DNA Dangling‐End‐Induced Colloidal Stabilization of Gold Nanoparticles for Colorimetric Single‐Nucleotide Polymorphism Genotyping

Abstract

A single-nucleotide polymorphism (SNP) detection method was developed by combining single-base primer extension and salt-induced aggregation of gold nanoparticles densely functionalized with double-stranded DNA (dsDNA-AuNP). The dsDNA-AuNPs undergo rapid aggregation in a medium of high ionic strength, whereas particles having a single-base protrusion at the outermost surface disperse stably, allowing detection of a single-base difference in length by color changes. When SNP typing primers are used as analytes to hybridize to the single-stranded DNA on the AuNP surface, the resulting dsDNA-AuNP works as a visual indicator of single-base extension. A set of four extension reaction mixtures is prepared using each of ddNTPs and subsequently subjected to the aggregation assay. Three mixtures involving ddNTP that is not complementary to the SNP site in the target produce the aggregates that exhibit a purple color. In contrast, one mixture with the complementary ddNTP generates the single-base protrusion and appears red. This method could potentially be used in clinical diagnostics for personalized medicine.

Directed Assembly of Gold Nanorods by Terminal‐Base Pairing of Surface‐Grafted DNA

“…These anomalous colloidal behaviors have been observed irrespective of the composition (metal and polymer), size (5–300 nm), and shape (sphere, rod, and platelet) of the particle core. In addition, they have also been observed, regardless of the base sequence of the inner region of the dsDNA layers . These facts indicate that the colloidal properties originate from the physicochemical characters of the outermost surface of the DNA layer.…”

“…By contrast, when the complementary ssDNAs are added to form DNA duplexes on the AuNP surface, the resultant double‐stranded (ds) DNA–AuNPs are spontaneously and rapidly aggregated under the same conditions. Interestingly, the dsDNA–AuNPs continue to stably disperse when a terminal mismatch or a single‐nucleotide overhang exists on the periphery of the dsDNA layer surrounding the AuNP core. These anomalous colloidal behaviors have been observed irrespective of the composition (metal and polymer), size (5–300 nm), and shape (sphere, rod, and platelet) of the particle core.…”

“…Interestingly, the dsDNA–AuNPs continue to stably disperse when a terminal mismatch or a single‐nucleotide overhang exists on the periphery of the dsDNA layer surrounding the AuNP core. These anomalous colloidal behaviors have been observed irrespective of the composition (metal and polymer), size (5–300 nm), and shape (sphere, rod, and platelet) of the particle core. In addition, they have also been observed, regardless of the base sequence of the inner region of the dsDNA layers .…”

Modulation of Interparticle Distance in Discrete Gold Nanoparticle Dimers and Trimers by DNA Single‐Base Pairing

“…By contrast, no aggregation takes place under the same conditions, when the surface dsDNA has a terminal single‐base mismatch at the outermost surface of the dsDNA–NP. This colloidal stabilization is predominantly ascribed to the interparticle entropic repulsion induced by the fraying motion of the terminal unpaired nucleobases …”

Naked-eye fingerprinting of single nucleotide polymorphisms on psoriasis patients

“…Gold standard methods to genotype HLA alleles rely either on sequencing, or on PCR with sequence-specific-primers (SSP-PCR), [20][21][22] [26][27][28][29] When comparing simplified, colorimetric SNP detection assays with state-of-the-art instrumental techniques, the main issues are specificity and sensitivity. 24 Although several reports have developed different strategies to deal with these issues, as a matter of fact, a great majority of commercial diagnostic tests for SNP genotyping currently rely on instrumental assays, mirroring the drawbacks that molecular strategies face when transferred to real-world samples.…”