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A handheld microfluidic manifold for massively multiplexed CRISPR-based nucleic acid detection.

Sijbren Kramer1,2, Ryungeun Song3,4, Yujia Huang1

  • 1Department of Molecular Biology, Princeton University, Princeton, New Jersey, 08544, USA.

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Summary

Microfluidic SHINE (mSHINE) enables over 100-plex nucleic acid detection using a portable device. This CRISPR-based technology offers sensitive, rapid, and field-deployable pathogen and single-nucleotide variant detection.

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Area of Science:

  • Molecular Biology
  • Biotechnology
  • Medical Diagnostics

Background:

  • Multiplexed nucleic acid detection is difficult to perform outside labs, with field-deployable methods limited in multiplexing capability.
  • CRISPR-based technologies offer sensitive and deployable nucleic acid detection.
  • The COVID-19 pandemic highlighted the need for advanced diagnostic tools.

Purpose of the Study:

  • To develop a highly multiplexed, field-deployable nucleic acid detection system.
  • To enhance the capabilities of the CRISPR-based Streamlined Highlighting of Infections to Navigate Epidemics (SHINE) technology.
  • To enable rapid detection of pathogens and genetic variants outside of traditional laboratory settings.

Main Methods:

  • Introduction of microfluidic SHINE (mSHINE), a portable microfluidic manifold system.
  • Dilution of samples and direction into individual reaction chambers containing lyophilized SHINE reagents and mixing elements.
  • Manual sample loading via syringe followed by a sealing step for parallel, independent reactions.

Main Results:

  • mSHINE enables >100-plex nucleic acid detection with high sensitivity, comparable to the original SHINE.
  • Highly multiplexed pathogen detection is achieved in under 1 hour.
  • Detection of single-nucleotide variants, including drug susceptibility mutations, is demonstrated.

Conclusions:

  • mSHINE significantly advances the field of multiplexed nucleic acid testing, moving it beyond laboratory settings.
  • The technology offers a paradigm shift for patient benefit and public health through accessible, high-plex diagnostics.
  • mSHINE provides a sensitive, rapid, and portable solution for diverse nucleic acid detection needs.