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DNA-Tethered RNA Polymerase for Programmable In vitro Transcription and Molecular Computation

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Published on: December 29, 2021

Protein-to-DNA Converter with High Signal Gain.

Yan Shan Ang¹, Lin-Yue Lanry Yung¹

¹Department of Chemical & Biomolecular Engineering, National University of Singapore, Singapore 117585, Singapore.

|April 4, 2024

Summary

This summary is machine-generated.

We developed a novel protein-to-DNA converter called PEAR (proximity extension amplification reaction) for ultrasensitive protein detection. This robust system enhances DNA amplification reactions, enabling new molecular evaluation methods.

Keywords:

DNA circuit DNA nanotechnology isothermal amplification molecular computation protein quantification proximity activation

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Area of Science:

Biotechnology
Molecular Biology
Biochemistry

Background:

DNA isothermal amplification is limited to nucleic acid inputs.
Direct analysis of protein biomarkers using DNA amplification is challenging.
Existing DNA amplification methods struggle with nonspecific amplification.

Purpose of the Study:

To design a proximity activation mechanism converting protein input into DNA barcodes.
To develop a robust DNA exponential amplification reaction (PEAR) for protein detection.
To achieve ultrasensitive protein detection with high signal gain.

Main Methods:

Designed a proximity activation mechanism (PEAR) for protein-to-DNA conversion.
Optimized design parameters including enzymes, probes, template sequences (NUPACK), and hairpin locks.
Experimentally verified the PEAR system's performance using three protein models.

Main Results:

The PEAR system demonstrated robustness against nonspecific DNA amplification.
Achieved target responsiveness with a dynamic range of 4-5 orders of magnitude.
Detected protein inputs down to femtomolar concentrations.

Conclusions:

The PEAR system provides a stable and robust protein-to-DNA converter module.
Enables high signal gain for DNA exponential amplification reactions with protein inputs.
Paves the way for complex molecular evaluations and ultrasensitive protein detection.