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From our previous work, it is known that phosphate-methylated d(TpT) forms parallel miniduplexes with an equal stability for the sp and Rp diastereoisomers. Therefore, it is concluded that the R P configuration (which is associated with location of the methyl group inside the helix groove) is unfavorable in the case of C-C base pairing. This conclusion was corroborated by AMBER molecular mechanics calculations, which showed that the larger propeller twist angle for C-C base pairing (∼41 o ), in comparison with T-T base pairing (∼25 o ), results in narrowing of the helix groove

the journal of organic chemistry

Conformation of the phosphate-methylated DNA dinucleotides d(CpC) and d(TpC). Formation of a parallel miniduplex exclusively for the S configuration at phosphorus