Left-handed DNA: intercalation of the cyanine thiazole orange and structural changes. A kinetic and thermodynamic approach.

The conditions under which different structures of left-handed DNA (poly(dG-me(5)dC)·poly(dG-me(5)dC)) can exist are investigated by spectrofluorometric, spectrophotometric, circular dichroism and calorimetric measurements and the kinetics of the transformations are analysed. The effects of temperature, salt and ethanol content on the transitions are also studied. The left-handed structure obtained by addition of either Mg(2+) ions or EtOH corresponds to Z-DNA, whereas the structure obtained using the mixture Mg(2+)/EtOH corresponds to the aggregate Z*-DNA. Upon addition of the fluorescent cyanine Thiazole Orange (TO), the transition Z → B immediately starts, whereas Z*-DNA retains its left-handed configuration in the presence of TO provided that the ratio [dye]/[polymer] ≤ 0.1. The equilibria and kinetics of the TO binding to Z*-DNA are investigated under the above conditions using the T-jump technique. The reaction mechanism consists of two series steps, the first one being characterized by the formation of an external electrostatic complex and the second corresponding to the dye penetration between the base pairs. A comparison with the B-DNA/TO system is drawn.

[1]  B. García,et al.  Solvent effects on the thermodynamics and kinetics of coralyne self-aggregation. , 2009, The journal of physical chemistry. B.

[2]  Bharathi,et al.  Role of DNA dynamics in Alzheimer's disease , 2008, Brain Research Reviews.

[3]  E. Vauthey,et al.  Ultrafast excited-state dynamics of oxazole yellow DNA intercalators. , 2007, The journal of physical chemistry. B.

[4]  S. Yarmoluk,et al.  Influence of cyanine dye structure on self-aggregation and interaction with nucleic acids: a kinetic approach to TO and BO binding. , 2007, Archives of biochemistry and biophysics.

[5]  Guliang Wang,et al.  Z-DNA, an active element in the genome. , 2007, Frontiers in bioscience : a journal and virtual library.

[6]  R. Wells,et al.  The involvement of non-B DNA structures in gross chromosomal rearrangements. , 2006, DNA repair.

[7]  M. Fuertes,et al.  Molecular mechanisms for the B-Z transition in the example of poly[d(G-C) x d(G-C)] polymers. A critical review. , 2006, Chemical reviews.

[8]  M. Kubista,et al.  LightUp® probes in clinical diagnostics , 2006, Molecular Aspects of Medicine.

[9]  A. Rich,et al.  Crystal structure of a junction between B-DNA and Z-DNA reveals two extruded bases , 2005, Nature.

[10]  S. Yarmoluk,et al.  Cyanine dyes as intercalating agents: kinetic and thermodynamic studies on the DNA/Cyan40 and DNA/CCyan2 systems. , 2005, Biophysical journal.

[11]  B. Armitage,et al.  DNA-templated assembly of helical cyanine dye aggregates: a supramolecular chain polymerization. , 2004, Accounts of chemical research.

[12]  A. Rich,et al.  Evidence that vaccinia virulence factor E3L binds to Z-DNA in vivo: Implications for development of a therapy for poxvirus infection. , 2004, Proceedings of the National Academy of Sciences of the United States of America.

[13]  Alexander Rich,et al.  Z-DNA: the long road to biological function , 2003, Nature Reviews Genetics.

[14]  A. Rich,et al.  A role for Z-DNA binding in vaccinia virus pathogenesis , 2003, Proceedings of the National Academy of Sciences of the United States of America.

[15]  Larry J Kricka,et al.  Stains, labels and detection strategies for nucleic acids assays , 2002, Annals of clinical biochemistry.

[16]  Robert M Clegg,et al.  Base-sequence specificity of Hoechst 33258 and DAPI binding to five (A/T)4 DNA sites with kinetic evidence for more than one high-affinity Hoechst 33258-AATT complex. , 2002, Journal of molecular biology.

[17]  Martha Kirby,et al.  Regulation of CSF1 Promoter by the SWI/SNF-like BAF Complex , 2001, Cell.

[18]  D. VanDerveer,et al.  Cations Mediate B-DNA Conformational Heterogeneity† , 2000 .

[19]  J. Chaires,et al.  Allosteric, chiral-selective drug binding to DNA. , 2000, Proceedings of the National Academy of Sciences of the United States of America.

[20]  D. Lilley,et al.  Location of cyanine-3 on double-stranded DNA: importance for fluorescence resonance energy transfer studies. , 2000, Biochemistry.

[21]  B. Kankia.  Hydration effects of Ni(2+) binding to synthetic polynucleotides with regularly alternating purine-pyrimidine sequences. , 2000, Nucleic acids research.

[22]  M. Fuertes,et al.  Empirical validation of a two-state kinetic model for the B-Z transition of double-stranded poly[d(G-m5C)] , 1999, JBIC Journal of Biological Inorganic Chemistry.

[23]  M. Kubista,et al.  The interactions between the fluorescent dye thiazole orange and DNA. , 1998, Biopolymers.

[24]  N. Farrell,et al.  A circular dichroism study of ethidium bromide binding to Z-DNA induced by dinuclear platinum complexes. , 1996, Journal of inorganic biochemistry.

