Encoded hydrogel microparticles with universal mismatch-incorporated DNA probes for highly specific multiplex detection of SNPs

Hyun June Moon, Seok Joon Mun, Jun Ho Lee, Yoon Ho Roh, Yong Jun Lim, Ki Wan Bong

Research output: Contribution to journalArticlepeer-review

2 Citations (Scopus)

Abstract

Hydrogel microparticle-based nucleic acid assays are an attractive detection platform based on their multiplexing capabilities with high sensitivity and specificity. A particular area of interest is single-nucleotide polymorphism (SNP) sensing, where multiple SNPs should be identified in a highly reliable yet economical manner. However, hydrogel microparticles leveraging probe-target hybridization as a key mechanism are hampered by small duplex stability differences arising from single base-pair mismatch. We have developed encoded hydrogel microparticles with DNA probes tailored for multiplex SNP detection. Within the DNA probes, we adopt a widely used base analog (5-nitroindole) so that it substitutes one of the base sequences among DNA probes. The effects of the modification of the probes’ structure on SNP sensing has been tested from multiple perspectives, such as specificity, sensitivity, and available assay temperatures at a given ionic strength. We have validated that our hydrogel microparticles exhibit much higher specificity for a single base-pair mismatch with minimal reduction in sensitivity. Our particles can also detect multiple SNPs located in different target strands, which is a significant challenge for conventional particles.

Original languageEnglish
Article number123480
JournalTalanta
Volume245
DOIs
Publication statusPublished - 2022 Aug 1

Bibliographical note

Funding Information:
This research was supported by the Engineering Research Center of Excellence Program through the National Research Foundation of Korea (NRF) funded by the Ministry of Science and ICT (MSIT, Republic of Korea) (grant number 2016R1A5A1010148 ), and the Next-Generation Biogreen 21 Program funded by the Rural Development Administration of Republic of Korea (grant number PJ016004 ). This research was also supported by the Basic Science Research Program through the National Research Foundation of Korea (NRF) funded by the Ministry of Education (Republic of Korea) (grant number 2018R1D1A1B07046577 ).

Publisher Copyright:
© 2022 Elsevier B.V.

Keywords

  • Encoded hydrogel microparticles
  • Multiplexed detection
  • Single nucleotide polymorphism
  • Universal mismatch

ASJC Scopus subject areas

  • Analytical Chemistry

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