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  • 5-b]pyridine  (1)
  • Escherichia coli  (1)
  • Key words Mutagen  (1)
  • Simian kidney cells  (1)
  • Water  (1)
  • 1
    ISSN: 0948-5023
    Keywords: Keywords  Hydrogen Bonds ; Protein-DNA Binding ; Specificity ; Water
    Source: Springer Online Journal Archives 1860-2000
    Topics: Chemistry and Pharmacology
    Notes: Abstract We extend our previous analysis of binding specificity of DNA-protein complexes to complexes containing water-mediated bridges. Inclusion of water bridges between phosphate and base, phosphate and sugar, as well as proteins and DNA, improves the prediction of specificity; six data sets studied in this paper yield correct predictions for all base pairs that have two or more hydrogen-bonds. Beside massive computation, our approach relies highly on experimental data. After deriving protein structures from DNA-protein complexes in which coordinates were established by X-ray diffraction techniques, we analysed all possible DNA sequences to which these proteins might bind, ranking them in terms of Lennard-Jones potential for the optimal docking configuration. Our prediction algorithm rests on the following assumptions: (1) specificity comes mainly from direct hydrogen bonding; (2) electrostatic forces stabilise DNA-protein complexes and contribute only weakly to specificity since they occur at the charged phosphate groups; (3) Van der Waals forces and electrostatic interactions between positively charged groups on the protein and phosphates on DNA can be neglected as they contribute primarily to the free energy of stabilisation as opposed to specificity.
    Type of Medium: Electronic Resource
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  • 2
    ISSN: 1431-4630
    Keywords: Key words Mutagen ; Single-strand phagemid vectors ; N-(deoxyguanosin-8-yl)-2-amino-1-methyl-6-phenylimidazo[4 ; 5-b]pyridine ; Simian kidney cells ; Escherichia coli
    Source: Springer Online Journal Archives 1860-2000
    Topics: Process Engineering, Biotechnology, Nutrition Technology
    Notes: Abstract  Site-specifically modified oligodeoxynucleotides were used to explore the mutagenic properties of a cooked food mutagen-derived DNA adduct, N-(deoxyguanosin-8-yl)-2-amino-1-methyl-6-phenylimidazo[4,5-b]pyridine (dG-C8-PhIP). A dG-C8-PhIP-modified oligodeoxynucleotide was prepared post-synthetically by reacting an oligodeoxynucleotide containing a single dG (5′-TCC TCC TCG CCT CTC T) with N-acetoxy-PhIP. The unmodified and dG-C8-PhIP-modified oligomers were inserted into single-strand (ss) phagemid vectors. These ss vectors were transfected into simian kidney (COS-7) cells. The progeny plasmid obtained was used to transform Escherichia coli DH10B. The transformants were analyzed by oligodeoxynucleotide hybridization and sequencing to determine the mutation frequency and spectrum. Preferential incorporation of dCMP, the correct base, was observed opposite dG-C8-PhIP. Targeted mutants showing G→T transversions were detected, along with a small number of G→A transitions and G→C transversions. Significant amounts of non-targeted mutations representing C→T transitions also were detected 5′ to the dG-C8-PhIP lesion. Thus, dG-C8-PhIP, a major DNA adduct induced by PhIP, is mutagenic in mammalian cells and may be involved in the initiation of human cancer.
    Type of Medium: Electronic Resource
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