[25]  H. Diebler,et al.  Spectrophotometric and kinetic studies of the binding of Ni2+, Co2+, and Mg2+ to poly(dG-dC).poly(dG-dC). Determination of the stoichiometry of the Ni2+-induced B--->Z transition. , 1993, Journal of inorganic biochemistry.

[26]  D. Porschke,et al.  Mechanism of intercalation into the DNA double helix by ethidium. , 1993, Biochemistry.

[27]  D E Wemmer,et al.  Stable fluorescent complexes of double-stranded DNA with bis-intercalating asymmetric cyanine dyes: properties and applications. , 1992, Nucleic acids research.

[28]  J. Kypr,et al.  Destabilization of the duplex and the high-salt Z-form of poly(dG-methyl5dC) by substitution of ethyl for the 5-methyl group. , 1991, International journal of biological macromolecules.

[29]  J. Chaires,et al.  Unusual binding of ethidium to a deoxyoligonucleotide containing a B-Z junction. , 1991, Biochemistry.

[30]  J. Chaires,et al.  Structure and stability of Z* DNA. , 1988, Journal of biomolecular structure & dynamics.

[31]  R. Clegg,et al.  Viscosity dependence of ethidium-DNA intercalation kinetics. , 1987, Biochemistry.

[32]  Olga Kennard,et al.  DNA conformation is determined by economics in the hydration of phosphate groups , 1986, Nature.

[33]  T. Thomas,et al.  A left-handed (Z) conformation of poly(dA-dC).poly(dG-dT) induced by polyamines. , 1986, Nucleic acids research.

[34]  J. Chaires,et al.  Thermodynamics of the B to Z transition in poly(m5dG-dC). , 1986, Proceedings of the National Academy of Sciences of the United States of America.

[35]  M Karplus,et al.  Transition from B to Z DNA: contribution of internal fluctuations to the configurational entropy difference. , 1985, Science.

[36]  K. Hall,et al.  Temperature‐dependent reversible transition of poly(dCdG) · poly(DcdG) in ethanolic and methanolic solutions , 1984, Biopolymers.

[37]  S. Brown,et al.  Binding of ethidium and bis(methidium)spermine to Z DNA by intercalation. , 1984, Nucleic Acids Research.

[38]  M. Behe,et al.  Critical amount of oligovalent ion binding required for the B-Z transition of poly (dG-m5dC). , 1984, Nucleic acids research.

[39]  T. Jovin,et al.  Z* DNA, the left‐handed helical form of poly[d(G‐C)] in MgCl2‐ethanol, is biologically active. , 1982, The EMBO journal.

[40]  M. Behe,et al.  Effects of methylation on a synthetic polynucleotide: the B--Z transition in poly(dG-m5dC).poly(dG-m5dC). , 1981, Proceedings of the National Academy of Sciences of the United States of America.

[41]  Jacques H. van Boom,et al.  Molecular structure of a left-handed double helical DNA fragment at atomic resolution , 1979, Nature.

[42]  T. Jovin,et al.  A temperature‐jump apparatus for fluorescence measurements , 1974 .

[43]  T M Jovin,et al.  Salt-induced co-operative conformational change of a synthetic DNA: equilibrium and kinetic studies with poly (dG-dC). , 1972, Journal of molecular biology.

[44]  C. Hélène,et al.  A quantitative analysis of proflavine binding to polyadenylic acid, polyuridylic acid, and transfer RNA. , 1971, European journal of biochemistry.

[45]  G. Schwarz.  Cooperative binding to linear biopolymers. 1. Fundamental static and dynamic properties. , 1970, European journal of biochemistry.

[46]  Joel H. Hildebrand,et al.  A Spectrophotometric Investigation of the Interaction of Iodine with Aromatic Hydrocarbons , 1949 .

[47]  J. Vaquero,et al.  Intercalating Cyanine Dyes for Nucleic Acid Detection , 2009 .

[48]  P. Champ,et al.  Distributions of Z-DNA and nuclear factor I in human chromosome 22: a model for coupled transcriptional regulation. , 2004, Nucleic acids research.

[49]  Jagannatha Rao,et al.  First evidence to show the topological change of DNA from B-DNA to Z-DNA conformation in the hippocampus of Alzheimer’s brain , 2002, NeuroMolecular Medicine.

[50]  S. Yarmoluk,et al.  Interaction of cyanine dyes with nucleic acids. XXI. Arguments for half-intercalation model of interaction. , 2001, Biopolymers.

[51]  M. Kawakami,et al.  Structure-activity of novel rhodacyanine dyes as antitumor agents. , 1998, Journal of medicinal chemistry.

[52]  L. Zhong,et al.  Poly[d(Gm5C)·d(Gm5C)] can assume the Z′ form: A CD study , 1990 .

[53]  S. Yagihara,et al.  Dielectric study on hydration of B‐, A‐, and Z‐DNA , 1990, Biopolymers.

[54]  Thomas M. Jovin,et al.  The Transition Between B-DNA and Z-DNA , 1987 .

[55]  Alfred Nordheim,et al.  THE CHEMISTRY AND BIOLOGY OF LEFT-HANDED Z-DNA , 1984 .