • (1990) Biochemistry , vol.29 , pp. 4227-4234
    • Koo, H.-S.1    Drak, J.2    Rice, J.A.3    Crothers, D.M.4
  • 31
    • 0032479186 scopus 로고    scopus 로고
    • Polymer chain statistics and conformational analysis of DNA molecules with bends or sections of different flexibility
    • Rivetti, C., Walker, C., and Bustamante, C. (1998) Polymer chain statistics and conformational analysis of DNA molecules with bends or sections of different flexibility Proc. Natl. Acad. Sci. U.S.A. 280, 41-59
    • (1998) Proc. Natl. Acad. Sci. U.S.A. , vol.280 , pp. 41-59
    • Rivetti, C.1    Walker, C.2    Bustamante, C.3
  • 32
    • 0037459086 scopus 로고    scopus 로고
    • Topological measurement of an A-tract bend angle: Variation of duplex winding
    • Tchernaenko, V., Halvorson, H. R., and Lutter, L. C. (2003) Topological measurement of an A-tract bend angle: Variation of duplex winding J. Mol. Biol. 326, 751-760
    • (2003) J. Mol. Biol. , vol.326 , pp. 751-760
    • Tchernaenko, V.1    Halvorson, H.R.2    Lutter, L.C.3
  • 33
    • 0037459036 scopus 로고    scopus 로고
    • Topological measurement of an A-tract bend angle: Comparison of the bent and straightened states
    • Tchernaenko, V., Radlinska, M., Drabik, C., Bujnicki, J., Halvorson, H. R., and Lutter, L. C. (2003) Topological measurement of an A-tract bend angle: Comparison of the bent and straightened states J. Mol. Biol. 326, 737-749
    • (2003) J. Mol. Biol. , vol.326 , pp. 737-749
    • Tchernaenko, V.1    Radlinska, M.2    Drabik, C.3    Bujnicki, J.4    Halvorson, H.R.5    Lutter, L.C.6
  • 34
    • 0035111541 scopus 로고    scopus 로고
    • Rotational dynamics of curved DNA fragments studied by fluorescence polarization anisotropy
    • Chirico, G., Collini, M., Tóth, K., Brun, N., and Langowski, J. (2001) Rotational dynamics of curved DNA fragments studied by fluorescence polarization anisotropy Eur. Biophys. J. 29, 597-606
    • (2001) Eur. Biophys. J. , vol.29 , pp. 597-606
    • Chirico, G.1    Collini, M.2    Tóth, K.3    Brun, N.4    Langowski, J.5
  • 37
    • 0036009329 scopus 로고    scopus 로고
    • DNA-cation interactions: Quo vadis?
    • Egli, M. (2002) DNA-cation interactions: Quo vadis? Chem. Biol. 9, 277-288
    • (2002) Chem. Biol. , vol.9 , pp. 277-288
    • Egli, M.1
  • 38
    • 0043037215 scopus 로고    scopus 로고
    • Cations as hydrogen bond donors: A view of electrostatic interactions in DNA
    • Subirana, J. A. and Soler-López, M. (2003) Cations as hydrogen bond donors: A view of electrostatic interactions in DNA Annu. Rev. Biophys. Biomol. Struct. 32, 27-45
    • (2003) Annu. Rev. Biophys. Biomol. Struct. , vol.32 , pp. 27-45
    • Subirana, J.A.1    Soler-López, M.2
  • 39
    • 8844269125 scopus 로고    scopus 로고
    • Nucleic acid crystallography: Current progress
    • Egli, M. (2004) Nucleic acid crystallography: Current progress Curr. Opin. Chem. Biol. 8, 580-591
    • (2004) Curr. Opin. Chem. Biol. , vol.8 , pp. 580-591
    • Egli, M.1
  • 41
    • 0033594498 scopus 로고    scopus 로고
    • A "hydrat-ion" spine in a B-DNA minor groove
    • Tereshko, V., Minasov, G., and Egli, M. (1999) A "hydrat-ion" spine in a B-DNA minor groove J. Am. Chem. Soc. 121, 3590-3595
    • (1999) J. Am. Chem. Soc. , vol.121 , pp. 3590-3595
    • Tereshko, V.1    Minasov, G.2    Egli, M.3
  • 44
    • 0033605083 scopus 로고    scopus 로고
    • Localization of ammonium ions in the minor groove of DNA duplexes in solution and the origin of A-tract bending
