메뉴 건너뛰기




Volumn 42, Issue 22, 2014, Pages 13981-13996

Ion distributions around left- and right-handed DNA and RNA duplexes: A comparative study

Author keywords

[No Author keywords available]

Indexed keywords

A RNA; ANION; DNA B; DNA Z; DOUBLE STRANDED DNA; DOUBLE STRANDED RNA; MAGNESIUM CHLORIDE; MAGNESIUM ION; POTASSIUM CHLORIDE; POTASSIUM ION; RNA; SODIUM CHLORIDE; SODIUM ION; UNCLASSIFIED DRUG; Z RNA; CATION; CHLORIDE; DIVALENT CATION; DNA A; MAGNESIUM; MONOVALENT CATION; POTASSIUM; SODIUM;

EID: 84927656679     PISSN: 03051048     EISSN: 13624962     Source Type: Journal    
DOI: 10.1093/nar/gku1107     Document Type: Article
Times cited : (53)

References (122)
  • 2
    • 0345552286 scopus 로고
    • The sequence (dC - dA)n. (dG - dT)n forms left-handed Z-DNA in negatively supercoiled plasmids
    • Nordheim, A. and Rich, A. (1983) The sequence (dC - dA)n. (dG - dT)n forms left-handed Z-DNA in negatively supercoiled plasmids. Proc. Natl Acad. Sci. U. S. A., 80, 1821.
    • (1983) Proc. Natl Acad. Sci. U. S. A. , vol.80 , pp. 1821
    • Nordheim, A.1    Rich, A.2
  • 3
    • 0021119770 scopus 로고
    • The chemistry and biology of left-handed Z-DNA
    • Rich, A., Nordheim, A. and Wang, A. H. (1984) The chemistry and biology of left-handed Z-DNA. Ann. Rev. Phys. Chem., 53, 791-846.
    • (1984) Ann. Rev. Phys. Chem. , vol.53 , pp. 791-846
    • Rich, A.1    Nordheim, A.2    Wang, A.H.3
  • 4
    • 0026752148 scopus 로고
    • Mapping Z-DNA in the human genome-computer-aided mapping revelas a nonrandom distribution of potential Z-DNA forming sequences in human genes
    • Schroth, G., Chou, P. and Ho, P. J. (1992) Mapping Z-DNA in the human genome-computer-aided mapping revelas a nonrandom distribution of potential Z-DNA forming sequences in human genes. J. Biol. Chem., 267, 11846.
    • (1992) J. Biol. Chem. , vol.267 , pp. 11846
    • Schroth, G.1    Chou, P.2    Ho, P.J.3
  • 5
    • 0023433855 scopus 로고
    • Supercoiling of the DNA template during transcription
    • Liu, L. F. and Wang, J. C. (1987) Supercoiling of the DNA template during transcription. Proc. Natl Acad. Sci. U. S. A., 84, 7024-7027.
    • (1987) Proc. Natl Acad. Sci. U. S. A. , vol.84 , pp. 7024-7027
    • Liu, L.F.1    Wang, J.C.2
  • 6
    • 0037168537 scopus 로고    scopus 로고
    • Z-DNA binding proteins can act as potent effectors of gene expression in vivo
    • Oh, D., Kim, Y. and Rich, A. (2002) Z-DNA binding proteins can act as potent effectors of gene expression in vivo. Proc. Natl Acad. Sci. U. S. A., 99, 16666.
    • (2002) Proc. Natl Acad. Sci. U. S. A. , vol.99 , pp. 16666
    • Oh, D.1    Kim, Y.2    Rich, A.3
  • 7
    • 0020710399 scopus 로고
    • Antibodies against Z-DNA react with the macronucleus but not the micronucleus of the hypotrichous ciliate stylonychia mytilus
    • Lipps, H. J. (1983) Antibodies against Z-DNA react with the macronucleus but not the micronucleus of the hypotrichous ciliate stylonychia mytilus. Cell, 32, 435-441.
    • (1983) Cell , vol.32 , pp. 435-441
    • Lipps, H.J.1
  • 9
    • 0033395227 scopus 로고    scopus 로고
    • Left-handed Z-DNA: Structure and function
    • Herbert, A. and Rich, A. (1999) Left-handed Z-DNA: structure and function. Genetica, 106, 37.
    • (1999) Genetica , vol.106 , pp. 37
    • Herbert, A.1    Rich, A.2
  • 10
    • 0021984352 scopus 로고
    • Left-handed DNA and the synaptic pairing reaction promoted by ustilago rec1 protein
    • Kmiec, E., Angelides, K. and Holloman, W. (1985) Left-handed DNA and the synaptic pairing reaction promoted by ustilago rec1 protein. Cell, 40, 139.
    • (1985) Cell , vol.40 , pp. 139
    • Kmiec, E.1    Angelides, K.2    Holloman, W.3
  • 11
    • 0023644785 scopus 로고
    • Left-handed Z-DNA binding by the reca protein of escherichia-coli
    • Blaho, J. and Wells, R. (1987) Left-handed Z-DNA binding by the reca protein of escherichia-coli. J. Biol. Chem., 262, 6082.
    • (1987) J. Biol. Chem. , vol.262 , pp. 6082
    • Blaho, J.1    Wells, R.2
  • 13
    • 0033546005 scopus 로고    scopus 로고
    • Crystal structure of the Z alpha domain of the human editing enzyme ADAR1 bound to left-handed Z-DNA
    • Schwartz, T., Rould, M., Lowenhaupt, K., Herbert, A. and Rich, A. (1999) Crystal structure of the Z alpha domain of the human editing enzyme ADAR1 bound to left-handed Z-DNA. Science, 284, 1841.
    • (1999) Science , vol.284 , pp. 1841
    • Schwartz, T.1    Rould, M.2    Lowenhaupt, K.3    Herbert, A.4    Rich, A.5
  • 14
    • 0037388031 scopus 로고    scopus 로고
    • DNA helix: The importance of being GC-rich
    • Vinogradov, A. (2003) DNA helix: the importance of being GC-rich. Nucleic Acids Res., 31, 1838.
    • (2003) Nucleic Acids Res. , vol.31 , pp. 1838
    • Vinogradov, A.1
  • 15
    • 13544272030 scopus 로고    scopus 로고
    • Distributions of Z-DNA and nuclear factor I in human chromosome 22; a model for coupled transcriptional regulation
    • Champ, P., Maurice, S., Vargason, J., Champ, T. and Ho, P. (2004) Distributions of Z-DNA and nuclear factor I in human chromosome 22; a model for coupled transcriptional regulation. Nucleic Acids Res., 32, 6501.
