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Volumn 45, Issue 4, 2006, Pages 1200-1211

Interaction between the Z-Type DNA duplex and 1,3-propanediamine: Crystal structure of d(CACGTG)2 at 1.2 Å resolution

Author keywords

[No Author keywords available]

Indexed keywords

AMINES; BROMINE; COBALT; CRYSTAL STRUCTURE; DNA; HYDRATION; METHANOL; X RAYS;

EID: 31544457042     PISSN: 00062960     EISSN: None     Source Type: Journal    
DOI: 10.1021/bi051569l     Document Type: Article
Times cited : (9)

References (61)
  • 2
    • 0015527119 scopus 로고
    • Salt-induced co-operative conformational change of a synthetic DNA: Equilibrium and kinetic studies with poly (dG-dC)
    • Pohl, F. M., and Jovin, T. M. (1972) Salt-induced co-operative conformational change of a synthetic DNA: Equilibrium and kinetic studies with poly (dG-dC), J. Mol. Biol. 67, 375-396.
    • (1972) J. Mol. Biol. , vol.67 , pp. 375-396
    • Pohl, F.M.1    Jovin, T.M.2
  • 3
    • 0345552286 scopus 로고
    • n forms left-handed Z-DNA in negatively supercoiled plasmids
    • n forms left-handed Z-DNA in negatively supercoiled plasmids, Proc. Natl. Acad. Sci. U.S.A. 80, 1821-1825.
    • (1983) Proc. Natl. Acad. Sci. U.S.A. , vol.80 , pp. 1821-1825
    • Nordheim, A.1    Rich, A.2
  • 4
    • 0020584610 scopus 로고
    • Facile transition of poly[d(TG)·d(CA)] into a left-handed helix in physiological conditions
    • Haniford, D. B., and Pulleyblank, D. E. (1983) Facile transition of poly[d(TG)·d(CA)] into a left-handed helix in physiological conditions, Nature 302, 632-634.
    • (1983) Nature , vol.302 , pp. 632-634
    • Haniford, D.B.1    Pulleyblank, D.E.2
  • 6
    • 0028087782 scopus 로고
    • n does not differ from that of Z-DNA
    • n does not differ from that of Z-DNA, Proc. Natl. Acad. Sci. U.S.A. 91, 9549-9553.
    • (1994) Proc. Natl. Acad. Sci. U.S.A. , vol.91 , pp. 9549-9553
    • Ho, P.S.1
  • 7
    • 0000684866 scopus 로고
    • Energetics of B-to-Z transition in DNA
    • Peck, L. J., and Wang, J. C. (1983) Energetics of B-to-Z transition in DNA, Proc. Natl. Acad. Sci. U.S.A. 80, 6206-6210.
    • (1983) Proc. Natl. Acad. Sci. U.S.A. , vol.80 , pp. 6206-6210
    • Peck, L.J.1    Wang, J.C.2
  • 8
    • 0019932819 scopus 로고
    • Left-handed Z-DNA is induced by supercoiling in physiological ionic conditions
    • Singleton, C. K., Klysik, J., Stirdivant, S. M., and Wells, R. D. (1982) Left-handed Z-DNA is induced by supercoiling in physiological ionic conditions, Nature 299, 312-316.
    • (1982) Nature , vol.299 , pp. 312-316
    • Singleton, C.K.1    Klysik, J.2    Stirdivant, S.M.3    Wells, R.D.4
  • 9
    • 0019849130 scopus 로고
    • Antibodies to left-handed Z-DNA bind to interband regions of Drosophila polytene chromosomes
    • Nordheim, A., Pardue, M. L., Lafer, E. M., Moller, A., Stollar, B. D., and Rich, A. (1981) Antibodies to left-handed Z-DNA bind to interband regions of Drosophila polytene chromosomes, Nature 294, 417-422.