    • Hud, N. V., Sklenář, V., and Feigon, J. (1999) Localization of ammonium ions in the minor groove of DNA duplexes in solution and the origin of A-tract bending J. Mol. Biol. 286, 651-660
    • (1999) J. Mol. Biol. , vol.286 , pp. 651-660
    • Hud, N.V.1    Sklenář, V.2    Feigon, J.3
  • 46
    • 0034681195 scopus 로고    scopus 로고
    • Sequence-specific binding of counterions to B-DNA
    • Denisov, V. P. and Halle, B. (2000) Sequence-specific binding of counterions to B-DNA Proc. Natl. Acad. Sci. U.S.A. 97, 629-633
    • (2000) Proc. Natl. Acad. Sci. U.S.A. , vol.97 , pp. 629-633
    • Denisov, V.P.1    Halle, B.2
  • 47
    • 0019843568 scopus 로고
    • Structure of a B-DNA dodecamer. III. Geometry of hydration
    • Drew, H. R. and Dickerson, R. E. (1981) Structure of a B-DNA dodecamer. III. Geometry of hydration J. Mol. Biol. 151, 535-556
    • (1981) J. Mol. Biol. , vol.151 , pp. 535-556
    • Drew, H.R.1    Dickerson, R.E.2
  • 48
    • 77649270492 scopus 로고    scopus 로고
    • Sequence recognition of DNA by protein-induced conformational transitions
    • Watkins, D., Mohan, S., Koudelka, G. B., and Williams, L. D. (2009) Sequence recognition of DNA by protein-induced conformational transitions J. Mol. Biol. 396, 1145-1164
    • (2009) J. Mol. Biol. , vol.396 , pp. 1145-1164
    • Watkins, D.1    Mohan, S.2    Koudelka, G.B.3    Williams, L.D.4
  • 50
    • 0034327565 scopus 로고    scopus 로고
    • Flexible structure of DNA: Ion dependence of minor-groove structure and dynamics
    • Hamelberg, D., McFail-Isom, L., Williams, L. D., and Wilson, W. D. (2000) Flexible structure of DNA: Ion dependence of minor-groove structure and dynamics J. Am. Chem. Soc. 122, 10513-10520
    • (2000) J. Am. Chem. Soc. , vol.122 , pp. 10513-10520
    • Hamelberg, D.1    McFail-Isom, L.2    Williams, L.D.3    Wilson, W.D.4
  • 51
    • 0028597967 scopus 로고
    • DNA bending by asymmetric phosphate neutralization
    • Strauss, J. K. and Maher, L. J., III (1994) DNA bending by asymmetric phosphate neutralization Science 266, 1829-1834
    • (1994) Science , vol.266 , pp. 1829-1834
    • Strauss, J.K.1    Maher Iii., L.J.2
  • 53
    • 1242269406 scopus 로고    scopus 로고
    • Molecular dynamics simulations of DNA curvature and flexibility: Helix phasing and premelting
    • Beveridge, D. L., Dixit, S. B., Barreiro, G., and Thayer, K. M. (2004) Molecular dynamics simulations of DNA curvature and flexibility: Helix phasing and premelting Biopolymers 73, 380-403
    • (2004) Biopolymers , vol.73 , pp. 380-403
    • Beveridge, D.L.1    Dixit, S.B.2    Barreiro, G.3    Thayer, K.M.4
  • 54
    • 0042121115 scopus 로고    scopus 로고
    • DNA analysis servers: Plot.it, bend.it, model.it and IS
    • Vlahoviček, K., Kaján, L., and Pongor, S. (2003) DNA analysis servers: plot.it, bend.it, model.it and IS Nucleic Acids Res. 31, 3686-3687 (http://hydra.icgeb.trieste.it/dna/index.php)
    • (2003) Nucleic Acids Res. , vol.31 , pp. 3686
    • Vlahoviček, K.1    Kaján, L.2    Pongor, S.3
  • 55
    • 0030576982 scopus 로고    scopus 로고
    • Correlation of intrinsic DNA curvature with DNA property periodicity
    • Gabrielian, A. and Pongor, S. (1996) Correlation of intrinsic DNA curvature with DNA property periodicity FEBS Lett. 393, 65-68
    • (1996) FEBS Lett. , vol.393 , pp. 65-68
    • Gabrielian, A.1    Pongor, S.2
  • 56
    • 0017956313 scopus 로고
    • On the theory of the excluded-volume effect of a polyelectrolyte in a 1-1 electrolyte solution
