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Modular protein-oligonucleotide signal exchange.

Deepak K Agrawal1,2, Rebecca Schulman1,3,4

  • 1Department of Chemical and Biomolecular Engineering, Johns Hopkins University, 3400 N Charles St, Baltimore, MD 21218, USA.

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|May 23, 2020
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Summary

This study introduces a novel biomolecular method to track protein concentrations in real-time by monitoring DNA output changes. This DNA reporting system offers a simple, versatile tool for sensing diverse protein levels.

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Area of Science:

  • Biochemistry
  • Molecular Biology
  • Synthetic Biology

Background:

  • Measuring real-time protein concentration changes dynamically remains a significant challenge in biological research.
  • Existing methods often lack the ability to quantitatively report both increases and decreases in protein levels simultaneously.
  • A need exists for innovative biosensing platforms that can translate protein concentration dynamics into easily measurable signals.

Purpose of the Study:

  • To develop a novel biomolecular reaction process for real-time, in situ reporting of input protein concentrations.
  • To establish a method that uses DNA oligonucleotide outputs to quantitatively reflect changes in protein levels.
  • To demonstrate the versatility and applicability of this system for clinically relevant proteins.

Main Methods:

  • Utilized DNA oligonucleotide aptamers for selective protein binding.
  • Employed toehold-mediated DNA strand-displacement for reversible DNA binding.
  • Designed a system where protein concentration directly influences the concentration of an output DNA strand.
  • Implemented four distinct exchange processes to monitor human α-thrombin and vascular endothelial growth factor.

Main Results:

  • Successfully demonstrated a biomolecular system that reports input protein concentration via output DNA strand concentration.
  • Showcased the ability to independently select output DNA sequences regardless of the target protein.
  • Validated the system's performance with clinically relevant proteins like α-thrombin and vascular endothelial growth factor.
  • Confirmed that multiple exchange processes can operate in tandem to report on distinct or identical proteins simultaneously.

Conclusions:

  • The developed biomolecular reaction process provides a robust and simple method for real-time protein quantification.
  • This approach enables the creation of devices capable of diverse output responses to specific protein concentration changes.
  • The system offers a promising pathway for advanced biosensing applications and diagnostics.