Label-Free Colorimetric Detection of Specific Sequences in Genomic DNA Amplified by the Polymerase Chain Reaction

TLDR

The study proposes a colorimetric assay that uses electrostatic interactions to detect specific sequences and single‑nucleotide polymorphisms in PCR‑amplified DNA. The assay is label‑free, requires no DNA or nanoparticle modification, and achieves PCR‑level sensitivity. Single‑stranded DNA adsorbs onto negatively charged gold nanoparticles with a rate that depends on sequence length and temperature, stabilizing the particles against salt‑induced aggregation; binding and hybridization occur in solution in under one minute, enabling rapid detection of SNPs such as those linked to long QT syndrome in clinical samples.

Abstract

We document the surprising result that single-stranded DNA adsorbs on negatively charged gold nanoparticles (Au-nps) with a rate that depends on sequence length and temperature. After ss-DNA adsorbs on Au-nps, we find that the particles are stabilized against salt-induced aggregation. These observations can be rationalized on the basis of electrostatics and form the basis for a colorimetric assay to identify specific sequences and single nucleotide polymorphisms on polymerase chain reaction (PCR)-amplified DNA. The assay is label-free, requires no covalent modification of the DNA or Au-np surfaces, and takes on the sensitivity of PCR. Most important, binding of target and probe takes place in solution where hybridization occurs in less than 1 min. As an example, we test PCR-amplified genomic DNA from clinical samples for single nucleotide polymorphisms (SNPs) associated with a fatal arrhythmia known as long QT syndrome.