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Guanine and 8‑Azaguanine in Anomeric DNA Hybrid Base Pairs: Stability, Fluorescence Sensing, and Efficient Mismatch Discrimination with α‑d‑Nucleosides

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journal contribution
posted on 2018-05-17, 00:00 authored by Jiang Liu, Sachin A. Ingale, Frank Seela
The α-anomers of 8-aza-2′-deoxyguanosine (αGd*) and 2′-deoxyguanosine (αGd) were site-specifically incorporated in 12-mer duplexes opposite to the four canonical DNA constituents dA, dG, dT, and dC. Oligodeoxyribonucleotides containing αGd* display significant fluorescence at slightly elevated pH (8.0). Oligodeoxyribonucleotides incorporating β-anomeric 8-aza-2′-deoxyguanosine (Gd*) and canonical dG were studied for comparison. For αGd* synthesis, an efficient purification of anomeric 8-azaguanine nucleosides was developed on the basis of protected intermediates, and a new αGd* phosphoramidite was prepared. Differences were observed for sugar conformations (N vs S) and pKa values of anomeric nucleosides. Duplex stability and mismatch discrimination were studied employing UV-dependent melting and fluorescence quenching. A gradual fluorescence change takes place in duplex DNA when the α-nucleoside αGd* was positioned opposite to the four canonical β-nucleosides. The strongest fluorescence decrease appeared in duplexes incorporating αGd*-Cd base pair matches. Decreasing fluorescence corresponds to increasing Tm values. For mismatch discrimination, the α-anomers αGd* and αGd are more efficient than the corresponding β-nucleosides. Duplexes with single “purine–purine” αGd*-αGd* or αGd-αGd base pairs are significantly more stable than those displaying β-d configuration. CD spectra indicate that single mutations by α-anomeric nucleosides do not affect the global structure of B-DNA.

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