Gel Shift Assay: Demonstration of Enhanced Binding of O1igo(δ)-L-Ornithine-Oligodeoxynucleotide Conjugates to Complementary DNA and RNA

Abstract

An increase in melting temperature for DNA:DNA duplexes had been observed previously (Zhu et al. Antisense Res. Dev. 3:349–356, 1993) when an oligo(δ)ornithine moiety was covalently appended to a short oligodeoxynucleotide. We now report the analysis of duplex formation by electrophoretic gel shift analysis. In the particular example studied, an increase in T_m of 4°C was found to correspond to about a fivefold increase in binding constant. A similar enhancement by the appended cationic peptide was observed when the target strand was RNA. The use of a competitive assay format for avoidance of adsorptive loss at low concentrations (<10^-7 M) of the oligonucleotide-oligo(δ)ornithine conjugate is presented.