    • (2004) Nucleic Acids Res. , vol.32 , pp. 6501
    • Champ, P.1    Maurice, S.2    Vargason, J.3    Champ, T.4    Ho, P.5
  • 16
    • 33644543741 scopus 로고    scopus 로고
    • Z-DNA-forming sequences generate large-scale deletions in mammalian cells
    • Wang, G., Christensen, L. and Vasquez, K. (2006) Z-DNA-forming sequences generate large-scale deletions in mammalian cells. Proc. Natl Acad. Sci. U. S. A., 103, 2677.
    • (2006) Proc. Natl Acad. Sci. U. S. A. , vol.103 , pp. 2677
    • Wang, G.1    Christensen, L.2    Vasquez, K.3
  • 17
    • 33745698705 scopus 로고    scopus 로고
    • Molecular mechanisms for the B-Z transition in the example of poly[d (G-C).d (G-C)] polymers. A critical review
    • Fuertes, M. A., Cepeda, V, Alonso, C. and Pérez, J. M. (2006) Molecular mechanisms for the B-Z transition in the example of poly[d (G-C).d (G-C)] polymers. A critical review. Chem. Rev., 106, 2045-2064.
    • (2006) Chem. Rev. , vol.106 , pp. 2045-2064
    • Fuertes, M.A.1    Cepeda, V.2    Alonso, C.3    Pérez, J.M.4
  • 18
    • 0021112288 scopus 로고
    • DNA structural dynamics-longitudinal breathing as a possible mechanism for the B-reversible-Z transition
    • Harvey, S. (1983) DNA structural dynamics-longitudinal breathing as a possible mechanism for the B-reversible-Z transition. Nucleic Acids Res., 11, 4867.
    • (1983) Nucleic Acids Res. , vol.11 , pp. 4867
    • Harvey, S.1
  • 19
    • 0021524222 scopus 로고
    • Characterization of intermediate conformational states in the BZ transition of poly (dG - dC) · poly (dG - DC)
    • Goto, S. (1984) Characterization of intermediate conformational states in the BZ transition of poly (dG - dC) · poly (dG - dC). Biopolymers, 23, 2211.
    • (1984) Biopolymers , vol.23 , pp. 2211
    • Goto, S.1
  • 20
    • 0024854284 scopus 로고
    • Raison d'etre and structural model for the B-Z transition of poly d (G-C) &poly d (G-C)
    • Saenger, W. and Hienemann, U. (1989) Raison d'etre and structural model for the B-Z transition of poly d (G-C) &poly d (G-C). FEBS Lett., 257, 223.
    • (1989) FEBS Lett. , vol.257 , pp. 223
    • Saenger, W.1    Hienemann, U.2
  • 21
    • 0025167309 scopus 로고
    • Evidence for a new Z-type left-handed DNA helix - Properties of Z (WC)-DNA
    • Ansevin, A. and Wang, A. (1990) Evidence for a new Z-type left-handed DNA helix - properties of Z (WC)-DNA. Nucleic Acids Res, 18, 6119.
    • (1990) Nucleic Acids Res , vol.18 , pp. 6119
    • Ansevin, A.1    Wang, A.2
  • 22
    • 21244504339 scopus 로고    scopus 로고
    • The stretched intermediate model of B-Z DNA transition
    • Lim, W. and Feng, Y (2005) The stretched intermediate model of B-Z DNA transition. Biophys. J., 88, 1593.
    • (2005) Biophys. J. , vol.88 , pp. 1593
    • Lim, W.1    Feng, Y.2
  • 23
    • 27144542066 scopus 로고    scopus 로고
    • Crystal structure of a junction between B-DNA and Z-DNA reveals two extruded bases
    • Ha, S. C, Lowenhaupt, K., Rich, A., Kim, YG. and Kim, K. K. (2005) Crystal structure of a junction between B-DNA and Z-DNA reveals two extruded bases. Nature, 437, 1183.
    • (2005) Nature , vol.437 , pp. 1183
    • Ha, S.C.1    Lowenhaupt, K.2    Rich, A.3    Kim, Y.G.4    Kim, K.K.5
  • 24
    • 84871800584 scopus 로고    scopus 로고
    • Reaction path ensemble of the B-Z-DNA transition: A comprehensive atomistic study
    • Moradi, M., Babin, V., Roland, C and Sagui, C (2012) Reaction path ensemble of the B-Z-DNA transition: a comprehensive atomistic study. Nucleic Acids Res., 41, 33-43.
    • (2012) Nucleic Acids Res. , vol.41 , pp. 33-43
    • Moradi, M.1    Babin, V.2    Roland, C.3    Sagui, C.4
  • 26
    • 0021868206 scopus 로고
    • Salt- and solvent-dependent conformational transitions of ribo-CGCGCG duplex
    • Adamiak, R. W., Galat, A. and Skalski, B. (1985) Salt- and solvent-dependent conformational transitions of ribo-CGCGCG duplex. Biochim. Biophys. Acta, 825, 345-352.
    • (1985) Biochim. Biophys. Acta , vol.825 , pp. 345-352
    • Adamiak, R.W.1    Galat, A.2    Skalski, B.3
  • 28
    • 0030779674 scopus 로고    scopus 로고
    • Solution structure of RNA duplexes containing alternating CG base pairs: NMR study of r (CGCGCG) 2 and 2' - O - Me (CGCGCG)2 under low salt conditions
    • Popenda, M., Biala, E., Milecki, J. and Adamiak, R. W. (1997) Solution structure of RNA duplexes containing alternating CG base pairs: NMR study of r (CGCGCG) 2 and 2' - O - Me (CGCGCG)2 under low salt conditions. Nucleic Acids Res., 25, 4589-4598.
    • (1997) Nucleic Acids Res. , vol.25 , pp. 4589-4598
    • Popenda, M.1    Biala, E.2    Milecki, J.3    Adamiak, R.W.4
  • 29
    • 3843130804 scopus 로고    scopus 로고
    • High salt solution structure of a left-handed RNA double helix
    • Popenda, M., Milecki, J. and Adamiak, R. W. (2004) High salt solution structure of a left-handed RNA double helix. Nucleic Acids Res., 32, 4044.
    • (2004) Nucleic Acids Res. , vol.32 , pp. 4044
    • Popenda, M.1    Milecki, J.2    Adamiak, R.W.3
  • 31
    • 34047263964 scopus 로고    scopus 로고
    • A left-handed RNA double helix bound by the Z-alpha domain of the RNA-editing enzyme ADAR1
    • Placido, D., Brown, B., Lowenhaupt, K., Rich, A. and Athanasiadis, A. (2007) A left-handed RNA double helix bound by the Z-alpha domain of the RNA-editing enzyme ADAR1. Structure, 15, 395.
