Sensitive Detection of Single-Nucleotide Polymorphisms by Solid Nanopores Integrated With DNA Probed Nanoparticles.

Ling Zhi Wu,Zhi Xuan Wang,Li Li,Bi Qing Bao,Die Ma,Guo Hao Xi,Li Xing Weng,Yuan Ye

doi:10.3389/fbioe.2021.690747

Abstract

Single-nucleotide polymorphisms (SNPs) are the abundant forms of genetic variations, which are closely associated with serious genetic and inherited diseases, even cancers. Here, a novel SNP detection assay has been developed for single-nucleotide discrimination by nanopore sensing platform with DNA probed Au nanoparticles as transport carriers. The SNP of p53 gene mutation in gastric cancer has been successfully detected in the femtomolar concentration by nanopore sensing. The robust biosensing strategy offers a way for solid nanopore sensors integrated with varied nanoparticles to achieve single-nucleotide distinction with high sensitivity and spatial resolution, which promises tremendous potential applications of nanopore sensing for early diagnosis and disease prevention in the near future.

Highlights

Single-nucleotide polymorphisms (SNPs) primarily refer to single-nucleotide substitution that constitutes the most common genetic variation, with an average occurrence of ∼1/1,000 base pairs, which are closely associated with various cancers and tumors (Liu et al, 2017; Varona and Anderson, 2019; Megalathan et al, 2021)
By rational design of the polyA length, the gold nanoparticles are wrapped by DNA probes at single-molecular level, and the appended recognition blocks with an upright conformation favor DNA recognition (Qin and Lanry Yung, 2007; Yao et al, 2015; Zhu et al, 2016; FIGURE 1 | (A) The work principle of the SNP detection system
Single-nucleotide polymorphisms are the most abundant genetic variation, which are responsible for genetic disease prevalent in a population

Summary

INTRODUCTION

Single-nucleotide polymorphisms (SNPs) primarily refer to single-nucleotide substitution that constitutes the most common genetic variation, with an average occurrence of ∼1/1,000 base pairs, which are closely associated with various cancers and tumors (Liu et al, 2017; Varona and Anderson, 2019; Megalathan et al, 2021). Based on the pore materials, nanopores have been developed into two major types of biological and solid-state pores, and both take their respective advantages to achieve single-molecule identification toward clinical detection (Wang et al, 2017, 2018, 2020; Meng et al, 2019). The DNA probes wrapped on Au nanoparticles favor hybridization with SNP sequences with a high selectivity for single-nucleotide discrimination (Ang and Lanry Yung, 2012; Venta et al, 2013, 2014; Karmi et al, 2021). The distinction of SNP mutations can be achieved by observing the differences of signals between the monomers and dimers of nanoparticles translocated through the hole by a nanopore platform. With high selectivity, efficiency, and simplicity, this method can be used to successfully distinguish single-nucleotide variations of DNA targets independent of the nanopore morphology

MATERIALS AND METHODS

RESULTS AND DISCUSSION

CONCLUSION

DATA AVAILABILITY STATEMENT