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Biosens. Bioelectron., Sep 09 2023, 241 S0956-5663(23)00612-7 | https://doi.org/10.1016/j.bios.2023.115670 Multiplex genotyping of SNPs in genomic DNA via hydrogel-based assay mediated with MutS and polyethylene glycol.

Seok Joon Mun ^a,1, Wookyoung Jang ^a,1, Hyun-Seung Park ^b,c, Yong Jun Lim ^a, Tae-Jin Yang ^b, Ki Wan Bong ^a

^aDepartment of Chemical and Biological Engineering, Korea University, Seoul, 02841, Republic of Korea

^bDepartment of Agriculture, Forestry and Bioresources, Plant Genomics and Breeding Institute, Natural Products Research Institute, Research Institute of Agriculture and Life Sciences, College of Agriculture and Life Sciences, Seoul National University, Seoul, 08826, Republic of Korea

^cDepartment of Integrative Biological Sciences and Industry, Convergence Research Center for Natural Products, Sejong University, Seoul, 05006, Republic of Korea

¹These authors contributed equally to this work.

Corresponding authors: Tae-Jin Yang, Ki Wan Bong

Abstract

The simultaneous genotyping of multiple single nucleotide polymorphisms (SNPs) in genomic DNA derived from organisms holds significant potential for applications such as precision medicine and food product authentication. However, conventional assay technologies including qPCR-based techniques, microarrays, and hydrogel-based assays face limitations in efficient multiplexing of SNPs, particularly for large-size DNA beyond kilobase scales, due to constraints in multiplex capability, specificity, or sensitivity. In this study, a hydrogel-based multiplex SNP genotyping platform specifically designed for genomic DNA is presented. This platform integrates the ligation detection reaction (LDR) and rolling circle amplification (RCA) techniques within a hydrogel-based multiplex sensing system, enabling adaptable and sensitive SNP genotyping for genomic DNA. To enhance the specificity of the assay, MutS protein and polyethylene glycol are introduced into the protocol, reducing the non-specific ligation and RCA reactions synergistically. With significant specificity improvement of over 10-fold, three types of SNPs within an artificially constructed ∼1000 bp double-stranded DNA (dsDNA) are successfully genotyped with double-digit picomolar sensitivity. Furthermore, the practical applicability of the developed process for the origin identification of raw materials is demonstrated by genotyping three types of SNPs within genomic DNA obtained from two closely related plant species, Korean ginseng (Panax ginseng) and American ginseng (Panax quinquefolius), containing ca. 3.5 gigabase genome size. Of notable significance, this study marks the premiere achievement in PCR-free multiplex genotyping of SNPs in genomic DNA using a single fluorophore.

논문정보

형식Research article
게재일2023년 09월 (BRIC 등록일 2023-09-26)
연구진국내 연구진
분야 바이오·의료융합 > 바이오센싱 및 나노바이오물질

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