    • (1981) Nature , vol.294 , pp. 417-422
    • Nordheim, A.1    Pardue, M.L.2    Lafer, E.M.3    Moller, A.4    Stollar, B.D.5    Rich, A.6
  • 10
    • 0019887567 scopus 로고
    • The high salt form of poly(dG-dC)·poly(dG-dC) is left-handed Z-DNA: Raman spectra of crystals and solutions
    • Thamann, T. J., Lord, R. C., Wang, A. H., and Rich, A. (1981) The high salt form of poly(dG-dC)·poly(dG-dC) is left-handed Z-DNA: Raman spectra of crystals and solutions, Nucleic Acids Res. 9, 5443-5457.
    • (1981) Nucleic Acids Res. , vol.9 , pp. 5443-5457
    • Thamann, T.J.1    Lord, R.C.2    Wang, A.H.3    Rich, A.4
  • 11
    • 0024975168 scopus 로고
    • Stabilization of Z DNA in vivo by localized supercoiling
    • Rahmouni, A. R., and Wells, R. D. (1989) Stabilization of Z DNA in vivo by localized supercoiling, Science 246, 358-363.
    • (1989) Science , vol.246 , pp. 358-363
    • Rahmouni, A.R.1    Wells, R.D.2
  • 12
    • 0037803571 scopus 로고    scopus 로고
    • Timeline: Z-DNA: The long road to biological function
    • Rich, A., and Zhang, S. (2003) Timeline: Z-DNA: The long road to biological function, Nat. Rev. Genet. 4, 566-572.
    • (2003) Nat. Rev. Genet. , vol.4 , pp. 566-572
    • Rich, A.1    Zhang, S.2
  • 13
    • 0020173895 scopus 로고
    • n DNA sequences from right- to left-handed helical structure by salt, Co(III), or negative supercoiling
    • n DNA sequences from right- to left-handed helical structure by salt, Co(III), or negative supercoiling, Proc. Natl. Acad. Sci. U.S.A. 79, 4560-4564.
    • (1982) Proc. Natl. Acad. Sci. U.S.A. , vol.79 , pp. 4560-4564
    • Peck, L.J.1    Nordheim, A.2    Rich, A.3    Wang, J.C.4
  • 14
    • 0020434670 scopus 로고
    • Interaction between antibodies to Z-form deoxyribonucleic acid and double-stranded polynucleotides
    • Malfoy, B., Rousseau, N., and Leng, M. (1982) Interaction between antibodies to Z-form deoxyribonucleic acid and double-stranded polynucleotides, Biochemistry 21, 5463-5467.
    • (1982) Biochemistry , vol.21 , pp. 5463-5467
    • Malfoy, B.1    Rousseau, N.2    Leng, M.3
  • 15
    • 0020953847 scopus 로고
    • Left-handed DNA: From synthetic polymers to chromosomes
    • Jovin, T. M., et al. (1983) Left-handed DNA: From synthetic polymers to chromosomes, J, Biomol. Struct. Dyn. 1, 21-57.
    • (1983) J. Biomol. Struct. Dyn. , vol.1 , pp. 21-57
    • Jovin, T.M.1
  • 16
    • 0019544304 scopus 로고
    • Effects of methylation on a synthetic polynucleotide: The B-Z transition in poly(dG-m5dC)· poly(dG-m5dC)
    • Behe, M., and Felsenfeld, G. (1981) Effects of methylation on a synthetic polynucleotide: The B-Z transition in poly(dG-m5dC)· poly(dG-m5dC), Proc. Natl. Acad. Sci. U.S.A. 78, 1619-1623.
    • (1981) Proc. Natl. Acad. Sci. U.S.A. , vol.78 , pp. 1619-1623
    • Behe, M.1    Felsenfeld, G.2
  • 18
    • 0026316202 scopus 로고
    • Structure of the pure-spermine form of Z-DNA (magnesium free) at 1-Å resolution
    • Egli, M., Williams, L. D., Gao, Q., and Rich, A. (1991) Structure of the pure-spermine form of Z-DNA (magnesium free) at 1-Å resolution, Biochemistry 30, 11388-11402.
