A Synthetic Nucleoside Probe that Discerns a DNA Adduct from Unmodified DNA

ArticleinJournal of the American Chemical Society 129(16):4882-3 · April 2007with24 Reads
DOI: 10.1021/ja070688g · Source: PubMed
Selective pairing of engineering nucleosides in DNA duplexes provides a potential means to probe structurally modified DNA bases (i.e., DNA adducts) and address challenges associated with correlating adduct chemical structure with biological impact. The current study provides the first example of a thermodynamically stable DNA base pair that is comprised of a biologically relevant carcinogen-DNA adduct and a synthetic nucleoside probe. O-6-Benzylguanine is a mutagenic DNA adduct; molecular modeling indicates that a novel diaminonaphthyl-derived nucleoside (dNap):O-6-benzylguanine base pair may be stabilized by a combination of hydrogen-bonding and hydrophobic interactions. The nucleoside dNap was synthetically incorporated into oligonucleotides, and a series of duplexes were evaluated by thermal denaturation studies. The bulky DNA adduct O-6-benzylguanine forms a highly stable and orthogonal base pair with dNap. Data indicate pi-stacking potential, self-pairing capacity, isomeric selectivity, 1:1 duplex stoichiometry, and a B-form DNA structure. Further studies are required to understand the physical determinants of adduct:probe pair stability for the design of probes for diverse forms of DNA damage and for the development of adduct-probe-based molecular techniques.
    • "Nucleoside phosphoramidites (PA) of 5-fluoro-C, 5-bromo-C, 5-iodo-C, difluorotoluene, 5-propynyl-C, protected abasic site and pyrrolo-C were purchased from Glen Research Corporation (Sterling, VA, USA). 1,7,NH2-15N3-2-13C1-dG-phosphoramidite and perimidin-2-one nucleoside (dPER) phosphoramidite were prepared as reported previously (42,49,50). O4-ethyl-5-chloro-2′-deoxyuridine phosphoramidite was synthesized and incorporated into the oligodeoxynucleotide following the methods of Kang et al. (39). "
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    • "In the rapidly and efficiently detection of genome sequence variation and mutation, gene expression spectrum analysis, disease diagnosis, drug screening, pathogen detection, disease-related genome sequence, copy number changes and the detection of nucleotide sequence polymorphism, DNA chip has a broad perspectives in application(Shaon,1996,p.639-643). Synthetic oligonucleotide molecular probe can find out the mutation and its properties through the analysis of hybridization signal, and it is expected to open up a series study methods of DNA chemical modification and DNA damage detection(Gong, 2007, p.4882-4883). "
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