    • Odijk, T. and Houwaart, A. C. (1978) On the theory of the excluded-volume effect of a polyelectrolyte in a 1-1 electrolyte solution J. Polym. Sci., Polym. Phys. Ed. 16, 627-639
    • (1978) J. Polym. Sci., Polym. Phys. Ed. , vol.16 , pp. 627-639
    • Odijk, T.1    Houwaart, A.C.2
  • 58
    • 0346504050 scopus 로고    scopus 로고
    • Free solution mobility of small single-stranded oligonucleotides with variable charge densities
    • Dong, Q., Stellwagen, E., Dagle, J. M., and Stellwagen, N. C. (2003) Free solution mobility of small single-stranded oligonucleotides with variable charge densities Electrophoresis 24, 3323-3329
    • (2003) Electrophoresis , vol.24 , pp. 3323-3329
    • Dong, Q.1    Stellwagen, E.2    Dagle, J.M.3    Stellwagen, N.C.4
  • 59
    • 33847028397 scopus 로고    scopus 로고
    • Quantitative analysis of monovalent counterion binding to random-sequence, double-stranded DNA using the replacement ion method
    • Stellwagen, E., Dong, Q., and Stellwagen, N. C. (2007) Quantitative analysis of monovalent counterion binding to random-sequence, double-stranded DNA using the replacement ion method Biochemistry 46, 2050-2058
    • (2007) Biochemistry , vol.46 , pp. 2050-2058
    • Stellwagen, E.1    Dong, Q.2    Stellwagen, N.C.3
  • 61
    • 34648828234 scopus 로고    scopus 로고
    • Electrophoretic mobility is a reporter of hairpin structure in single-stranded DNA oligomers
    • Stellwagen, E., Abdulla, A., Dong, Q., and Stellwagen, N. C. (2007) Electrophoretic mobility is a reporter of hairpin structure in single-stranded DNA oligomers Biochemistry 46, 10931-10941
    • (2007) Biochemistry , vol.46 , pp. 10931-10941
    • Stellwagen, E.1    Abdulla, A.2    Dong, Q.3    Stellwagen, N.C.4
  • 62
    • 80054989510 scopus 로고    scopus 로고
    • Tandem GA residues on opposite sides of the loop in molecular beacon-like DNA hairpins compact the loop and increase hairpin stability
    • Chang, C. Y. and Stellwagen, N. C. (2011) Tandem GA residues on opposite sides of the loop in molecular beacon-like DNA hairpins compact the loop and increase hairpin stability Biochemistry 50, 9148-9157
    • (2011) Biochemistry , vol.50 , pp. 9148-9157
    • Chang, C.Y.1    Stellwagen, N.C.2
  • 63
    • 0022418377 scopus 로고
    • Sequence dependence of the curvature of DNA: A test of the phasing hypothesis
    • Hagerman, P. J. (1985) Sequence dependence of the curvature of DNA: A test of the phasing hypothesis Biochemistry 24, 7033-7037
    • (1985) Biochemistry , vol.24 , pp. 7033-7037
    • Hagerman, P.J.1
  • 64
    • 0031047279 scopus 로고    scopus 로고
    • Intrusion of counterions into the spine of hydration in the minor groove of B-DNA: Fractional occupancy of electronegative pockets
    • Young, M. A., Jayaram, B., and Beveridge, D. L. (1997) Intrusion of counterions into the spine of hydration in the minor groove of B-DNA: Fractional occupancy of electronegative pockets J. Am. Chem. Soc. 119, 59-69
    • (1997) J. Am. Chem. Soc. , vol.119 , pp. 59-69
    • Young, M.A.1    Jayaram, B.2    Beveridge, D.L.3
  • 65
    • 4043179941 scopus 로고    scopus 로고
    • DNA and its counterions: A molecular dynamics study
    • Várnal, P. and Zakrzewska, K. (2004) DNA and its counterions: A molecular dynamics study Nucleic Acids Res. 32, 4269-4280
    • (2004) Nucleic Acids Res. , vol.32 , pp. 4269-4280
    • Várnal, P.1    Zakrzewska, K.2
  • 66
    • 0035689884 scopus 로고    scopus 로고
    • Do orientation effects contribute to the molecular weight dependence of the free solution mobility of DNA?