    • (2007) Structure , vol.15 , pp. 395
    • Placido, D.1    Brown, B.2    Lowenhaupt, K.3    Rich, A.4    Athanasiadis, A.5
  • 32
    • 0001533502 scopus 로고
    • Measurement of the repulsive force between polyelectrolyte molecules in ionic solution: Hydration forces between parallel DNA double helices
    • Rau, DC, Lee, B. and Parsegian, V. A. (1984) Measurement of the repulsive force between polyelectrolyte molecules in ionic solution: hydration forces between parallel DNA double helices. Proc. Natl Acad. Sci. U. S. A., 81, 2621-2625.
    • (1984) Proc. Natl Acad. Sci. U. S. A. , vol.81 , pp. 2621-2625
    • Rau, D.C.1    Lee, B.2    Parsegian, V.A.3
  • 33
    • 67449096141 scopus 로고    scopus 로고
    • Physical chemistry of DNA viruses
    • Knobler, C and Gelbart, W. (2009) Physical chemistry of DNA viruses. Annu. Rev. Phys. Chem., 60, 367-383.
    • (2009) Annu. Rev. Phys. Chem. , vol.60 , pp. 367-383
    • Knobler, C.1    Gelbart, W.2
  • 34
    • 67349123194 scopus 로고    scopus 로고
    • Comparative enzymology and structural biology of RNA self-cleavage
    • Fedor, M. (2009) Comparative enzymology and structural biology of RNA self-cleavage. Annu. Rev. Biophys., 38, 271-299.
    • (2009) Annu. Rev. Biophys. , vol.38 , pp. 271-299
    • Fedor, M.1
  • 36
    • 33847682251 scopus 로고    scopus 로고
    • Charge density of divalent metal cations determines RNA stability
    • Koculi, E., Hyeon, C, Thirumalai, D and Woodson, S. A. (2007) Charge density of divalent metal cations determines RNA stability. J. Am. Chem. Soc, 129, 2676-2682.
    • (2007) J. Am. Chem. Soc , vol.129 , pp. 2676-2682
    • Koculi, E.1    Hyeon, C.2    Thirumalai, D.3    Woodson, S.A.4
  • 38
    • 41949124146 scopus 로고    scopus 로고
    • Molecular dynamics simulations of nucleic acid-protein complexes
    • MacKerrell, A. Jr. and Nilsson, L. (2008) Molecular dynamics simulations of nucleic acid-protein complexes. Curr Opin. Struct. Biol, 18, 194-199.
    • (2008) Curr Opin. Struct. Biol , vol.18 , pp. 194-199
    • MacKerrell, A.1    Nilsson, L.2
  • 39
  • 40
    • 0026059567 scopus 로고
    • Structure of the B-DNA decamer C-C-A-A-C-G-T-T-G-G and comparison with isomorphous decamers C-C-A-A-G-A-T-T-G-G and C-C-A-G-G-C-C-T-G-G
    • Prive, GG, Yanagi, K. and Dickerson, R. E. (1991) Structure of the B-DNA decamer C-C-A-A-C-G-T-T-G-G and comparison with isomorphous decamers C-C-A-A-G-A-T-T-G-G and C-C-A-G-G-C-C-T-G-G. J. Mol. Biol, 217, 177-199.
    • (1991) J. Mol. Biol , vol.217 , pp. 177-199
    • Prive, G.G.1    Yanagi, K.2    Dickerson, R.E.3
  • 41
    • 0032387836 scopus 로고    scopus 로고
    • Structure of the potassium form of CGCGAATTCGCG: DNA deformation by electrostatic collapse around inorganic cations
    • Shui, X., Sines, CC, McFail-Isom, L., Van Derveer, D and Williams, L. D (1998) Structure of the potassium form of CGCGAATTCGCG: DNA deformation by electrostatic collapse around inorganic cations. Biochemistry, 37, 16877-16887.
    • (1998) Biochemistry , vol.37 , pp. 16877-16887
    • Shui, X.1    Sines, C.C.2    McFail-Isom, L.3    Van Derveer, D.4    Williams, L.D.5
  • 42
    • 0032499635 scopus 로고    scopus 로고
    • The B-DNA dodecamer at high resolution reveals a spine of water on sodium
    • Shui, X., McFail-Isom, L., Hu, G. and Williams, L. D. (1998) The B-DNA dodecamer at high resolution reveals a spine of water on sodium. Biochemistry, 37, 8341-8355.
    • (1998) Biochemistry , vol.37 , pp. 8341-8355
    • Shui, X.1    McFail-Isom, L.2    Hu, G.3    Williams, L.D.4
  • 43
    • 0033594498 scopus 로고    scopus 로고
    • A 'hydration' spine in a B-DNA minor groove
    • Tereshko, V., Minasov, G. and Egli, M. (1999) A 'hydration' 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
  • 45
    • 0033571104 scopus 로고    scopus 로고
    • The crystal structure of the dimerization initiation site of genomic HIV-1 RNA reveals an extended duplex with two adenine bulges
    • Ennifar, E., Yusupov, M., Walter, P., Marquet, R., Ehresmann, B., Ehresmann, C. and Dumas, P. (1999) The crystal structure of the dimerization initiation site of genomic HIV-1 RNA reveals an extended duplex with two adenine bulges. Struct. Fold. Des., 7, 1439-1449.
    • (1999) Struct. Fold. Des. , vol.7 , pp. 1439-1449
    • Ennifar, E.1    Yusupov, M.2    Walter, P.3    Marquet, R.4    Ehresmann, B.5    Ehresmann, C.6    Dumas, P.7
  • 46
    • 0034655642 scopus 로고    scopus 로고
    • Hexahydrated magnesium ions bind in the deep major groove and at the outer mouth of A-form nucleic acid duplexes
    • Robinson, H., Gao, Y. G., Sanishvili, R., Joachimiak, A. and Wang, A. H. J. (2000) Hexahydrated magnesium ions bind in the deep major groove and at the outer mouth of A-form nucleic acid duplexes. Nucleic Acids Res., 28, 1760-1766.
