Multiple detection of single nucleotide polymorphism by microarray-based resonance light scattering assay with enlarged gold nanoparticle probes

Abstract

The mapping of specific single nucleotide polymorphisms (SNPs) in patients' genome is a critical process for the development of personalized therapy. In this work, a DNA microarray-based resonance light scattering (RLS) assay has been developed for multiplexed detection of breast cancer related SNPs with high sensitivity and selectivity. After hybridization of the desired target single-stranded DNAs (ssDNAs) with the ssDNA probes on a microarray, the polyvalent ssDNA modified 13 nm gold nanoparticles (GNPs) are employed to label the hybridization reaction through the formation of a three-stranded DNA system. The H2O2-mediated enlargement of GNPs is then used to enhance the RLS signal. The microarray-based RLS assay provides a detection limit of 10 pM (S/N = 3) for the target ssDNA and determines an allele frequency as low as 1.0% in the target ssDNA cocktail. Combined with an asymmetric PCR technique, the proposed assay shows good accuracy and sensitivity in profiling 4 SNPs related to breast cancer of three selected cell lines.

Gold nanoparticles as sensitive optical probes

“…54 A colorimetric assay in conjunction with a resonance light scattering technique provides a LOD of 10 pM for DNA, showing a potential for the analysis of single nucleotide polymorphisms in breast cancer. 55 Another way to improve DNA detection sensitivity is through the control of the size of Au NP aggregates. Huge aggregates lead to precipitation of Au NPs and a decrease of absorbance, diminishing the sensitivity.…”

High-efficiency and high-fidelity ssDNA circularisation via the pairing of five 3′-terminal bases to assist LR-LAMP for the genotyping of single-nucleotide polymorphisms

“…The relatively common SNP-detection approaches include molecular-hybridisation-based methods, such as allele-specific oligonucleotide, molecular beacon (MB), high-resolution melting and DNA chip technologies. 8–10 However, such methods usually require strict control of the operation and reaction conditions. Other emerging tools, i.e.…”

“…The relatively common SNP-detection approaches include molecular-hybridisation-based methods, such as allele-specific oligonucleotide, molecular beacon (MB), high-resolution melting and DNA chip technologies. [8][9][10] However, such methods usually require strict control of the operation and reaction conditions. Other emerging tools, i.e., enzyme-based technologies, have also been developed rapidly, such as polymerase-based approaches (including polymerase chain reaction (PCR) and allele-specific PCR (AS-PCR), 11 enzyme-cleavage-based approaches (including restriction fragment length polymorphism and lambda exonuclease), exonuclease III or Argonaute (Ago) protein-based SNP detection methods 12,13 and the promising ligase-based approaches (including ligase chain reaction, ligation-polymerase chain reaction and ligation-rolling circle amplification (LRCA).…”

Improvement of Molecular Diagnosis Using Domain‐Level Single‐Nucleotide Variants by Eliminating Unexpected Secondary Structures

“…[4] Therefore, SNVs identification is crucial for physiology and medicine. Many efforts have been devoted to SNVs identification,s uch as microarray-basedm ethods, [5] sequestrationassisted assays, [6] and PCR-basedm ethods. [7] However,i nt he process of recognizingS NV,t he unexpected secondary struc-ture of target DNA formed by intermolecularb ase pairs creates ah ighere nergy barrier for intermolecular hybridization, which has been clearly demonstrated by Gao et al They found that the presence of secondary structures in as ingle short DNA strandsignificantly slowed the process of DNA hybridization.…”