Highly multiplex PCR assays by coupling the 5'-flap endonuclease activity of Taq DNA polymerase and molecular beacon reporters

• Published in: Proceedings of the National Academy of Sciences - PNAS 2022-03, Vol.119 (9), p.1
• Main Authors: Huang, Qiuying, Chen, Dongmei, Du, Chen, Liu, Qiaoqiao, Lin, Su, Liang, Lanlan, Xu, Ye, Liao, Yiqun, Li, Qingge
• Format: Article
• Language: English
• Subjects: Assaying; Biological Sciences; Chemical compounds; Chromosome Deletion; Chromosomes, Human, Y; Coupling (molecular); Deoxyribonucleic acid; DNA; DNA polymerase; DNA Primers; DNA-directed DNA polymerase; E coli; Endonuclease; Escherichia coli - genetics; Flap Endonucleases - metabolism; Fluorescence; Fluorescent Dyes - chemistry; Fluorophores; Humans; Hybrids; Limit of Detection; Multiplex Polymerase Chain Reaction - methods; Multiplexing; Mutation; Nucleic acids; Polymerase chain reaction; Real time; Respiratory diseases; Taq Polymerase - metabolism; Target detection
• ISSN: 0027-8424; 1091-6490
• DOI: 10.1073/pnas.2110672119

Real-time PCR is the most utilized nucleic acid testing tool in clinical settings. However, the number of targets detectable per reaction are restricted by current modes. Here, we describe a single-step, multiplex approach capable of detecting dozens of targets per reaction in a real-time PCR thermal cycler. The approach, termed MeltArray, utilizes the 5'-flap endonuclease activity of DNA polymerase to cleave a mediator probe into a mediator primer that can bind to a molecular beacon reporter, which allows for the extension of multiple mediator primers to produce a series of fluorescent hybrids of different melting temperatures unique to each target. Using multiple molecular beacon reporters labeled with different fluorophores, the overall number of targets is equal to the number of the reporters multiplied by that of mediator primers per reporter. The use of MeltArray was explored in various scenarios, including in a 20-plex assay that detects human Y chromosome microdeletions, a 62-plex assay that determines serovars, a 24-plex assay that simultaneously identifies and quantitates respiratory pathogens, and a minisequencing assay that identifies mutations, and all of these different assays were validated with clinical samples. MeltArray approach should find widespread use in clinical settings owing to its combined merits of multiplicity, versatility, simplicity, and accessibility.