    • (2000) Nucleic Acids Res. , vol.28 , pp. 1760-1766
    • Robinson, H.1    Gao, Y.G.2    Sanishvili, R.3    Joachimiak, A.4    Wang, A.H.J.5
  • 48
    • 0043037215 scopus 로고    scopus 로고
    • Cations as hydrogen bond donors: A view of electrostatic interactions in DNA
    • Subirana, J. A. and Soler-Lopez, 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-Lopez, M.2
  • 49
    • 0034714010 scopus 로고    scopus 로고
    • 1 angstrom crystal structure of B-DNA real sequence specific and groove specific bending of DNA by magnesium and calcium
    • Chiu, T. K. and Dickerson, R. E. (2000) 1 angstrom crystal structure of B-DNA real sequence specific and groove specific bending of DNA by magnesium and calcium. J. Mol. Biol., 301, 915.
    • (2000) J. Mol. Biol. , vol.301 , pp. 915
    • Chiu, T.K.1    Dickerson, R.E.2
  • 50
    • 0038719800 scopus 로고    scopus 로고
    • A crystallographic study of the binding of 13 metal ions to two related RNA duplexes
    • Ennifar, E., Walter, P. and Dumas, P. (2003) A crystallographic study of the binding of 13 metal ions to two related RNA duplexes. Nucleic Acids Res., 31, 2671-2682.
    • (2003) Nucleic Acids Res. , vol.31 , pp. 2671-2682
    • Ennifar, E.1    Walter, P.2    Dumas, P.3
  • 51
    • 36248966494 scopus 로고    scopus 로고
    • The 1.3 angstrom resolution structure of the RNA tridecamer r (GCGUUUGAAACGC): Metal ion binding correlates with base unstacking and groove contraction
    • Timsit, Y. and Bombard, S. (2007) The 1.3 angstrom resolution structure of the RNA tridecamer r (GCGUUUGAAACGC): metal ion binding correlates with base unstacking and groove contraction. RNA, 13, 2098-2107.
    • (2007) RNA , vol.13 , pp. 2098-2107
    • Timsit, Y.1    Bombard, S.2
  • 52
    • 0033585580 scopus 로고    scopus 로고
    • The Dickerson-Drew B-DNA dodecamer revisited at atomic resolution
    • Tereshko, V., Minasov, G. and Egli, M. (1999) The Dickerson-Drew B-DNA dodecamer revisited at atomic resolution. J. Am. Chem. Soc., 121, 470-471.
    • (1999) J. Am. Chem. Soc. , vol.121 , pp. 470-471
    • Tereshko, V.1    Minasov, G.2    Egli, M.3
  • 53
    • 0033600794 scopus 로고    scopus 로고
    • Absence of minor groove monovalent cations in the crosslinked dodecamer CGCGAATTCGCG
    • Chiu, T. K., Kaczor-Grzeskowiak, M. and Dickerson, R. E. (1999) Absence of minor groove monovalent cations in the crosslinked dodecamer CGCGAATTCGCG. J. Mol. Biol., 292, 589-608.
    • (1999) J. Mol. Biol. , vol.292 , pp. 589-608
    • Chiu, T.K.1    Kaczor-Grzeskowiak, M.2    Dickerson, R.E.3
  • 55
    • 57649130782 scopus 로고    scopus 로고
    • A repulsive field: Advances in the electrostatics of the ion atmosphere
    • Chu, V., Bai, Y., Lipfert, J., Herschlag, D. and Doniach, S. (2008) A repulsive field: advances in the electrostatics of the ion atmosphere. Curr. Opin. Chem. Biol., 12, 619-625.
    • (2008) Curr. Opin. Chem. Biol. , vol.12 , pp. 619-625
    • Chu, V.1    Bai, Y.2    Lipfert, J.3    Herschlag, D.4    Doniach, S.5
  • 56
    • 77951687980 scopus 로고    scopus 로고
    • Electrostatics of strongly charged biological polymers: Ion-mediated interactions and self-organization in nucleic acids and proteins
    • Wong, G. C. L. and Pollack, L. (2010) Electrostatics of strongly charged biological polymers: ion-mediated interactions and self-organization in nucleic acids and proteins. Annu. Rev. Phys. Chem., 61, 171-189.
    • (2010) Annu. Rev. Phys. Chem. , vol.61 , pp. 171-189
    • Wong, G.C.L.1    Pollack, L.2
  • 57
    • 36848999901 scopus 로고    scopus 로고
    • Quantitative and comprehensive decomposition of the ion atmosphere around nucleic acids
    • Bai, Y., Greenfeld, M., Travers, K., Chu, V., Lipfert, J., Doniach, S. and Herschlag, D. (2007) Quantitative and comprehensive decomposition of the ion atmosphere around nucleic acids. J. Am. Chem. Soc., 129, 14981-14988.
    • (2007) J. Am. Chem. Soc. , vol.129 , pp. 14981-14988
    • Bai, Y.1    Greenfeld, M.2    Travers, K.3    Chu, V.4    Lipfert, J.5    Doniach, S.6    Herschlag, D.7
  • 58
    • 0030763137 scopus 로고    scopus 로고
    • Localization of divalent metal ions in the minor groove of DNA A-tracts
    • Hud, N. V. and Feigon, J. (1997) Localization of divalent metal ions in the minor groove of DNA A-tracts. J. Am. Chem. Soc., 119, 5756-5757.
    • (1997) J. Am. Chem. Soc. , vol.119 , pp. 5756-5757
    • Hud, N.V.1    Feigon, J.2
  • 59
    • 0033605083 scopus 로고    scopus 로고
    • Localization of ammonium ions in the minor groove of DNA duplexes in solution and the origin of DNA A-tract bending
    • Hud, N. V., Sklenar, V. and Feigon, J. (1999) Localization of ammonium ions in the minor groove of DNA duplexes in solution and the origin of DNA A-tract bending. J. Mol. Biol., 286, 651-660.
    • (1999) J. Mol. Biol. , vol.286 , pp. 651-660
    • Hud, N.V.1    Sklenar, V.2    Feigon, J.3
  • 60
    • 0033801089 scopus 로고    scopus 로고
    • Localisation and dynamics of sodium counterions around DNA in solution from molecular dynamics simulation
    • Bonvin, A. (2000) Localisation and dynamics of sodium counterions around DNA in solution from molecular dynamics simulation. Eur. Biophys. J., 29, 57-60.
    • (2000) Eur. Biophys. J. , vol.29 , pp. 57-60
    • Bonvin, A.1
  • 61
    • 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
  • 62
    • 2542583798 scopus 로고    scopus 로고
    • Competitive Na+ and Rb+ binding in the minor groove of DNA
    • Marincola, F. C., Denisov, V. P. and Halle, B. (2004) Competitive Na+ and Rb+ binding in the minor groove of DNA. J. Am. Chem. Soc., 126, 6739-6750.
