Positively Charged Base Surrogate for Highly Stable Base Pairing through Electrostatic and Stacking Interactions

Base pairs of cationic dyes (p-methylstilbazole) were incorporated into oligodeoxyribonucleotides (ODNs). This base pair greatly stabilized the duplex through electrostatic and stacking interactions. The melting temperature of modified ODN was higher than those of neutral dyes and native base pairs. Further stabilization of the duplex was observed when the number of cationic dyes increased.