    • Stellwagen, N. C., Bossi, A., Gelfi, C., and Righetti, P. G. (2001) Do orientation effects contribute to the molecular weight dependence of the free solution mobility of DNA? Electrophoresis 22, 4311-4315
    • (2001) Electrophoresis , vol.22 , pp. 4311-4315
    • Stellwagen, N.C.1    Bossi, A.2    Gelfi, C.3    Righetti, P.G.4
  • 67
    • 38849198534 scopus 로고    scopus 로고
    • Continuum transport model of Ogston sieving in patterned nanofilter arrays for separation of rod-like biomolecules
    • Li, Z. R., Liu, G. R., Chen, Y. Z., Wang, J.-S., Bow, H., Cheng, Y., and Han, J. (2008) Continuum transport model of Ogston sieving in patterned nanofilter arrays for separation of rod-like biomolecules Electrophoresis 29, 329-339
    • (2008) Electrophoresis , vol.29 , pp. 329-339
    • Li, Z.R.1    Liu, G.R.2    Chen, Y.Z.3    Wang, J.-S.4    Bow, H.5    Cheng, Y.6    Han, J.7
  • 68
    • 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. Mod. Phys. 72, 813-872
    • (2000) Rev. Mod. Phys. , vol.72 , pp. 813-872
    • Viovy, J.-L.1
  • 69
    • 0141885303 scopus 로고    scopus 로고
    • Unified description of electrophoresis and diffusion for DNA and other polyions
    • Stellwagen, E., Lu, Y. J., and Stellwagen, N. C. (2003) Unified description of electrophoresis and diffusion for DNA and other polyions Biochemistry 42, 11745-11750
    • (2003) Biochemistry , vol.42 , pp. 11745-11750
    • Stellwagen, E.1    Lu, Y.J.2    Stellwagen, N.C.3
  • 70
    • 0028797753 scopus 로고
    • Gel electrophoresis measurement of counterion condensation on DNA
    • Ma, C. and Bloomfield, V. A. (1994) Gel electrophoresis measurement of counterion condensation on DNA Biopolymers 35, 211-216
    • (1994) Biopolymers , vol.35 , pp. 211-216
    • Ma, C.1    Bloomfield, V.A.2
  • 71
    • 0030069829 scopus 로고
    • Trivalent counterion condensation of DNA measured by pulse gel electrophoresis
    • Li, A. Z., Qi, L. J., Shih, H. H., and Marx, K. A. (1995) Trivalent counterion condensation of DNA measured by pulse gel electrophoresis Biopolymers 38, 367-376
    • (1995) Biopolymers , vol.38 , pp. 367-376
    • Li, A.Z.1    Qi, L.J.2    Shih, H.H.3    Marx, K.A.4
  • 72
    • 0031880566 scopus 로고    scopus 로고
    • A gel electrophoresis study of the competitive effects of monovalent counterion on the extent of divalent counterions binding to DNA
    • Li, A., Huang, H., Re, X., Qi, L. J., and Marx, K. A. (1998) A gel electrophoresis study of the competitive effects of monovalent counterion on the extent of divalent counterions binding to DNA Biophys. J. 74, 964-973
    • (1998) Biophys. J. , vol.74 , pp. 964-973
    • Li, A.1    Huang, H.2    Re, X.3    Qi, L.J.4    Marx, K.A.5
  • 73
    • 70350212819 scopus 로고    scopus 로고
    • Mesoscale modeling of polyelectrolyte electrophoresis
    • Grass, K. and Holm, C. (2010) Mesoscale modeling of polyelectrolyte electrophoresis Faraday Discuss. 144, 57-70
    • (2010) Faraday Discuss. , vol.144 , pp. 57-70
    • Grass, K.1    Holm, C.2
  • 74
    • 73449131221 scopus 로고    scopus 로고
    • Mesoscale hydrodynamic simulation of short polyelectrolytes in electric fields
    • Frank, S. and Winkler, R. G. (2009) Mesoscale hydrodynamic simulation of short polyelectrolytes in electric fields J. Chem. Phys. 131, 234905
    • (2009) J. Chem. Phys. , vol.131 , pp. 234905
