The research projects comprising this Program are designed to provide insights into the biological role of exocyclic nucleic acid derivatives in carcinogenesis. The central theme of this multidisciplinary program focuses on the relationship of molecular structure to biological function. By applying experimental systems which reflect mutagenic spectra of a single species of DNA adduct and by using modern chemical techniques to establish primary and three-dimensional structures of DNA adducts, we hope to define fundamental structure-activity relationships that will assist in elucidating mechanisms of chemical mutagenesis. The specific objectives of this Program research include development of sensitive and specific methods for detection and quantitation of exocyclic DNA adducts and determination of the chemical structures of such adducts. In several studies, we will use synthetic duplex oligodeoxynucleotides as sequence-defined models for DNA. We also propose to extend the general usefulness of solid-phase DNA synthesis by developing new nucleoside protecting groups which will permit site-specific incorporation of alkali-sensitive adducts into oligodeoxynuc- leotides. Synthetic routes will be designed by which desired exocyclic adducts and DNA crosslinks can conveniently be prepared. Exocyclic adducts will be incorporated site-specifically into shuttle vectors and other genomes and their mutational spectra will be determined in mammalian cells and bacteria. We will attempt to relate biological properties of exocyclic adducts to their three-dimensional structure, as determined by two-dimensional NMR and computer-assisted molecular modelling techniques. Recent developments in these areas of research make it possible to assign the structure and conformation, in solution, of duplex DNA containing up to 20 base pairs. Refinement of certain parameters is required for molecular modelling studies; we will concentrate our efforts on the general equations governing solvent terms which will be applied to energy minimization programs used to model the tertiary structure of DNA.

National Institute of Health (NIH)
National Cancer Institute (NCI)
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State University New York Stony Brook
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Stony Brook
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Minetti, Conceição A S A; Remeta, David P; Iden, Charles R et al. (2015) Impact of thymine glycol damage on DNA duplex energetics: Correlations with lesion-induced biochemical and structural consequences. Biopolymers 103:491-508
Völker, Jens; Plum, G Eric; Gindikin, Vera et al. (2014) Impact of bulge loop size on DNA triplet repeat domains: Implications for DNA repair and expansion. Biopolymers 101:1-12
Li, Mengxia; Völker, Jens; Breslauer, Kenneth J et al. (2014) APE1 incision activity at abasic sites in tandem repeat sequences. J Mol Biol 426:2183-98
Braunlin, William; Völker, Jens; Plum, G Eric et al. (2013) DNA meter: Energy tunable, quantitative hybridization assay. Biopolymers 99:408-17
Völker, Jens; Gindikin, Vera; Klump, Horst H et al. (2012) Energy landscapes of dynamic ensembles of rolling triplet repeat bulge loops: implications for DNA expansion associated with disease states. J Am Chem Soc 134:6033-44
Lukin, Mark; Minetti, Conceicao A S A; Remeta, David P et al. (2011) Novel post-synthetic generation, isomeric resolution, and characterization of Fapy-dG within oligodeoxynucleotides: differential anomeric impacts on DNA duplex properties. Nucleic Acids Res 39:5776-89
Völker, Jens; Plum, G Eric; Klump, Horst H et al. (2010) Energetic coupling between clustered lesions modulated by intervening triplet repeat bulge loops: allosteric implications for DNA repair and triplet repeat expansion. Biopolymers 93:355-69
Zaliznyak, Tanya; Lukin, Mark; El-khateeb, Mahmoud et al. (2010) NMR structure of duplex DNA containing the alpha-OH-PdG.dA base pair: a mutagenic intermediate of acrolein. Biopolymers 93:391-401
Minetti, Conceição A S A; Remeta, David P; Johnson, Francis et al. (2010) Impact of alpha-hydroxy-propanodeoxyguanine adducts on DNA duplex energetics: opposite base modulation and implications for mutagenicity and genotoxicity. Biopolymers 93:370-82
Minetti, Conceicao A S A; Remeta, David P; Dickstein, Rian et al. (2010) Energetic signatures of single base bulges: thermodynamic consequences and biological implications. Nucleic Acids Res 38:97-116

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