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:
-
[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
- 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; OSTI ID: 1798465
- 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. https://doi.org/10.1093/nar/gkaa405
Agrawal, Deepak K., and Schulman, Rebecca. Fri .
"Modular protein-oligonucleotide signal exchange". United Kingdom. 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 = {Fri May 22 00:00:00 EDT 2020},
month = {Fri May 22 00:00:00 EDT 2020}
}
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