    • Frank, S.1    Winkler, R.G.2
  • 76
    • 0042889435 scopus 로고    scopus 로고
    • Polyelectrolytes in electric fields
    • Netz, R. R. (2003) Polyelectrolytes in electric fields J. Phys. Chem. B 107, 8208-8217
    • (2003) J. Phys. Chem. B , vol.107 , pp. 8208-8217
    • Netz, R.R.1
  • 77
    • 0017895903 scopus 로고
    • The molecular theory of polyelectrolyte solutions with applications to the electrostatic properties of polynucleotides
    • Manning, G. (1978) The molecular theory of polyelectrolyte solutions with applications to the electrostatic properties of polynucleotides Q. Rev. Biophys. 11, 179-246
    • (1978) Q. Rev. Biophys. , vol.11 , pp. 179-246
    • Manning, G.1
  • 78
    • 0017820499 scopus 로고
    • Thermodynamic analysis of ion effects on the binding and conformational equilibria of proteins and nucleic acids: The roles of ion association or release, screening, and ion effects on water activity
    • Record, M. T., Jr., Anderson, C. F., and Lohman, T. M. (1978) Thermodynamic analysis of ion effects on the binding and conformational equilibria of proteins and nucleic acids: The roles of ion association or release, screening, and ion effects on water activity Q. Rev. Biophys. 11, 103-178
    • (1978) Q. Rev. Biophys. , vol.11 , pp. 103-178
    • Record Jr., M.T.1    Anderson, C.F.2    Lohman, T.M.3
  • 79
    • 4243642135 scopus 로고
    • Comparison of theories for the translational and rotational diffusion coefficients of rod-like macromolecules. Application to short DNA fragments
    • Tirado, M. M., López Martínez, C. L., and García de la Torre, J. (1984) Comparison of theories for the translational and rotational diffusion coefficients of rod-like macromolecules. Application to short DNA fragments J. Chem. Phys. 81, 2047-2052
    • (1984) J. Chem. Phys. , vol.81 , pp. 2047-2052
    • Tirado, M.M.1    López Martínez, C.L.2    García De La Torre, J.3
  • 80
  • 81
    • 84985638035 scopus 로고
    • Diffusion coefficients for rigid macromolecules with irregular shapes that allow rotational-translational coupling
    • Wegener, W. A. (1981) Diffusion coefficients for rigid macromolecules with irregular shapes that allow rotational-translational coupling Biopolymers 20, 303-326
    • (1981) Biopolymers , vol.20 , pp. 303-326
    • Wegener, W.A.1
  • 82
    • 84985641587 scopus 로고
    • Transport properties of particles with segmental flexibility. I. Hydrodynamic resistance and diffusion coefficients of a freely hinged particle
    • Harvey, S. C. (1979) Transport properties of particles with segmental flexibility. I. Hydrodynamic resistance and diffusion coefficients of a freely hinged particle Biopolymers 18, 1081-1104
    • (1979) Biopolymers , vol.18 , pp. 1081-1104
    • Harvey, S.C.1
  • 83
    • 0025253261 scopus 로고
    • Computer simulation of hydrodynamic properties of semiflexible macromolecules: Randomly broken chains, wormlike chains, and analysis of properties of DNA
    • García Molina, J. J., López Martínez, M. C., and García de la Torre, J. (1990) Computer simulation of hydrodynamic properties of semiflexible macromolecules: Randomly broken chains, wormlike chains, and analysis of properties of DNA Biopolymers 29, 883-900
    • (1990) Biopolymers , vol.29 , pp. 883-900
    • García Molina, J.J.1    López Martínez, M.C.2    García De La Torre, J.3
