POLYNUCLEOTIDE BLOCK POLYMERS CONSISTING OF A DNA-RNA HYBRID JOINED TO A DNA-DNA DUPLEX - SYNTHESIS AND CHARACTERIZATION OF DGN-RCIDCK DUPLEXES

Abstract

The synthesis of several nucleic acid block polymers of the general type dGn .cntdot. rCidCk is described. The key steps in the procedure were the joining of dCk oligomers, protected at the 3''-OH with an acetyl group, to rCi oligomers by T4 DNA ligase and the purification of the products by RPC-5 column chromatography. The block polymers were characterized by 20% polyacrylamide gel electrophoresis, UV and circular dichroism spectra, analytical Cs2SO4 buoyant density analyses, helix-coil transitions and S1 nuclease studies. NMR studies on 1 member of this series, dGn .cntdot. rC11dC16, were reported recently. The NMR studies and the results described here indicate that these block polymers are linear duplexes with 2 adjoining conformations, yet are H-bonded and base-stacked throughout with minimal disruption of the helix at the junction of the 2 conformations. Computer model building studies predict that these nucleic acids contain a bend at the junction region.