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

Department of Medicinal Chemistry and The Cancer Center, University of Minnesota, Minneapolis, Minnesota 55455, USA.
Journal of the American Chemical Society (Impact Factor: 12.11). 04/2007; 129(16):4882-3. 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.

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    ABSTRACT: Endogenous 5-methylcytosine (MeC) residues are found at all CG dinucleotides of the p53 tumor suppressor gene, including the mutational ‘hotspots’ for smoking induced lung cancer. MeC enhances the reactivity of its base paired guanine towards carcinogenic diolepoxide metabolites of polycyclic aromatic hydrocarbons (PAH) present in cigarette smoke. In the present study, the structural basis for these effects was investigated using a series of unnatural nucleoside analogs and a representative PAH diolepoxide, benzo[a]pyrene diolepoxide (BPDE). Synthetic DNA duplexes derived from a frequently mutated region of the p53 gene (5′-CCCGGCACCC GC[15N3,13C1-G]TCCGCG-3′, + strand) were prepared containing [15N3, 13C1]-guanine opposite unsubstituted cytosine, MeC, abasic site, or unnatural nucleobase analogs. Following BPDE treatment and hydrolysis of the modified DNA to 2′-deoxynucleosides, N2-BPDE-dG adducts formed at the [15N3, 13C1]-labeled guanine and elsewhere in the sequence were quantified by mass spectrometry. We found that C-5 alkylcytosines and related structural analogs specifically enhance the reactivity of the base paired guanine towards BPDE and modify the diastereomeric composition of N2-BPDE-dG adducts. Fluorescence and molecular docking studies revealed that 5-alkylcytosines and unnatural nucleobase analogs with extended aromatic systems facilitate the formation of intercalative BPDE–DNA complexes, placing BPDE in a favorable orientation for nucleophilic attack by the N2 position of guanine.
    Full-text · Article · May 2011 · Nucleic Acids Research
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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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    ABSTRACT: The DNA chemical damage is a very important researching project in chemistry, life science and related fields.In this paper, the biological function of DNA damage, the reason causing damage and the detecting technologyof DNA damage are summarized and discussed.
    Preview · Article · Jul 2010
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