    • (2004) J. Am. Chem. Soc. , vol.126 , pp. 6739-6750
    • Marincola, F.C.1    Denisov, V.P.2    Halle, B.3
  • 63
    • 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., 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.3    Moulaei, T.4    Hud, N.V.5    Williams, L.D.6
  • 64
    • 0017895903 scopus 로고
    • 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
  • 65
    • 0000533571 scopus 로고
    • Ionic distributions and competitive association on DNA mixed salt solutions
    • Bacquet, R. J. and Rossky, P. J. (1988) Ionic distributions and competitive association on DNA mixed salt solutions. J. Phys. Chem., 92, 3604-3612.
    • (1988) J. Phys. Chem. , vol.92 , pp. 3604-3612
    • Bacquet, R.J.1    Rossky, P.J.2
  • 66
    • 84990642018 scopus 로고
    • The interaction of Na (I), Ca (II), and Mg (II) metal-ions with duplex DNA - A theoretical modeling study
    • York, D. M., Darden, T., Deerfield, D. and Pedersen, L. G. (1992) The interaction of Na (I), Ca (II), and Mg (II) metal-ions with duplex DNA - a theoretical modeling study. Intl. J. Quant. Chem., 19, 145-166.
    • (1992) Intl. J. Quant. Chem. , vol.19 , pp. 145-166
    • York, D.M.1    Darden, T.2    Deerfield, D.3    Pedersen, L.G.4
  • 67
    • 0031249752 scopus 로고    scopus 로고
    • Monovalent and divalent salt effects on electrostatic free energies defined by the nonlinear Poisson-Boltzmann equation: Application to DNA binding reaction
    • Chen, S. W. W. and Honig, B. (1997) Monovalent and divalent salt effects on electrostatic free energies defined by the nonlinear Poisson-Boltzmann equation: application to DNA binding reaction. J. Phys. Chem. B, 101, 9113-9118.
    • (1997) J. Phys. Chem. B , vol.101 , pp. 9113-9118
    • Chen, S.W.W.1    Honig, B.2
  • 68
    • 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
  • 69
    • 0032851951 scopus 로고    scopus 로고
    • Sodium and chlorine ions as part of the DNA solvation shell
    • Feig, M. and Pettitt, B. M. (1999) Sodium and chlorine ions as part of the DNA solvation shell. Biophys. J., 77, 1769-1781.
    • (1999) Biophys. J. , vol.77 , pp. 1769-1781
    • Feig, M.1    Pettitt, B.M.2
  • 70
    • 0034725528 scopus 로고    scopus 로고
    • Water and ion binding around RNA and DNA (C, G) oligomers
    • Auffinger, P. and Westhof, E. (2000) Water and ion binding around RNA and DNA (C, G) oligomers. J. Mol. Biol., 300, 1113-1131.
    • (2000) J. Mol. Biol. , vol.300 , pp. 1113-1131
    • Auffinger, P.1    Westhof, E.2
  • 71
    • 1242347628 scopus 로고    scopus 로고
    • Theoretical methods for the simulation of nucleic acids
    • Orozco, M., Pérez, A., Noy, A. and Luque, F. J. (2003) Theoretical methods for the simulation of nucleic acids. Chem. Soc. Rev., 32, 350-364.
    • (2003) Chem. Soc. Rev. , vol.32 , pp. 350-364
    • Orozco, M.1    Pérez, A.2    Noy, A.3    Luque, F.J.4
  • 72
    • 4143138536 scopus 로고    scopus 로고
    • Exploring the counterion atmosphere around DNA: What can be learned from molecular dynamics simulations?
    • Rueda, M., Cubero, E., Laughton, C. A. and Orozco, M. (2004) Exploring the counterion atmosphere around DNA: what can be learned from molecular dynamics simulations?. Biophys. J., 87, 800-811.
    • (2004) Biophys. J. , vol.87 , pp. 800-811
    • Rueda, M.1    Cubero, E.2    Laughton, C.A.3    Orozco, M.4
  • 74
    • 4043179941 scopus 로고    scopus 로고
    • DNA and its counterions: A molecular dynamics study
    • Várnai, P. and Zakrzewska, K. (2004) DNA and its counterions: a molecular dynamics study. Nucleic Acids Res., 320, 4269-4280.
    • (2004) Nucleic Acids Res. , vol.320 , pp. 4269-4280
    • Várnai, P.1    Zakrzewska, K.2
  • 75
    • 28144433340 scopus 로고    scopus 로고
    • Ion atmosphere around nucleic acid
    • Taubes, C. H., Mohanty, U. and Chu, S. (2005) Ion atmosphere around nucleic acid. J. Phys. Chem. B, 109, 21267-21272.
    • (2005) J. Phys. Chem. B , vol.109 , pp. 21267-21272
    • Taubes, C.H.1    Mohanty, U.2    Chu, S.3
  • 76
    • 34347404466 scopus 로고    scopus 로고
    • Nucleic acid solvation: From outside to insight
    • Auffinger, P. and Hashem, Y. (2007) Nucleic acid solvation: from outside to insight. Curr. Opin. Struct. Biol., 17, 325-333.
    • (2007) Curr. Opin. Struct. Biol. , vol.17 , pp. 325-333
    • Auffinger, P.1    Hashem, Y.2
  • 77
    • 38349110269 scopus 로고    scopus 로고
    • Simulation of the pressure and temperature folding/unfolding equilibrium of a small RNA hairpin
    • Garcia, A. E. and Paschek, D. (2008) Simulation of the pressure and temperature folding/unfolding equilibrium of a small RNA hairpin. J. Am. Chem. Soc., 130, 815.
    • (2008) J. Am. Chem. Soc. , vol.130 , pp. 815
    • Garcia, A.E.1    Paschek, D.2
  • 78
    • 84868242573 scopus 로고    scopus 로고
    • Competitive binding of cations to duplex DNA revealed through molecular dynamics simulations
    • Yoo, J. and Aksimentiev, A. (2012) Competitive binding of cations to duplex DNA revealed through molecular dynamics simulations. J. Phys. Chem. B, 116, 12946-12954.
    • (2012) J. Phys. Chem. B , vol.116 , pp. 12946-12954
    • Yoo, J.1    Aksimentiev, A.2
  • 79
    • 84860477162 scopus 로고    scopus 로고
    • Frontiers in molecular dynamics simulations of DNA
    • Perez, A., Luque, F. J. and Orozco, M. (2012) Frontiers in molecular dynamics simulations of DNA. Acc. Chem. Res., 45, 196-205.
    • (2012) Acc. Chem. Res. , vol.45 , pp. 196-205
    • Perez, A.1    Luque, F.J.2    Orozco, M.3
  • 80
    • 84892157404 scopus 로고    scopus 로고
    • Classical electrostatics for biomolecular simulations
    • Cisneros, G. A., Karttunen, M., Ren, P. and Sagui, C. (2014) Classical electrostatics for biomolecular simulations. Chem. Rev., 114, 779-814.