    • (1991) Biochemistry , vol.30 , pp. 11388-11402
    • Egli, M.1    Williams, L.D.2    Gao, Q.3    Rich, A.4
  • 19
    • 0020480141 scopus 로고
    • A Z-like form of poly(dA-dC)·poly(dG-dT) in solution?
    • Vorlickova, M., Kypr, J., Stokrova, S., and Sponar, J. (1982) A Z-like form of poly(dA-dC)·poly(dG-dT) in solution? Nucleic Acids Res. 10, 1071-1080.
    • (1982) Nucleic Acids Res. , vol.10 , pp. 1071-1080
    • Vorlickova, M.1    Kypr, J.2    Stokrova, S.3    Sponar, J.4
  • 20
    • 0020480683 scopus 로고
    • Conformational transitions of poly(dA-dT)poly(dA-dT) in ethanolic solutions
    • Vorlickova, M., Sedlacek, P., Kypr, J., and Sponar, J. (1982) Conformational transitions of poly(dA-dT)poly(dA-dT) in ethanolic solutions, Nucleic Acids Res. 10, 6969-6979.
    • (1982) Nucleic Acids Res. , vol.10 , pp. 6969-6979
    • Vorlickova, M.1    Sedlacek, P.2    Kypr, J.3    Sponar, J.4
  • 21
    • 0020480142 scopus 로고
    • Conformational transitions of poly(dA-dC)·poly(dG-dT) induced by high salt or in ethanolic solution
    • Zimmer, C., Tymen, S., Marck, C., and Guschlbauer, W. (1982) Conformational transitions of poly(dA-dC)·poly(dG-dT) induced by high salt or in ethanolic solution, Nucleic Acids Res. 10, 1081-1091.
    • (1982) Nucleic Acids Res. , vol.10 , pp. 1081-1091
    • Zimmer, C.1    Tymen, S.2    Marck, C.3    Guschlbauer, W.4
  • 22
    • 0019955810 scopus 로고
    • Potential Z-DNA forming sequences are highly dispersed in the human genome
    • Hamada, H., and Kakunaga, T. (1982) Potential Z-DNA forming sequences are highly dispersed in the human genome, Nature 298, 396-398.
    • (1982) Nature , vol.298 , pp. 396-398
    • Hamada, H.1    Kakunaga, T.2
  • 23
    • 2742558049 scopus 로고
    • A novel repeated element with Z- DNA-forming potential is widely found in evolutionarily diverse eukaryotic genomes
    • Hamada, H., Petrino, M. G., and Kakunaga, T. (1982) A novel repeated element with Z- DNA-forming potential is widely found in evolutionarily diverse eukaryotic genomes, Proc. Natl. Acad. Sci. U.S.A. 79, 6465-6469.
    • (1982) Proc. Natl. Acad. Sci. U.S.A. , vol.79 , pp. 6465-6469
    • Hamada, H.1    Petrino, M.G.2    Kakunaga, T.3
  • 24
    • 0020355988 scopus 로고
    • Negatively supercoiled plasmids contain left-handed Z DNA segments as detected by specific antibody binding
    • Nordheim, A., Lafer, E. M., Peck, L. J., Wang, J. C., Stollar, B. D., and Rich, A. (1982) Negatively supercoiled plasmids contain left-handed Z DNA segments as detected by specific antibody binding. Cell 31, 309-318.
    • (1982) Cell , vol.31 , pp. 309-318
    • Nordheim, A.1    Lafer, E.M.2    Peck, L.J.3    Wang, J.C.4    Stollar, B.D.5    Rich, A.6
  • 25
    • 0024554495 scopus 로고
    • A new DNA binding and dimerization motif in immunoglobulin enhancer binding, daughterless, MyoD, and myc proteins
    • Murre, C., McCaw, P. S., and Baltimore, D. (1989) A new DNA binding and dimerization motif in immunoglobulin enhancer binding, daughterless, MyoD, and myc proteins, Cell 56, 777-783.
