‘Switch-on’ DNA sensor based on poly (p-phenylene vinylenes) bound tentacle probes

Abstract

Abstract The development of highly sensitive and selective DNA sensors has fuelled applications in a wide range of fields including medical diagnostics, forensics, biodefense, food contamination and environment monitoring. We demonstrate a novel superquenching based DNA sensor with “switch-on” readout using poly(p-phenylenevinylene) (PPV) coated magnetic beads (PPV-MagSi) and quencher functionalized tentacle probes (TP). The sensor design utilizes signal amplification properties of PPV and cooperativity of TPs to monitor hybridization of target oligonucleotides (ONs). The switch-on sensor exhibits excellent sensitivity and selectively discriminates mismatches in the target DNA sequence. Two novel anionic PPVs – poly (6,6′-((2-methyl-5-((E)-4-((E)-prop-1-en-1-yl)styryl)-1,4-phenylene)-bis(oxy) dihexanoic acid) (PMDH) and poly (6,6′-((2-((E)-2,5-bis(2-methoxyethoxy)-4-((E)-prop-1-en-1-yl)styryl)-5-methyl-1,4-phenylene)-bis-(oxy)) di-hexanoic acid) (PDMonoG) were tested and compared against each other as part of the sensor design. The employed hairpin TPs possess further advantages of avoiding labelling of target ON, increased selectivity and sensitivity; faster assay time, and capability of magnetically controlled deployment and separation of PPV-MagSi beads.