  • 84
    • 0024117839 scopus 로고
    • Diffusion coefficients of segmentally flexible macromolecules with two subunits: A study of broken rods
    • Mellado, P., Iniesta, A., Diaz, F. G., and García de la Torre, J. (1988) Diffusion coefficients of segmentally flexible macromolecules with two subunits: A study of broken rods Biopolymers 27, 1771-1786
    • (1988) Biopolymers , vol.27 , pp. 1771-1786
    • Mellado, P.1    Iniesta, A.2    Diaz, F.G.3    García De La Torre, J.4
  • 85
    • 79953907770 scopus 로고    scopus 로고
    • Monovalent cation size and DNA conformational stability
    • Stellwagen, E., Muse, J. M., and Stellwagen, N. C. (2011) Monovalent cation size and DNA conformational stability Biochemistry 50, 3084-3094
    • (2011) Biochemistry , vol.50 , pp. 3084-3094
    • Stellwagen, E.1    Muse, J.M.2    Stellwagen, N.C.3
  • 86
    • 0024285807 scopus 로고
    • Evidence from base-pair kinetics for two types of adenine tract structures in solution: Their relation to DNA curvature
    • Leroy, J. L., Charretier, E., Kochoyan, M., and Guéron, M. (1988) Evidence from base-pair kinetics for two types of adenine tract structures in solution: Their relation to DNA curvature Biochemistry 27, 8894-8898
    • (1988) Biochemistry , vol.27 , pp. 8894-8898
    • Leroy, J.L.1    Charretier, E.2    Kochoyan, M.3    Guéron, M.4
  • 87
    • 0037107340 scopus 로고    scopus 로고
    • Alteration of A·T base-pair opening kinetics by the ammonium cation in DNA A-tracts
    • Snoussi, K. and Leroy, L.-L. (2002) Alteration of A·T base-pair opening kinetics by the ammonium cation in DNA A-tracts Biochemistry 41, 12467-12474
    • (2002) Biochemistry , vol.41 , pp. 12467-12474
    • Snoussi, K.1    Leroy, L.-L.2
  • 88
    • 0027299077 scopus 로고
    • Counterion-type characteristic effects on intrinsic bending components of calf thymus DNA; Hydrodynamic investigations
    • Reinert, K.-E. (1993) Counterion-type characteristic effects on intrinsic bending components of calf thymus DNA; hydrodynamic investigations J. Biomol. Struct. Dyn. 10, 991-1000
    • (1993) J. Biomol. Struct. Dyn. , vol.10 , pp. 991-1000
    • Reinert, K.-E.1
  • 89
    • 0031787749 scopus 로고    scopus 로고
    • Counterion condensation revisited
    • Manning, G. S. and Ray, J. (1998) Counterion condensation revisited J. Biomol. Struct. Dyn. 16, 461-476
    • (1998) J. Biomol. Struct. Dyn. , vol.16 , pp. 461-476
    • Manning, G.S.1    Ray, J.2
  • 90
    • 0032686953 scopus 로고    scopus 로고
    • Counterion and coion distribution functions in the counterion condensation theory of polyelectrolytes
    • Ray, J. and Manning, G. S. (1999) Counterion and coion distribution functions in the counterion condensation theory of polyelectrolytes Macromolecules 332, 4588-4595
    • (1999) Macromolecules , vol.332 , pp. 4588-4595
    • Ray, J.1    Manning, G.S.2
  • 92
    • 84857311171 scopus 로고    scopus 로고
    • RNA and its ionic cloud: Solution scattering experiments and atomically detailed simulations
    • Kirmizialtin, S., Pabit, S. A., Meisburger, S. P., Pollack, L., and Elber, R. (2012) RNA and its ionic cloud: Solution scattering experiments and atomically detailed simulations Biophys. J. 102, 819-828
    • (2012) Biophys. J. , vol.102 , pp. 819-828
