Nanoparticle-Based Discrimination of Single-Nucleotide Polymorphism in Long DNA Sequences

Area of Science:

• Biotechnology
• Nanotechnology
• Molecular Biology

Background:

• Circulating DNA (ctDNA) analysis in liquid biopsies offers revolutionary potential for cancer detection.
• Secondary structures in short ctDNA fragments (around 150 bases) can hinder the detection of cancer-associated mutations.
• Accurate detection of single nucleotide polymorphisms (SNPs) is crucial for identifying these mutations.

Purpose of the Study:

• To develop a novel assay capable of discriminating single nucleotide polymorphisms in clinically relevant single-stranded DNA (ssDNA) sequences.
• To overcome the challenge of secondary structures in ctDNA that impede mutation detection.
• To establish a sensitive method for detecting low concentrations of mutated ctDNA.

Main Methods:

• Utilized an assay based on gold nanoparticles (65 nm) stabilized with DNA (Au@DNA).
• Employed a preincubation step to facilitate sequential bridging of Au@DNA nanoparticles.
• Tested the assay with clinically relevant ssDNA sequences ranging from 70 to 140 bases.

Main Results:

• The Au@DNA nanoparticle assay successfully discriminated single nucleotide polymorphisms in the tested ssDNA sequences.
• The assay demonstrated sensitivity in detecting mutations down to 100 pM concentration.
• The preincubation step was identified as critical for achieving single base discrimination.

Conclusions:

• The developed Au@DNA nanoparticle assay provides a promising method for detecting cancer-associated mutations in ctDNA.
• This assay can overcome the limitations posed by ctDNA secondary structures.
• The technology advances the field of liquid biopsies for more sensitive and accurate cancer detection.