Abstract

Nucleic acid amplification has permeated every field in the life sciences since the introduction of the classic polymerase chain reaction (PCR) method in 1983. Yet, despite its fundamental reach, PCR has been constrained within the walls of a laboratory, due to its requirement for a sophisticated thermocycling machine, limiting external application in low-resource settings. New isothermal amplification strategies are seeking to break through traditional laboratory boundaries by providing nucleic acid replication at constant temperatures. Of these methods, recombinase polymerase amplification (RPA) is one of the fastest developing, experiencing rapid uptake and market, even though it was introduced comparatively late. Critically, RPA's technology potentiates highly accessible and sensitive nucleic acid amplification outside of laboratory, and even self-testing. Here we provide a comprehensive review of the equipment-free simplicity of RPA over its first decade of development. Our review includes key knowledge of RPA technology, such as its reaction components, mechanism, sensitivities and specificities, and distinctive detection methods. The review also provides know-how for developing RPA assays, and information about commercially available RPA reaction kits and accessories. We summarise critical RPA experimental tips and issues available through data mining the published literature, to assist researchers in mastering the RPA reaction. We also outline influential hotspots of RPA development, and conclude with outlooks for future development and implications for eclipsing PCR and further revolutionising the life sciences.

Highlights

  • Introduction and overviewRecent advances in isothermal nucleic acid amplification have provided simplified incubation conditions for artificial nucleic acid replication, requiring only a constant temperature rather than thermocycling

  • The most wellestablished methods are exemplified by nucleic acid sequencebased amplification (NASBA, known as transcription mediated amplification, TMA), signal-mediated amplification of ribonucleic acid (RNA) technology (SMART), helicase-dependent amplification (HDA), recombinase polymerase amplification (RPA), rolling circle amplification (RCA), multiple displacement amplification (MDA), loop-mediated isothermal amplification (LAMP) and strand displacement amplification (SDA); readers can refer to details of these methods in a few reviews.[2,3,4,5]

  • All the lateral flow devices except for the PCRD Nucleic Acid Detection device are based on sandwich assay using gold nanoparticles as tracer; the PCRD Nucleic Acid Detection device employs carbon nanoparticles, which can be more sensitive than the gold nanoparticles.[59,60]

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Summary

Introduction and overview

Recent advances in isothermal nucleic acid amplification have provided simplified incubation conditions for artificial nucleic acid replication, requiring only a constant temperature rather than thermocycling. We subsequently provide know-how about developing RPA assays, including design and selection of oligonucleotides ( primer, probe and template); the information about commercially available RPA reaction kits and accessories are provided For those interested in the technical implementation of RPA, we summarise critical RPA experimental tips and issues available through data mining the published literature to assist researchers better master RPA reaction. Jia Li vision at the University of the Sunshine Coast, developing rapid and novel virus detection biosensors towards point-of-care Afterwards, she has been working as a post-doc in the University of Freiburg under Alexander von Humboldt Fellowship, researching in assay development for micro-total diagnostic systems. Addition, the nucleic acid labelling during RPA, and RPA amplicon clean-up and post-amplification treatment are important details for successful RPA detection We provide these practical information summarised from the RPA literature to serve as a guideline for RPA assay design. This section elucidates the clinical/field performance of RPA via data mining of RPA literature, which are succinctly collated (Tables 4 and 5)

Reaction components
Mechanism
27 RNA samples of
66 Napier grass samples from various geographical locations in western Kenya
Commercial kits and instrumentation by TwistDxTM
Influence of temperature and agitation
Nucleic acid labelling during RPA
Amplicon clean-up and post-amplification treatment
Sensitivities and specificities
Distinctive RPA detection methods
Flocculation assay detection
Hot spots for RPA development
Quantitative RPA – digital RPA
Multiplex RPA
RPA in a suitcase for mobile laboratory
Microfluidic integration of RPA assays
Findings
One-step RPA assays

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