Gel shift assay: demonstration of enhanced binding of oligo(delta)-L-ornithine-oligodeoxynucleotide conjugates to complementary DNA and RNA.
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(delta)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 Tm of 4 degrees 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(delta)ornithine conjugate is presented.
Zhu
T
T
Center for Advanced Biotechnology and Medicine, Piscataway, NJ 08854, USA.
Pooyan
S
S
Wei
Z
Z
Leibowitz
M J
MJ
Stein
S
S
D001483:Base Sequence; D001665:Binding Sites; D004247:DNA / Q000737:chemistry*; D004591:Electrophoresis, Polyacrylamide Gel; D009691:Nucleic Acid Denaturation; D009838:Oligodeoxyribonucleotides / Q000138:chemical synthesis / Q000737:chemistry*; D016376:Oligonucleotides, Antisense / Q000138:chemical synthesis / Q000737:chemistry*; D009952:Ornithine / Q000031:analogs & derivatives* / Q000737:chemistry; D012313:RNA / Q000737:chemistry; D013816:Thermodynamics
D009838:Oligodeoxyribonucleotides; D016376:Oligonucleotides, Antisense; D012313:RNA; D004247:DNA; D009952:Ornithine