Simultaneous recognition of nucleobase and sites of DNA damage: effect of tethered cation on the binding affinity.

BACKGROUND The 3,5-diamino-N-(3-aminopropyl)-6-chloropyrazine-2-carboxamide (DCPC-NH(2)) has been synthesized and characterized by Mass and (1)H NMR. The selective binding of the ligand to thymine (T) target base is investigated by the melting temperature (T(m)) and fluorescence measurements. METHODS Thermal denaturation study of DNA duplex containing T target base revealed the DeltaT(m) of 5.1 degrees C, while least influence was observed for other target bases. The fluorescence of the ligand DCPC-NH(2) is quenched only upon adding the DNA containing T target base. RESULTS The binding constant for the interaction of the ligand to T target base containing DNA duplex was determined to be 4.7 (+/-0.3)x10(6) M(-1). The tethered cation in the ligand is found to enhance the binding constant. The ligand binds to both a target nucleotide and an AP site on the complimentary strand for the target strand in a DNA duplex. GENERAL SIGNIFICANCE Interestingly, the electronic behavior of the ligand depends on the bases flanking the AP site. Its fluorescence is quenched with guanine flanking bases, while it is enhanced with DNA duplex containing T bases flanking an AP site. Finally, the binding modes were visualized by molecular modeling.

[1]  N. Grover,et al.  Binding and kinetics studies of oxidation of DNA by oxoruthenium(IV) , 1993 .

[2]  Balachandran Unni Nair,et al.  Unprecedented dual binding behaviour of acridine group of dye: a combined experimental and theoretical investigation for the development of anticancer chemotherapeutic agents. , 2006, Biochimica et biophysica acta.

[3]  G. Chang,et al.  Macromodel—an integrated software system for modeling organic and bioorganic molecules using molecular mechanics , 1990 .

[4]  Keitaro Yoshimoto,et al.  Fluorescence detection of guanine-adenine transition by a hydrogen bond forming small compound. , 2003, Chemical communications.

[5]  Masaki Mishima,et al.  Small-molecule ligand induces nucleotide flipping in (CAG)n trinucleotide repeats , 2005, Nature chemical biology.

[6]  P. Dervan,et al.  Programmable oligomers for minor groove DNA recognition. , 2006, Journal of the American Chemical Society.

[7]  Jie Chen,et al.  Thermodynamics of the interaction of aluminum ions with DNA: implications for the biological function of aluminum. , 2005, Journal of inorganic biochemistry.

[8]  R. Stein,et al.  First evidence on induced topological changes in supercoiled DNA by an aluminium d-aspartate complex , 2003, JBIC Journal of Biological Inorganic Chemistry.

[9]  N. Teramae,et al.  Strong and selective binding of amiloride to thymine base opposite AP sites in DNA duplexes: simultaneous binding to DNA phosphate backbone. , 2006, Chemical communications.

[10]  P. T. Perumal,et al.  DNA-DNA cross-linking mediated by bifunctional [SalenAlIII]+ complex. , 2008, Biochimica et biophysica acta.

[11]  I. Tinoco,et al.  Absorbance melting curves of RNA. , 1989, Methods in enzymology.

[12]  C. Burrows,et al.  Oxidative Nucleobase Modifications Leading to Strand Scission. , 1998, Chemical reviews.

[13]  Keitaro Yoshimoto,et al.  Use of abasic site-containing DNA strands for nucleobase recognition in water. , 2003, Journal of the American Chemical Society.

[14]  M. Braña,et al.  Intercalators as anticancer drugs. , 2001, Current pharmaceutical design.

[15]  P. Dervan,et al.  Molecular recognition of DNA by small molecules. , 2001, Bioorganic & medicinal chemistry.

[16]  P. Dervan,et al.  Recognition of the DNA minor groove by pyrrole-imidazole polyamides. , 2003, Current opinion in structural biology.

[17]  J. Barton,et al.  Insights into finding a mismatch through the structure of a mispaired DNA bound by a rhodium intercalator , 2007, Proceedings of the National Academy of Sciences.

[18]  N. Teramae,et al.  Alloxazine as a ligand for selective binding to adenine opposite AP sites in DNA duplexes and analysis of single-nucleotide polymorphisms. , 2008, Organic & biomolecular chemistry.

[19]  David E. Graves and Luminita M. Velea.  Intercalative Binding of Small Molecules to Nucleic Acids , 2000 .

[20]  Keitaro Yoshimoto,et al.  Fluorescence detection of cytosine/guanine transversion based on a hydrogen bond forming ligand. , 2004, Talanta.

[21]  J. Doudna,et al.  Metal-binding sites in the major groove of a large ribozyme domain. , 1996, Structure.

[22]  Y. Liang,et al.  Applications of isothermal titration calorimetry in protein folding and molecular recognition , 2006, Journal of the Iranian Chemical Society.

[23]  Shinsuke Sando,et al.  Scanning of guanine–guanine mismatches in DNA by synthetic ligands using surface plasmon resonance , 2001, Nature Biotechnology.

[24]  A. Wang,et al.  Synthesis, structure and thermodynamic properties of 8-methylguanine-containing oligonucleotides: Z-DNA under physiological salt conditions. , 1996, Nucleic acids research.

[25]  Norio Teramae,et al.  A Pyrazine-based Fluorescence-enhancing Ligand with a High Selectivity for Thymine in AP Site-containing DNA Duplexes , 2008, Analytical sciences : the international journal of the Japan Society for Analytical Chemistry.

[26]  B. Nair,et al.  Synthesis, characterization and binding studies of chromium(III) complex containing an intercalating ligand with DNA. , 2003, Journal of inorganic biochemistry.

[27]  V. Uma,et al.  A new dinuclear biphenylene bridged copper(II) complex: DNA cleavage under hydrolytic conditions. , 2006, Biochimica et biophysica acta.