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Mun SJ, Jang W, Park HS, Lim YJ, Yang TJ, Bong KW. Multiplex genotyping of SNPs in genomic DNA via hydrogel-based assay mediated with MutS and polyethylene glycol. Biosens Bioelectron 2023; 241:115670. [PMID: 37714061 DOI: 10.1016/j.bios.2023.115670] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2023] [Revised: 08/30/2023] [Accepted: 09/03/2023] [Indexed: 09/17/2023]
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.
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Affiliation(s)
- Seok Joon Mun
- Department of Chemical and Biological Engineering, Korea University, Seoul, 02841, Republic of Korea
| | - Wookyoung Jang
- Department of Chemical and Biological Engineering, Korea University, Seoul, 02841, Republic of Korea
| | - Hyun-Seung Park
- Department 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; Department of Integrative Biological Sciences and Industry, Convergence Research Center for Natural Products, Sejong University, Seoul, 05006, Republic of Korea
| | - Yong Jun Lim
- Department of Chemical and Biological Engineering, Korea University, Seoul, 02841, Republic of Korea
| | - Tae-Jin Yang
- Department 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.
| | - Ki Wan Bong
- Department of Chemical and Biological Engineering, Korea University, Seoul, 02841, Republic of Korea.
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Abstract
Due to their hydrophilic, biocompatible, and highly tunable nature, hydrogel materials have attracted strong interest in the recent years for numerous biotechnological applications. In particular, their solution-like environment and non-fouling nature in complex biological samples render hydrogels as ideal substrates for biosensing applications. Hydrogel coatings, and later, gel dot surface microarrays, were successfully used in sensitive nucleic acid assays and immunoassays. More recently, new microfabrication techniques for synthesizing encoded particles from hydrogel materials have enabled the development of hydrogel-based suspension arrays. Lithography processes and droplet-based microfluidic techniques enable generation of libraries of particles with unique spectral or graphical codes, for multiplexed sensing in biological samples. In this review, we discuss the key questions arising when designing hydrogel particles dedicated to biosensing. How can the hydrogel material be engineered in order to tune its properties and immobilize bioprobes inside? What are the strategies to fabricate and encode gel particles, and how can particles be processed and decoded after the assay? Finally, we review the bioassays reported so far in the literature that have used hydrogel particle arrays and give an outlook of further developments of the field.
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Affiliation(s)
- Gaelle C. Le Goff
- Novartis Institutes for Biomedical Research, 250 Massachusetts
Avenue, Cambridge 02139, USA
- Department of Chemical Engineering, Massachusetts Institute of
Technology, 77 Massachusetts Avenue, Cambridge, MA 02139, USA
| | - Rathi L. Srinivas
- Department of Chemical Engineering, Massachusetts Institute of
Technology, 77 Massachusetts Avenue, Cambridge, MA 02139, USA
| | - W. Adam Hill
- Novartis Institutes for Biomedical Research, 250 Massachusetts
Avenue, Cambridge 02139, USA
| | - Patrick S. Doyle
- Department of Chemical Engineering, Massachusetts Institute of
Technology, 77 Massachusetts Avenue, Cambridge, MA 02139, USA
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Sun XT, Liu M, Xu ZR. Microfluidic fabrication of multifunctional particles and their analytical applications. Talanta 2014; 121:163-77. [DOI: 10.1016/j.talanta.2013.12.060] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/26/2013] [Revised: 12/20/2013] [Accepted: 12/25/2013] [Indexed: 12/21/2022]
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Guarrotxena N, Bazan GC. Antitags: SERS-encoded nanoparticle assemblies that enable single-spot multiplex protein detection. ADVANCED MATERIALS (DEERFIELD BEACH, FLA.) 2014; 26:1941-1946. [PMID: 24338905 DOI: 10.1002/adma.201304107] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/15/2013] [Revised: 11/04/2013] [Indexed: 06/03/2023]
Abstract
Simultaneous detection of multiple proteins on a single spot can be efficiently achieved by using multiplexed surface-enhanced Raman spectroscopy (SERS)-encoded nanoparticle 'antitags' consisting of poly(ethylene glycol) (PEG)-protected silver dimers (and higher aggregates) and antibody-tagging entities. The effective SERS-based multivariate deconvolution approach guarantees an accurate and successful distinguishable identification of single and multiple proteins in complex samples. Their potential application in multiplexed SERS bioimaging technology can be easily envisaged.
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Affiliation(s)
- Nekane Guarrotxena
- Instituto de Ciencia y Tecnología de Polímeros (ICTP), Consejo Superior de Investigaciones Científicas (CSIC), Juan de la Cierva 3, Madrid, 28006, Spain
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Breul AM, Hager MD, Schubert US. Fluorescent monomers as building blocks for dye labeled polymers: synthesis and application in energy conversion, biolabeling and sensors. Chem Soc Rev 2013; 42:5366-407. [DOI: 10.1039/c3cs35478d] [Citation(s) in RCA: 190] [Impact Index Per Article: 17.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
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