    • (2014) Chem. Rev. , vol.114 , pp. 779-814
    • Cisneros, G.A.1    Karttunen, M.2    Ren, P.3    Sagui, C.4
  • 81
    • 36449007976 scopus 로고
    • The effect of long-range electrostatic interactions in simulations of macromolecular crystals: A comparison of the Ewald and truncated list methods
    • York, D. M., Darden, T. A. and Pedersen, L. G. (1993) The effect of long-range electrostatic interactions in simulations of macromolecular crystals: a comparison of the Ewald and truncated list methods. J. Chem. Phys., 99, 8345-8348.
    • (1993) J. Chem. Phys. , vol.99 , pp. 8345-8348
    • York, D.M.1    Darden, T.A.2    Pedersen, L.G.3
  • 82
    • 33846823909 scopus 로고
    • Particle mesh Ewald: An N log (N) method for Ewald sums in large systems
    • Darden, T. A., York, D. M. and Pedersen, L. G. (1993) Particle mesh Ewald: an N log (N) method for Ewald sums in large systems. J. Chem. Phys., 98, 10089-10092.
    • (1993) J. Chem. Phys. , vol.98 , pp. 10089-10092
    • Darden, T.A.1    York, D.M.2    Pedersen, L.G.3
  • 83
    • 0029110156 scopus 로고
    • Towards the accurate modeling of DNA: The importance of long-range electrostatics
    • York, D. M., Yang, W., Lee, H., Darden, T. A. and Pedersen, L. G. (1995) Towards the accurate modeling of DNA: the importance of long-range electrostatics. J. Am. Chem. Soc., 117, 5001-5002.
    • (1995) J. Am. Chem. Soc. , vol.117 , pp. 5001-5002
    • York, D.M.1    Yang, W.2    Lee, H.3    Darden, T.A.4    Pedersen, L.G.5
  • 85
    • 70549103338 scopus 로고    scopus 로고
    • Dependence of A-RNA simulations on the choice of the force field and salt strength
    • Besseova, I., Otyepka, M., Reblova, K. and Sponer, J. (2009) Dependence of A-RNA simulations on the choice of the force field and salt strength. Phys. Chem. Chem. Phys., 11, 10701-10711.
    • (2009) Phys. Chem. Chem. Phys. , vol.11 , pp. 10701-10711
    • Besseova, I.1    Otyepka, M.2    Reblova, K.3    Sponer, J.4
  • 86
    • 77953802958 scopus 로고    scopus 로고
    • Computational exploration of mobile ion distributions around RNA duplex
    • Kirmizialtin, S. and Elber, R. (2010) Computational exploration of mobile ion distributions around RNA duplex. J. Phys. Chem. B, 114, 8207-8220.
    • (2010) J. Phys. Chem. B , vol.114 , pp. 8207-8220
    • Kirmizialtin, S.1    Elber, R.2
  • 87
    • 84867761593 scopus 로고    scopus 로고
    • Simulations of A-RNA duplexes. The effect of sequence, solute force field, water model, and salt concentration
    • Besseova, I., Barnas, P., Kuhrova, P., Kosinova, P., Otyepka, M. and Sponer, J. (2012) Simulations of A-RNA duplexes. The effect of sequence, solute force field, water model, and salt concentration. J. Phys. Chem. B, 116, 9899-9916.
    • (2012) J. Phys. Chem. B , vol.116 , pp. 9899-9916
    • Besseova, I.1    Barnas, P.2    Kuhrova, P.3    Kosinova, P.4    Otyepka, M.5    Sponer, J.6
  • 88
    • 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
  • 89
    • 84857256519 scopus 로고    scopus 로고
    • The ionic atmosphere around A-RNA: Poisson-Boltzmann and molecular dynamics simulations
    • Kirmizialtin, S., Silalahi, A. R., Elber, R. and Fenley, M. O. (2012) The ionic atmosphere around A-RNA: Poisson-Boltzmann and molecular dynamics simulations. Biophys. J., 102, 829-838.
    • (2012) Biophys. J. , vol.102 , pp. 829-838
    • Kirmizialtin, S.1    Silalahi, A.R.2    Elber, R.3    Fenley, M.O.4
  • 90
    • 34250318638 scopus 로고    scopus 로고
    • Refinement of the AMBER force field for nucleic acids: Improving the description of α/γ conformers
    • Perez, A., Marchan, I., Svozil, D., Sponer, J., Cheatham, T. E., Laughton, C. A. and Orozco, M. (2007) Refinement of the AMBER force field for nucleic acids: improving the description of α/γ conformers. Biophys. J., 92, 3817-3829.
    • (2007) Biophys. J. , vol.92 , pp. 3817-3829
    • Perez, A.1    Marchan, I.2    Svozil, D.3    Sponer, J.4    Cheatham, T.E.5    Laughton, C.A.6    Orozco, M.7
  • 92
    • 80052820313 scopus 로고    scopus 로고
    • Refinement of the Cornell et al. Nucleic acids force field based on reference quantum chemical calculations of glycosidic torsion profiles
    • Zgarbova, M., Otyepka, M., Sponer, J., Mladek, A., Banas, P, Cheatham, T. E. and Jurecka, P (2011) Refinement of the Cornell et al. nucleic acids force field based on reference quantum chemical calculations of glycosidic torsion profiles. J. Chem. Theory Comput., 7, 2886-2902.
    • (2011) J. Chem. Theory Comput. , vol.7 , pp. 2886-2902
    • Zgarbova, M.1    Otyepka, M.2    Sponer, J.3    Mladek, A.4    Banas, P.5    Cheatham, T.E.6    Jurecka, P.7
  • 94
    • 0004016501 scopus 로고
    • Comparison of simple potential functions for simulating liquid water
    • Jorgensen, W. L., Chandrasekhar, J., Madura, J. and Klein, M. L. (1983) Comparison of simple potential functions for simulating liquid water. J. Chem. Phys., 79, 926-935.
    • (1983) J. Chem. Phys. , vol.79 , pp. 926-935
    • Jorgensen, W.L.1    Chandrasekhar, J.2    Madura, J.3    Klein, M.L.4
  • 95
    • 0015244752 scopus 로고
    • Structural and functional defects in mammalian ribosomes after potassium deficiency
    • Naslund, PH. and Hultin, T. (1971) Structural and functional defects in mammalian ribosomes after potassium deficiency. Biochim. Biophys. Acta, 254, 104-116.