    • (1989) Cell , vol.56 , pp. 777-783
    • Murre, C.1    McCaw, P.S.2    Baltimore, D.3
  • 26
    • 0019318942 scopus 로고
    • High-salt d(CpGpCpG), a left-handed Z′ DNA double helix
    • Drew, H., Takano, T., Tanaka, S., Itakura, K., and Dickerson, R. E. (1980) High-salt d(CpGpCpG), a left-handed Z′ DNA double helix, Nature 286, 567-573.
    • (1980) Nature , vol.286 , pp. 567-573
    • Drew, H.1    Takano, T.2    Tanaka, S.3    Itakura, K.4    Dickerson, R.E.5
  • 31
    • 0029037450 scopus 로고
    • Sequence-dependent microheterogeneity of Z-DNA: The crystal and molecular structures of d(CACGCG)·d(CGCGTG) and d(CGCACG)·d(CGTGCG)
    • Sadasivan, C., and Gautham, N. (1995) Sequence-dependent microheterogeneity of Z-DNA: The crystal and molecular structures of d(CACGCG)·d(CGCGTG) and d(CGCACG)·d(CGTGCG), J. Mol. Biol. 248, 918-930.
    • (1995) J. Mol. Biol. , vol.248 , pp. 918-930
    • Sadasivan, C.1    Gautham, N.2
  • 32
    • 0032128296 scopus 로고    scopus 로고
    • Structure of d(CACGCG)· d(CGCGTG) in crystals grown in the presence of ruthenium(III) hexammine chloride
    • Karthe, P., and Gautham, N. (1998) Structure of d(CACGCG)· d(CGCGTG) in crystals grown in the presence of ruthenium(III) hexammine chloride, Acta Crystallogr. D54, 501-509.
    • (1998) Acta Crystallogr. , vol.D54 , pp. 501-509
    • Karthe, P.1    Gautham, N.2
  • 33
    • 10244226776 scopus 로고    scopus 로고
    • Cobalt hexammine induced tautomeric shift in Z-DNA: The structure of d(CGCGCA)·d(TGCGCG) in two crystal forms
    • Thiyagarajan, S., Rajan, S. S., and Gautham, N. (2004) Cobalt hexammine induced tautomeric shift in Z-DNA: The structure of d(CGCGCA)·d(TGCGCG) in two crystal forms, Nucleic Acids Res. 32, 5945-5953.
    • (2004) Nucleic Acids Res. , vol.32 , pp. 5945-5953
    • Thiyagarajan, S.1    Rajan, S.S.2    Gautham, N.3
  • 34
    • 0024363293 scopus 로고
    • The molecular structure of the left-handed Z-DNA double helix at 1.0 angstrom atomic resolution. Geometry, conformation, and ionic interactions of d(CGCGCG)
    • Gessner, R. V., Frederick, C. A., Quigley, G. J., Rich, A., and Wang, A. H.-J. (1989) The molecular structure of the left-handed Z-DNA double helix at 1.0 angstrom atomic resolution. Geometry, conformation, and ionic interactions of d(CGCGCG), J. Biol. Chem. 264, 7921-7935.
    • (1989) J. Biol. Chem. , vol.264 , pp. 7921-7935
    • Gessner, R.V.1    Frederick, C.A.2    Quigley, G.J.3    Rich, A.4    Wang, A.H.-J.5
  • 36
    • 0023140814 scopus 로고
    • Crystallographic R factor refinement by molecular dynamics
    • Brunger, A. T., Kuriyan, J., and Karplus, M. (1987) Crystallographic R factor refinement by molecular dynamics, Science 235. 458-460.