    • Kirmizialtin, S.1    Pabit, S.A.2    Meisburger, S.P.3    Pollack, L.4    Elber, R.5
  • 95
    • 0024519056 scopus 로고
    • An estimate of the extent of folding of nucleosomal DNA by laterally asymmetric neutralization of phosphate groups
    • Manning, G. S., Ebralidse, K. K., Mirzabekov, A. D., and Rich, A. (1989) An estimate of the extent of folding of nucleosomal DNA by laterally asymmetric neutralization of phosphate groups J. Biomol. Struct. Dyn. 6, 877-889
    • (1989) J. Biomol. Struct. Dyn. , vol.6 , pp. 877-889
    • Manning, G.S.1    Ebralidse, K.K.2    Mirzabekov, A.D.3    Rich, A.4
  • 96
    • 0038036670 scopus 로고    scopus 로고
    • Comments on selected aspects of nucleic acid electrostatics
    • Manning, G. S. (2003) Comments on selected aspects of nucleic acid electrostatics Biopolymers 69, 137-143
    • (2003) Biopolymers , vol.69 , pp. 137-143
    • Manning, G.S.1
  • 97
    • 33646158918 scopus 로고    scopus 로고
    • The contribution of transient counterion imbalances to DNA bending fluctuations
    • Manning, G. S. (2006) The contribution of transient counterion imbalances to DNA bending fluctuations Biophys. J. 90, 3208-3215
    • (2006) Biophys. J. , vol.90 , pp. 3208-3215
    • Manning, G.S.1
  • 98
    • 4243189532 scopus 로고
    • Electrostatic persistence length of a wormlike polyelectrolyte
    • Skolnick, J. and Fixman, M. (1977) Electrostatic persistence length of a wormlike polyelectrolyte Macromolecules 10, 944-948
    • (1977) Macromolecules , vol.10 , pp. 944-948
    • Skolnick, J.1    Fixman, M.2
  • 100
    • 60349115060 scopus 로고    scopus 로고
    • Poly(dA:dT) tracts: Major determinants of nucleosome organization
    • Segal, E. and Widom, J. (2009) Poly(dA:dT) tracts: Major determinants of nucleosome organization Curr. Opin. Struct. Biol. 19, 65-71
    • (2009) Curr. Opin. Struct. Biol. , vol.19 , pp. 65-71
    • Segal, E.1    Widom, J.2
  • 101
    • 70350686719 scopus 로고    scopus 로고
    • The role of DNA shape in protein-DNA recognition
    • Rohs, R., West, S. M., Sosinsky, A., Liu, P., Mann, R. S., and Honig, B. (2009) The role of DNA shape in protein-DNA recognition Nature 461, 1248-1253
    • (2009) Nature , vol.461 , pp. 1248-1253
    • Rohs, R.1    West, S.M.2    Sosinsky, A.3    Liu, P.4    Mann, R.S.5    Honig, B.6
  • 103
    • 0030896406 scopus 로고    scopus 로고
    • Temperature-dependent ultraviolet resonance Raman spectroscopy of the premelting state of dA·dT DNA
    • Chan, S. S., Austin, R. H., Mukerji, I., and Spiro, T. G. (1997) Temperature-dependent ultraviolet resonance Raman spectroscopy of the premelting state of dA·dT DNA Biophys. J. 72, 1512-1529
    • (1997) Biophys. J. , vol.72 , pp. 1512-1529
    • Chan, S.S.1    Austin, R.H.2    Mukerji, I.3    Spiro, T.G.4
  • 104
    • 0034633947 scopus 로고    scopus 로고
    • The curvature of da tracts is temperature dependent
    • Jerkovic, B. and Bolton, P. H. (2000) The curvature of dA tracts is temperature dependent Biochemistry 39, 12121-12127
    • (2000) Biochemistry , vol.39 , pp. 12121-12127
    • Jerkovic, B.1    Bolton, P.H.2
  • 105
    • 0037039286 scopus 로고    scopus 로고
    • 3 tract: Evidence for a premelting transition and three-centered H-bonds
    • 3 tract: Evidence for a premelting transition and three-centered H-bonds Biochemistry 41, 69-77
    • (2002) Biochemistry , vol.41 , pp. 69-77