    • (1971) Biochim. Biophys. Acta , vol.254 , pp. 104-116
    • Naslund, P.H.1    Hultin, T.2
  • 96
    • 0015502853 scopus 로고
    • Ribosome size distribution in extracts of potassium-depleted Escherichia coli
    • Ennis, H. L. and Artman, M. (1972) Ribosome size distribution in extracts of potassium-depleted Escherichia coli. Biochem. Biophys. Res. Commun., 48, 161-168.
    • (1972) Biochem. Biophys. Res. Commun. , vol.48 , pp. 161-168
    • Ennis, H.L.1    Artman, M.2
  • 97
    • 84855389998 scopus 로고    scopus 로고
    • A study of the hydration of the alkali metal ions in aqueous solution
    • Mahler, J. and Persson, I. (2012) A study of the hydration of the alkali metal ions in aqueous solution. Inorg. Chem., 51, 425-438.
    • (2012) Inorg. Chem. , vol.51 , pp. 425-438
    • Mahler, J.1    Persson, I.2
  • 98
    • 0142025560 scopus 로고
    • Structure and dynamics of hydrated ions
    • Ohtaki, H. and Radnai, T. (1993) Structure and dynamics of hydrated ions. Chem. Rev., 93, 1157.
    • (1993) Chem. Rev. , vol.93 , pp. 1157
    • Ohtaki, H.1    Radnai, T.2
  • 100
    • 0033984826 scopus 로고    scopus 로고
    • A new table of the thermodynamic quantities of ionic hydration: Values and some applications (enthalpy-entropy compensation and Born radii)
    • Schmid, R., Miah, A. M. and Sapunov, VN. (2000) A new table of the thermodynamic quantities of ionic hydration: values and some applications (enthalpy-entropy compensation and Born radii). Phys. Chem. Chem. Phys., 2, 97-102.
    • (2000) Phys. Chem. Chem. Phys. , vol.2 , pp. 97-102
    • Schmid, R.1    Miah, A.M.2    Sapunov, V.N.3
  • 102
    • 0038539610 scopus 로고    scopus 로고
    • The Mg2+ binding sites of the 5S rRNA loop E motif as investigated by molecular dynamics simulations
    • Auffinger, P, Bielecki, L. and Westhof, E. (2003) The Mg2+ binding sites of the 5S rRNA loop E motif as investigated by molecular dynamics simulations. Chem. Biol, 10, 551-561.
    • (2003) Chem. Biol , vol.10 , pp. 551-561
    • Auffinger, P.1    Bielecki, L.2    Westhof, E.3
  • 104
    • 0346366808 scopus 로고    scopus 로고
    • Symmetric K+ and Mg2+ ion-binding sites in the 5S rRNA loop E inferred from molecular dynamics simulations
    • Auffinger, P, Bielecki, L. and Westhof, E. (2004) Symmetric K+ and Mg2+ ion-binding sites in the 5S rRNA loop E inferred from molecular dynamics simulations. J. Mol. Biol, 335, 555-571.
    • (2004) J. Mol. Biol , vol.335 , pp. 555-571
    • Auffinger, P.1    Bielecki, L.2    Westhof, E.3
  • 105
    • 16244363320 scopus 로고    scopus 로고
    • Metal ions and RNA folding: A highly charged topic with a dynamic future
    • Woodson, S. A. (2005) Metal ions and RNA folding: a highly charged topic with a dynamic future. Curr. Opin. Chem. Biol, 9, 104-109.
    • (2005) Curr. Opin. Chem. Biol , vol.9 , pp. 104-109
    • Woodson, S.A.1
  • 106
    • 20444496846 scopus 로고    scopus 로고
    • Determining the Mg2+ stoichiometry for folding an RNA metal ion core
    • Das, R., Travers, K. J., Bai, Y. and Herschlag, D. (2005) Determining the Mg2+ stoichiometry for folding an RNA metal ion core. J. Am. Chem. Soc, 127, 8272-8273.
    • (2005) J. Am. Chem. Soc , vol.127 , pp. 8272-8273
    • Das, R.1    Travers, K.J.2    Bai, Y.3    Herschlag, D.4
  • 107
    • 33749032381 scopus 로고    scopus 로고
    • Mg2+-RNA interaction free energies and their relationship to the folding of RNA tertiary structures
    • Grilley, D., Soto, A. M. and Draper, D. E. (2006) Mg2+-RNA interaction free energies and their relationship to the folding of RNA tertiary structures. Proc. Natl Acad. Sci. U. S. A., 103, 14003-14008.
    • (2006) Proc. Natl Acad. Sci. U. S. A. , vol.103 , pp. 14003-14008
    • Grilley, D.1    Soto, A.M.2    Draper, D.E.3
  • 108
    • 33749646478 scopus 로고    scopus 로고
    • Simulation of Ca2+ and Mg2+ solvation using polarizable atomic multipole potential
    • Jiao, D., King, C, Grossfield, A., Darden, T and Ren, P (2006) Simulation of Ca2+ and Mg2+ solvation using polarizable atomic multipole potential. J. Phys. Chem. B, 110, 18553-18559.
    • (2006) J. Phys. Chem. B , vol.110 , pp. 18553-18559
    • Jiao, D.1    King, C.2    Grossfield, A.3    Darden, T.4    Ren, P.5
  • 109
    • 7544244858 scopus 로고    scopus 로고
    • Molecular dynamics simulations of the d (CCAACGTTGG)2 decamer in crystal environment: Comparison of atomic point-charge, extra-point and polarizable force fields
    • Baucom, J., Transue, T, Fuentes-Cabrera, M. A., Krahn, J. M., Darden, T and Sagui, C. (2004) Molecular dynamics simulations of the d (CCAACGTTGG)2 decamer in crystal environment: comparison of atomic point-charge, extra-point and polarizable force fields. J. Chem. Phys., 121, 6998-7008.
    • (2004) J. Chem. Phys. , vol.121 , pp. 6998-7008
    • Baucom, J.1    Transue, T.2    Fuentes-Cabrera, M.A.3    Krahn, J.M.4    Darden, T.5    Sagui, C.6
  • 110
    • 33745727284 scopus 로고    scopus 로고
    • Molecular dynamics simulations of DNA with polarizable force fields: Convergence of an ideal B-DNA structure to the crystallographic structure
    • Babin, V., Baucom, J., Darden, T. A. and Sagui, C. (2006) Molecular dynamics simulations of DNA with polarizable force fields: convergence of an ideal B-DNA structure to the crystallographic structure. J. Phys. Chem. B, 110, 11571-11581.
