Spacer Control the Dynamic of Triplex Formation between Oligonucleotide-Modified Gold Nanoparticles

A novel method was developed to control the dynamic of triplex formation between oligonucleotide-modified gold nanoparticles in the presence of complementary strand. The solution containing the oligonucleotide 5′-SH-ACA CAC ACA CAC CTT TCT TTC CTT TCT TTC-3′(oligo-1)-modified gold nanoparticles was red in color. Due to triplex formation, there was a tiny change in color on addition of the complementary oligonucleotide 5′-GAA AGA AAG GAA AGA AAG-3′(oligo-3). The addition of oligonucleotide 5′-GTG TGT GTG TGT-3′(oligo-2) induced the spacer portion of oligo-1 to change from single strand to rigid duplex structure and protrude from the surface of the gold colloid, removing the physisorption between oligo-1 and the gold nanoparticles successfully. Therefore, when the oligo-2 was added accompanied by oligo-3 at pH 5.6 and 6.0 μM spermine, larger aggregates were formed and the color of the solution changed from red to blue within 20 min. The oligo-2 hybridized with the spacer portion of oligo-1 and had no effect on the stability of triplex DNA; thereby, the melting temperatures of the triplex DNA were 51 and 53 °C in the absence and presence of oligo-2, respectively. Oligo-3 played a crucial role in the triplex formation between nanoparticles. When oligo-3 was replaced with 5′-GAA AGA AAG TAA AGA AAG-3′ (oligo-4, single-base mismatched) and 5′-GAA AGT AAG GAA TGA AAG-3′ (oligo-5, double-base mismatched), respectively, the melting temperature decreased from 53 to 41 °C and eventually to 33 °C