    • (1987) Science , vol.235 , pp. 458-460
    • Brunger, A.T.1    Kuriyan, J.2    Karplus, M.3
  • 37
    • 45949114594 scopus 로고
    • TOM: A FRODO subpackage for protein-ligand fitting with interactive energy minimization
    • Cambillau, C., and Horjales, E. (1987) TOM: A FRODO subpackage for protein-ligand fitting with interactive energy minimization, J. Mol. Graphics 5, 174-177.
    • (1987) J. Mol. Graphics , vol.5 , pp. 174-177
    • Cambillau, C.1    Horjales, E.2
  • 39
    • 0028221644 scopus 로고
    • Comparative studies of high resolution Z-DNA crystal structures. Part 1: Common hydration patterns of alternating dC-dG
    • Gessner, R. V., Quigley, G. J., and Egli, M. (1994) Comparative studies of high resolution Z-DNA crystal structures. Part 1: Common hydration patterns of alternating dC-dG, J. Mol. Biol. 236, 1154-1168.
    • (1994) J. Mol. Biol. , vol.236 , pp. 1154-1168
    • Gessner, R.V.1    Quigley, G.J.2    Egli, M.3
  • 40
    • 0022400608 scopus 로고
    • Structural studies of DNA fragments: The G.T wobble base pair in A, B and Z DNA; the G·A base pair in B-DNA
    • Kennard, O. (1985) Structural studies of DNA fragments: The G.T wobble base pair in A, B and Z DNA; the G·A base pair in B-DNA, J. Biomol. Struct. Dyn. 3, 205-226.
    • (1985) J. Biomol. Struct. Dyn. , vol.3 , pp. 205-226
    • Kennard, O.1
  • 41
    • 0035906709 scopus 로고    scopus 로고
    • Spermine: An "invisible" component in the crystals of B-DNA. A grand canonical Monte Carlo and molecular dynamics simulation study
    • Korolev, N., Lyubartsev, A. P., Nordenskiold, L., and Laaksonen, A. (2001) Spermine: An "invisible" component in the crystals of B-DNA. A grand canonical Monte Carlo and molecular dynamics simulation study, J. Mol. Biol. 308, 907-917.
    • (2001) J. Mol. Biol. , vol.308 , pp. 907-917
    • Korolev, N.1    Lyubartsev, A.P.2    Nordenskiold, L.3    Laaksonen, A.4
  • 42
    • 0018447541 scopus 로고
    • Crystal structure of putrescine diphosphate: A model system for amine-nucleic acid interactions
    • Woo, N. H., Seeman, N. C., and Rich, A. (1979) Crystal structure of putrescine diphosphate: A model system for amine-nucleic acid interactions, Biopolymers 18, 539-552.
    • (1979) Biopolymers , vol.18 , pp. 539-552
    • Woo, N.H.1    Seeman, N.C.2    Rich, A.3
  • 51
    • 0028265282 scopus 로고
    • The low-temperature crystal structure of the pure-spermine form of Z-DNA reveals binding of a spermine molecule in the minor groove
    • Bancroft, D., Williams, L. D., Rich, A., and Egli, M. (1994) The low-temperature crystal structure of the pure-spermine form of Z-DNA reveals binding of a spermine molecule in the minor groove, Biochemistry 33, 1073-1086.
    • (1994) Biochemistry , vol.33 , pp. 1073-1086
    • Bancroft, D.1    Williams, L.D.2    Rich, A.3    Egli, M.4
  • 52
    • 0023651156 scopus 로고
    • Sequence dependence of the B to Z transition in crystals and aqueous NaCl solutions for deoxyoligonucleotides containing all four canonical DNA bases
    • Wang, Y., Thomas, G. A., and Peticolas, W. L. (1987) Sequence dependence of the B to Z transition in crystals and aqueous NaCl solutions for deoxyoligonucleotides containing all four canonical DNA bases, Biochemistry 26, 5178-5186.
