Article

Synthesis and Reaction of DNA Oligomers Containing Modified Cytosines Related to Bisulfite Sequencing

Institute of Scientific and Industrial Research, Osaka University, 8-1 Mihogaoka, Ibaraki, Osaka 567-0047, Japan.
Organic Letters (Impact Factor: 6.32). 04/2009; 11(6):1377-9. DOI: 10.1021/ol900195z
Source: PubMed

ABSTRACT The synthesis of DNA oligomers containing N(4)-hydroxy-5,6-dihydrocytosine-6-sulfonate by using ligand-induced base flipping of cytosine followed by the simultaneous addition of bisulfite and hydroxylamine is reported. In contrast to C, the flipped-out 5-methylcytosine was selectively oxidized over thymines and cytosines in the duplex by potassium permanganate. Ligand-induced base flipping is a convenient and powerful strategy for the synthesis of modified cytosines and 5-methylcytosines related to bisulfite sequencing at the predetermined site of DNA.

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    • "OsO4 and reagents derived thereof were found to cis-hydroxylate dC bases with some selectivity (24, 25). Furthermore photochemical methods were reported (26, 27) that allow some discrimination and finally even compounds were reported that are added during bisulfite sequencing to trap intermediates of the bisulfite reaction (28). All reported approaches target the reactivity differences between dC and 5MedC imposed by the additional methyl group. "
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