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Title: Modular protein-oligonucleotide signal exchange

Abstract

While many methods are available to measure the concentrations of proteins in solution, the development of a method to quantitatively report both increases and decreases in different protein concentrations in real-time using changes in the concentrations of other molecules, such as DNA outputs, has remained a challenge. Here, we present a biomolecular reaction process that reports the concentration of an input protein in situ as the concentration of an output DNA oligonucleotide strand. This method uses DNA oligonucleotide aptamers that bind either to a specific protein selectively or to a complementary DNA oligonucleotide reversibly using toehold-mediated DNA strand-displacement. It is possible to choose the sequence of output strand almost independent of the sensing protein. Using this strategy, we implemented four different exchange processes to report the concentrations of clinically relevant human α-thrombin and vascular endothelial growth factor using changes in concentrations of DNA oligonucleotide outputs. These exchange processes can operate in tandem such that the same or different output signals can indicate changes in concentration of distinct or identical input proteins. The simplicity of our approach suggests a pathway to build devices that can direct diverse output responses in response to changes in concentrations of specific proteins.

Authors:
ORCiD logo [1];  [2]
  1. Department of Chemical and Biomolecular Engineering, Johns Hopkins University, 3400 N Charles St, Baltimore, MD 21218, USA;Department of Bioengineering, University of Colorado Medicine, Aurora, CO 80045, USA
  2. Department of Chemical and Biomolecular Engineering, Johns Hopkins University, 3400 N Charles St, Baltimore, MD 21218, USA;Department of Chemistry, Johns Hopkins University, 3400 N Charles St, Baltimore, Maryland 21218, USA;Department of Computer Science, Johns Hopkins University, 3400 N Charles St, Baltimore, Maryland 21218, USA
Publication Date:
Research Org.:
Johns Hopkins Univ., Baltimore, MD (United States)
Sponsoring Org.:
USDOE
OSTI Identifier:
1630481
Alternate Identifier(s):
OSTI ID: 1659413
Grant/Contract Number:  
SC0010595
Resource Type:
Published Article
Journal Name:
Nucleic Acids Research
Additional Journal Information:
Journal Name: Nucleic Acids Research Journal Volume: 48 Journal Issue: 12; Journal ID: ISSN 0305-1048
Publisher:
Oxford University Press
Country of Publication:
United Kingdom
Language:
English
Subject:
59 BASIC BIOLOGICAL SCIENCES; protein-nucleic acid interaction

Citation Formats

Agrawal, Deepak K., and Schulman, Rebecca. Modular protein-oligonucleotide signal exchange. United Kingdom: N. p., 2020. Web. doi:10.1093/nar/gkaa405.
Agrawal, Deepak K., & Schulman, Rebecca. Modular protein-oligonucleotide signal exchange. United Kingdom. doi:https://doi.org/10.1093/nar/gkaa405
Agrawal, Deepak K., and Schulman, Rebecca. Fri . "Modular protein-oligonucleotide signal exchange". United Kingdom. doi:https://doi.org/10.1093/nar/gkaa405.
@article{osti_1630481,
title = {Modular protein-oligonucleotide signal exchange},
author = {Agrawal, Deepak K. and Schulman, Rebecca},
abstractNote = {While many methods are available to measure the concentrations of proteins in solution, the development of a method to quantitatively report both increases and decreases in different protein concentrations in real-time using changes in the concentrations of other molecules, such as DNA outputs, has remained a challenge. Here, we present a biomolecular reaction process that reports the concentration of an input protein in situ as the concentration of an output DNA oligonucleotide strand. This method uses DNA oligonucleotide aptamers that bind either to a specific protein selectively or to a complementary DNA oligonucleotide reversibly using toehold-mediated DNA strand-displacement. It is possible to choose the sequence of output strand almost independent of the sensing protein. Using this strategy, we implemented four different exchange processes to report the concentrations of clinically relevant human α-thrombin and vascular endothelial growth factor using changes in concentrations of DNA oligonucleotide outputs. These exchange processes can operate in tandem such that the same or different output signals can indicate changes in concentration of distinct or identical input proteins. The simplicity of our approach suggests a pathway to build devices that can direct diverse output responses in response to changes in concentrations of specific proteins.},
doi = {10.1093/nar/gkaa405},
journal = {Nucleic Acids Research},
number = 12,
volume = 48,
place = {United Kingdom},
year = {2020},
month = {5}
}

Journal Article:
Free Publicly Available Full Text
Publisher's Version of Record
DOI: https://doi.org/10.1093/nar/gkaa405

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