Cidofovir (1-(S)-[3-hydroxy-2-(phosphonomethoxy)propyl]cytosine, CDV) is a potent inhibitor of poxvirus replication. Prior studies have shown that... » More

Cidofovir (1-(S)-[3-hydroxy-2-(phosphonomethoxy)propyl]cytosine, CDV) is a potent inhibitor of poxvirus replication. Prior studies have shown that the inhibition of replication involves effects of CDV incorporated into DNA on reactions catalyzed by both the 5?-to-3? polymerase and 3?-to-5? exonuclease activities of vaccinia virus DNA polymerase. However, the mechanism of inhibition of these DNA polymerase activities by the insertion of CDV into DNA remains unclear. While CDV and deoxycytidine share a common nucleobase, CDV is missing the deoxyribose sugar ring, containing instead an acyclic phosphonate with a hydroxyl equivalent to the 3?-hydroxyl of deoxycytidine. To study the structural consequences of the insertion of a CDV residue into DNA, we have solved using 1H NMR the solution structures of a dodecamer DNA duplex containing a CDV molecule at position 7 and of a control DNA duplex containing a deoxycytidine (C7). The overall ensembles of structures for both DNA duplexes were found to be very similar to each other. We observed a decrease of intensity (>50%) for the imino protons neighboring the CDV (bases G6 and T8), and a large chemical shift change for the cognate base (G18), implying higher proton exchange rates for this region. Furthermore, DNA duplex melting experiments revealed a lower Tm for the CDV-containing duplex (45.5°C) compared to the control (57.7°C). Our results suggest that on one hand, the CDV drug is well accommodated and stable within the dodecamer DNA duplex, but the stability of the complex is less than the control suggesting increased dynamics around the inserted CDV.

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