We report the solution structure of two heptanucleotides each containing a central N4-methoxycytosine, in one case paired with adenine on the opposite strand and the other with guanine. For the N4-methoxycytosine · adenine pair, only the imino form of the N4-methoxycytosine residue is observed and base pairing is in Watson-Crick geometry. However, rotation of the methoxy group about the N-OCH3 bond is not constrained to a particular orientation although it must be anti to the N3 of N4-methoxycytosine. The slow exchange on a proton NMR time scale between the single strand and double strand forms is attributed to the strong preference of the cis conformation of the OCH3 group in the single strand, which inhibits base pair formation. For the N4-methoxycytosine that is base paired with guanine, we observe an amino form in Watson-Crick geometry in slow exchange with a base paired imino form in wobble geometry. The amino form is predominant at low temperature whereas the imino form predominates above 313 K. We have measured the exchange rate between the two forms at 303 K and observed a value of approximately 1 s-1. The relative ratio of amino and imino forms of N4-methoxycytosine is influenced by both the base that is in front and the temperature. Our results explain the preferential replacement of dTTP by N4-methoxycytosine in primer elongation.
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