    • (1987) Biochemistry , vol.26 , pp. 5178-5186
    • Wang, Y.1    Thomas, G.A.2    Peticolas, W.L.3
  • 53
    • 0037079669 scopus 로고    scopus 로고
    • Polyaminenucleic acid interactions and the effects on structure in oriented DNA fibers
    • van Dam, L., Korolev, N., and Nordenskiold, L. (2002) Polyaminenucleic acid interactions and the effects on structure in oriented DNA fibers, Nucleic Acids Res. 30, 419-428.
    • (2002) Nucleic Acids Res. , vol.30 , pp. 419-428
    • Van Dam, L.1    Korolev, N.2    Nordenskiold, L.3
  • 54
    • 0029856643 scopus 로고    scopus 로고
    • Sequence-dependent effects of spermine on the thermodynamics of the B-DNA to Z-DNA transition
    • Howell, M. L., Schroth, G. P., and Ho, P. S. (1996) Sequence-dependent effects of spermine on the thermodynamics of the B-DNA to Z-DNA transition, Biochemistry 35, 15373-15382.
    • (1996) Biochemistry , vol.35 , pp. 15373-15382
    • Howell, M.L.1    Schroth, G.P.2    Ho, P.S.3
  • 55
    • 0031576993 scopus 로고    scopus 로고
    • Nine polymorphic crystal structures of d(CCGGGCCCGG), d(CCGGGCCm5CGG), d(Cm5CGGGCCm5CGG) and d(CCGGGCC(Br)5CGG) in three different conformations: Effects of spermine binding and methylation on the bending and condensation of A-DNA
    • Tippin, D. B., and Sundaralingam, M. (1997) Nine polymorphic crystal structures of d(CCGGGCCCGG), d(CCGGGCCm5CGG), d(Cm5CGGGCCm5CGG) and d(CCGGGCC(Br)5CGG) in three different conformations: Effects of spermine binding and methylation on the bending and condensation of A-DNA, J. Mol. Biol. 267, 1171-1185.
    • (1997) J. Mol. Biol. , vol.267 , pp. 1171-1185
    • Tippin, D.B.1    Sundaralingam, M.2
  • 56
    • 0025770871 scopus 로고
    • The importance of the specific Z-DNA structure and polyamines in carcinogenesis: Fact or fiction
    • Juranic, Z., Kidric, M., Tomin, R., Juranic, I., Spuzic, I., and Petrovic, J. (1991) The importance of the specific Z-DNA structure and polyamines in carcinogenesis: Fact or fiction, Med. Hypotheses 35, 353-357.
    • (1991) Med. Hypotheses , vol.35 , pp. 353-357
    • Juranic, Z.1    Kidric, M.2    Tomin, R.3    Juranic, I.4    Spuzic, I.5    Petrovic, J.6
  • 57
    • 0024342138 scopus 로고
    • Conformations in crystals and solutions of d(CACGTG), d(CCGCGG) and d(GGCGCC) studied by vibrational spectroscopy
    • Urpi, L., et al. (1989) Conformations in crystals and solutions of d(CACGTG), d(CCGCGG) and d(GGCGCC) studied by vibrational spectroscopy, Nucleic Acids Res. 17, 6669-6680.
    • (1989) Nucleic Acids Res. , vol.17 , pp. 6669-6680
    • Urpi, L.1
  • 60
    • 0023053306 scopus 로고
    • Solvation of the left-handed hexamer d(5BrC-G-5BrC-G-5BrC-G) in crystals grown at two temperatures
    • Chevrier, B., Dock, A. C., Hartmann, B., Leng, M., Moras, D., Thuong, M. T., and Westhof, E. (1986) Solvation of the left-handed hexamer d(5BrC-G-5BrC-G-5BrC-G) in crystals grown at two temperatures, J. Mol. Biol. 188, 707-719.
    • (1986) J. Mol. Biol. , vol.188 , pp. 707-719
    • Chevrier, B.1    Dock, A.C.2    Hartmann, B.3    Leng, M.4    Moras, D.5    Thuong, M.T.6    Westhof, E.7


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