    • (2006) J. Phys. Chem. B , vol.110 , pp. 11571-11581
    • Babin, V.1    Baucom, J.2    Darden, T.A.3    Sagui, C.4
  • 111
    • 33750904923 scopus 로고    scopus 로고
    • Molecular dynamics simulations of polarizable DNA in crystal environment
    • Babin, V., Baucom, J., Darden, T. A. and Sagui, C. (2006) Molecular dynamics simulations of polarizable DNA in crystal environment. Int. J. Quantum Chem., 106, 3260-3269.
    • (2006) Int. J. Quantum Chem. , vol.106 , pp. 3260-3269
    • Babin, V.1    Baucom, J.2    Darden, T.A.3    Sagui, C.4
  • 112
    • 22244482712 scopus 로고
    • Many-body effects in molecular-dynamics simulations of Na+ (H2O)n and Cl-(H2O)n clusters
    • Perera, L. and Berkowitz, M. L. (1991) Many-body effects in molecular-dynamics simulations of Na+ (H2O)n and Cl-(H2O)n clusters. J. Chem. Phys., 95, 1954-1963.
    • (1991) J. Chem. Phys. , vol.95 , pp. 1954-1963
    • Perera, L.1    Berkowitz, M.L.2
  • 113
    • 36449003625 scopus 로고
    • Photoelectron-spectroscopy of iodine anion solvated in water clusters
    • Markovich, G., Giniger, R., Levin, M. and Cheshnovsky, O. (1991) Photoelectron-spectroscopy of iodine anion solvated in water clusters. J. Chem. Phys., 95, 9416-9419.
    • (1991) J. Chem. Phys. , vol.95 , pp. 9416-9419
    • Markovich, G.1    Giniger, R.2    Levin, M.3    Cheshnovsky, O.4
  • 114
    • 22244474239 scopus 로고
    • Structure and dynamics of Cl-(H2O)20 clusters: The efect of the polarizability and the charge of the ion
    • Perera, L. and Berkowitz, M. L. (1992) Structure and dynamics of Cl-(H2O)20 clusters: the efect of the polarizability and the charge of the ion. J. Chem. Phys., 96, 8288-8294.
    • (1992) J. Chem. Phys. , vol.96 , pp. 8288-8294
    • Perera, L.1    Berkowitz, M.L.2
  • 115
    • 33748570423 scopus 로고
    • Stabilization energies of Cl-, Br-, and I-ions in water clusters
    • Perera, L. and Berkowitz, M. L. (1993) Stabilization energies of Cl-, Br-, and I-ions in water clusters. J. Chem. Phys., 99, 4222-4224.
    • (1993) J. Chem. Phys. , vol.99 , pp. 4222-4224
    • Perera, L.1    Berkowitz, M.L.2
  • 116
    • 22244459794 scopus 로고
    • Many-body effects in molecular-dynamics simulations of Na+ (H2O)n and Cl-(H2O)n clusters (VOL 95, PG 1954, 1991)
    • Perera, L. and Berkowitz, M. L. (1993) Many-body effects in molecular-dynamics simulations of Na+ (H2O)n and Cl-(H2O)n clusters (VOL 95, PG 1954, 1991). J. Chem. Phys., 99, 4236-4237.
    • (1993) J. Chem. Phys. , vol.99 , pp. 4236-4237
    • Perera, L.1    Berkowitz, M.L.2
  • 117
    • 22944493056 scopus 로고    scopus 로고
    • Surface solvation for an ion in a water cluster
    • Herce, D. H., Perera, L., Darden, T. A. and Sagui, C. (2004) Surface solvation for an ion in a water cluster. J. Chem. Phys., 122, 024513.
    • (2004) J. Chem. Phys. , vol.122 , pp. 024513
    • Herce, D.H.1    Perera, L.2    Darden, T.A.3    Sagui, C.4
  • 118
    • 0031592942 scopus 로고    scopus 로고
    • Structure and conformation of helical nucleic acids: Analysis program (SCHNAaP)
    • Lu, X. J., Hassan, M. A. E. and Hunter, C. A. (1997) Structure and conformation of helical nucleic acids: analysis program (SCHNAaP). J. Mol. Biol., 273, 668-680.
    • (1997) J. Mol. Biol. , vol.273 , pp. 668-680
    • Lu, X.J.1    Hassan, M.A.E.2    Hunter, C.A.3
  • 119
    • 0017098687 scopus 로고
    • RNA double helices generated from crystal-structures of double helical dinucleoside phosphates
    • Rosenberg, J. M., Seeman, N. C., Day, R. O. and Rich, A. (1976) RNA double helices generated from crystal-structures of double helical dinucleoside phosphates. Biochem. Biophys. Res. Commun., 69, 979-987.
    • (1976) Biochem. Biophys. Res. Commun. , vol.69 , pp. 979-987
    • Rosenberg, J.M.1    Seeman, N.C.2    Day, R.O.3    Rich, A.4
  • 120
    • 0027636867 scopus 로고
    • Sequence-selective metal-ion binding to DNA oligonucleotides
    • Froystein, N., Davis, J., Reid, B. and Sletten, E. (1993) Sequence-selective metal-ion binding to DNA oligonucleotides. Acta Chem. Scand., 47, 649-657.
    • (1993) Acta Chem. Scand. , vol.47 , pp. 649-657
    • Froystein, N.1    Davis, J.2    Reid, B.3    Sletten, E.4
  • 121
    • 0030929889 scopus 로고    scopus 로고
    • A magnesium ion core at the heart of a ribozyme domain
    • Cate, J., Hanna, R. and Doudna, J. (1997) A magnesium ion core at the heart of a ribozyme domain. Nat. Struct. Biol., 4, 553-558.
    • (1997) Nat. Struct. Biol. , vol.4 , pp. 553-558
    • Cate, J.1    Hanna, R.2    Doudna, J.3
  • 122
    • 33845469142 scopus 로고
    • Ribooligonucleotides r (C-G-C-G) analogues containing 8-substituted guanosine residues form left-handed duplexes with Z-form-like structures
    • Uesugi, S., Ohkuko, M., Urata, H., Ikehara, M., Kobayshi, Y. and Kyogoki, Y. (1984) Ribooligonucleotides r (C-G-C-G) analogues containing 8-substituted guanosine residues form left-handed duplexes with Z-form-like structures. Am. Chem. Soc., 106, 3675-3676.
    • (1984) Am. Chem. Soc. , vol.106 , pp. 3675-3676
    • Uesugi, S.1    Ohkuko, M.2    Urata, H.3    Ikehara, M.4    Kobayshi, Y.5    Kyogoki, Y.6


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.