    • Mukerji, I.1    Williams, A.P.2
  • 106
    • 33645912348 scopus 로고    scopus 로고
    • Examination of the premelting transition of DNA A-tracts using a fluorescent adenosine analogue
    • Augustyn, K. E., Wojtuszewski, K., Hawkins, M. E., Knutson, J. R., and Mukerji, I. (2006) Examination of the premelting transition of DNA A-tracts using a fluorescent adenosine analogue Biochemistry 45, 5039-5047
    • (2006) Biochemistry , vol.45 , pp. 5039-5047
    • Augustyn, K.E.1    Wojtuszewski, K.2    Hawkins, M.E.3    Knutson, J.R.4    Mukerji, I.5
  • 107
    • 0024589495 scopus 로고
    • A premelting conformational transition in poly(dA)-poly(dT) coupled to daunomycin binding
    • Herrera, J. E. and Chaires, J. B. (1989) A premelting conformational transition in poly(dA)-poly(dT) coupled to daunomycin binding Biochemistry 28, 1993-2000
    • (1989) Biochemistry , vol.28 , pp. 1993-2000
    • Herrera, J.E.1    Chaires, J.B.2
  • 108
    • 33845556449 scopus 로고
    • Limiting laws and counterion condensation in polyelectrolyte solutions. 7. Electrophoretic mobility and conductance
    • Manning, G. S. (1981) Limiting laws and counterion condensation in polyelectrolyte solutions. 7. Electrophoretic mobility and conductance J. Phys. Chem. 85, 1508-1515
    • (1981) J. Phys. Chem. , vol.85 , pp. 1508-1515
    • Manning, G.S.1
  • 109
    • 0037342517 scopus 로고    scopus 로고
    • Probing the electrostatic shielding of DNA with capillary electrophoresis
    • Stellwagen, E. and Stellwagen, N. C. (2003) Probing the electrostatic shielding of DNA with capillary electrophoresis Biophys. J. 84, 1855-1866
    • (2003) Biophys. J. , vol.84 , pp. 1855-1866
    • Stellwagen, E.1    Stellwagen, N.C.2
  • 110
    • 0026329869 scopus 로고
    • Helical repeat and chirality effects on DNA gel electrophoretic mobility
    • Drak, J. and Crothers, D. M. (1991) Helical repeat and chirality effects on DNA gel electrophoretic mobility Proc. Natl. Acad. Sci. U.S.A. 88, 3074-3078
    • (1991) Proc. Natl. Acad. Sci. U.S.A. , vol.88 , pp. 3074-3078
    • Drak, J.1    Crothers, D.M.2
  • 111
    • 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
  • 112
    • 0031037020 scopus 로고    scopus 로고
    • DNA mobility anomalies are determined primarily by polyacrylamide gel concentration, not gel pore size
    • Stellwagen, N. C. (1997) DNA mobility anomalies are determined primarily by polyacrylamide gel concentration, not gel pore size Electrophoresis 18, 34-44
    • (1997) Electrophoresis , vol.18 , pp. 34-44
    • Stellwagen, N.C.1
  • 113
    • 0346504001 scopus 로고    scopus 로고
    • Sequence-dependent bending in plasmid pUC19
    • Stellwagen, N. C. (2003) Sequence-dependent bending in plasmid pUC19 Electrophoresis 24, 3467-3475
    • (2003) Electrophoresis , vol.24 , pp. 3467-3475
    • Stellwagen, N.C.1
  • 114
    • 0020163379 scopus 로고
    • Intrinsic electrostatic properties and base sequence effects in the structure of oligonucleotides
    • Lavery, R., Pullman, B., and Zakrzewska, K. (1982) Intrinsic electrostatic properties and base sequence effects in the structure of oligonucleotides Biophys. Chem. 15, 343-351
    • (1982) Biophys. Chem. , vol.15 , pp. 343
    • Lavery, R.1    Pullman, B.2    Zakrzewska, K.3


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.