Base pairing involving deoxyinosine: implications for probe design

The thermal stability of oligodeoxyribonucleotide duplexes containing deoxyinoslne (1) residues matched with each of the four normal DNA bases were determined by optical melting techniques. The duplexes containing at least one I were obtained by nixing equimolar amounts of an oligonucleotide of sequence dCA3XA3G with one of sequence dCT3YT3G where X and Y were A, C, G, T, or I. Comparison of optical melting curves yielded relative stabilities for the I-containlng standard base pairs in an otherwise identical base-pair sequence. I:C pairs were found to be less stable than A:T pairs in these duplexes. Large neighboring-base effects upon stability were observed. For example, when (X,Y)=(I,A), the duplex is eight-fold more stable than when (X,Y)=(A,I). Independent of sequence effects the order of stabilities is: I:C > I:A > I:T = I:G. This order differs from that of deoxyguanosine which pairs less strongly with dA; otherwise each deoxy-lnosine base pair is less stable than its deoxyguanosine counterpart in the same sequence environment. Implications of these results for design of DNA oligonucleotide probes are discussed.