Modular DNA strand-displacement controllers for directing material expansion

doi:10.1038/s41467-018-06218-w

Title: Modular DNA strand-displacement controllers for directing material expansion

Abstract

Soft materials that swell or change shape in response to external stimuli show extensive promise in regenerative medicine, targeted therapeutics, and soft robotics. Generally, a stimulus for shape change must interact directly with the material, limiting the types of stimuli that may be used and necessitating high stimulus concentrations. Here, we show how DNA strand-displacement controllers within hydrogels can mediate size change by interpreting, amplifying, and integrating stimuli and releasing signals that direct the response. These controllers tune the time scale and degree of DNA-crosslinked hydrogel swelling and can actuate dramatic material size change in response to <100 nM of a specific biomolecular input. Controllers can also direct swelling in response to small molecules or perform logic. The integration of these stimuli-responsive materials with biomolecular circuits is a major step towards autonomous soft robotic systems in which sensing and actuation are implemented by biomolecular reaction networks.

Authors:

;

Publication Date:: 2018-09-14

Research Org.:: Johns Hopkins Univ., Baltimore, MD (United States)

Sponsoring Org.:: USDOE Office of Science (SC)

OSTI Identifier:: 1469248

Alternate Identifier(s):: OSTI ID: 1624113

Grant/Contract Number:: SC0015906; SC0010687

Resource Type:: Published Article

Journal Name:: Nature Communications

Additional Journal Information:: Journal Name: Nature Communications Journal Volume: 9 Journal Issue: 1; Journal ID: ISSN 2041-1723

Publisher:: Nature Publishing Group

Country of Publication:: United Kingdom

Language:: English

Subject:: 59 BASIC BIOLOGICAL SCIENCES; Science & Technology - Other Topics

Citation Formats


                    Fern, Joshua, and Schulman, Rebecca. Modular DNA strand-displacement controllers for directing material expansion.  United Kingdom: N. p., 2018. 
        Web.  doi:10.1038/s41467-018-06218-w.

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                    Fern, Joshua, & Schulman, Rebecca. Modular DNA strand-displacement controllers for directing material expansion.  United Kingdom.  doi:10.1038/s41467-018-06218-w.

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                    Fern, Joshua, and Schulman, Rebecca. Fri .  
        "Modular DNA strand-displacement controllers for directing material expansion".  United Kingdom.  doi:10.1038/s41467-018-06218-w.

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@article{osti_1469248,

  title        = {Modular DNA strand-displacement controllers for directing material expansion},

  author       = {Fern, Joshua and Schulman, Rebecca},

  abstractNote = {Soft materials that swell or change shape in response to external stimuli show extensive promise in regenerative medicine, targeted therapeutics, and soft robotics. Generally, a stimulus for shape change must interact directly with the material, limiting the types of stimuli that may be used and necessitating high stimulus concentrations. Here, we show how DNA strand-displacement controllers within hydrogels can mediate size change by interpreting, amplifying, and integrating stimuli and releasing signals that direct the response. These controllers tune the time scale and degree of DNA-crosslinked hydrogel swelling and can actuate dramatic material size change in response to <100 nM of a specific biomolecular input. Controllers can also direct swelling in response to small molecules or perform logic. The integration of these stimuli-responsive materials with biomolecular circuits is a major step towards autonomous soft robotic systems in which sensing and actuation are implemented by biomolecular reaction networks.},

  doi          = {10.1038/s41467-018-06218-w},

  journal      = {Nature Communications},

  number       = 1,

  volume       = 9,

  place        = {United Kingdom},

  year         = {2018},

  month        = {9}

}

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Title: Modular DNA strand-displacement controllers for directing material expansion

Abstract

Citation Formats

Enzyme-Free Nucleic Acid Logic Circuits journal, December 2006

Enzyme-Triggered Folding of Hydrogels: Toward a Mimic of the Venus Flytrap journal, July 2016

Reversible Logic Circuits Made of DNA journal, December 2011

Modulated degradation of hydrogels with thermo-responsive network in relation to their swelling behavior journal, April 1998

Biomimetic Hydrogel-Based Actuating Systems journal, June 2013

A DNA Aptamer That Binds Adenosine and ATP journal, January 1995

Smart micro/nanoparticles in stimulus-responsive drug/gene delivery systems journal, January 2016

Supramolecular Hydrogel Exhibiting Four Basic Logic Gate Functions To Fine-Tune Substance Release journal, April 2009

Mechanical Properties of a Reversible, DNA-Crosslinked Polyacrylamide Hydrogel journal, February 2004

Stimuli-responsive smart gating membranes journal, January 2016

A biochemical logic approach to biomarker-activated drug release journal, January 2012

Microscopic agents programmed by DNA circuits journal, January 2017

Enzyme-free colorimetric detection systems based on the DNA strand displacement competition reaction journal, May 2016

Structure-Switching Signaling Aptamers: Transducing Molecular Recognition into Fluorescence Signaling journal, April 2004

Chemotactic Response and Adaptation Dynamics in Escherichia coli journal, May 2010

On the biophysics and kinetics of toehold-mediated DNA strand displacement journal, September 2013

Dynamically Reshaping Signaling Networks to Program Cell Fate via Genetic Controllers journal, August 2013

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Cell-signalling dynamics in time and space journal, February 2006

A reversibly antigen-responsive hydrogel journal, June 1999

From The Cover: Triggered amplification by hybridization chain reaction journal, October 2004

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Programming biomolecular self-assembly pathways journal, January 2008

Colorimetric logic gates based on aptamer-crosslinked hydrogels journal, January 2012

Scaling Up Digital Circuit Computation with DNA Strand Displacement Cascades journal, June 2011

Control of DNA Strand Displacement Kinetics Using Toehold Exchange journal, December 2009

An Aptamer Cross-Linked Hydrogel as a Colorimetric Platform for Visual Detection journal, February 2010

Absolute metabolite concentrations and implied enzyme active site occupancy in Escherichia coli journal, June 2009

Stimuli-Responsive Hydrogel Membranes Coupled with Biocatalytic Processes journal, February 2009

Multi-Arm Junctions for Dynamic DNA Nanotechnology journal, May 2017

Signal integration, crosstalk mechanisms and networks in the function of inflammatory cytokines journal, December 2011

Programming colloidal phase transitions with DNA strand displacement journal, February 2015

NUPACK: Analysis and design of nucleic acid systems journal, November 2010

Proteome-pI: proteome isoelectric point database journal, October 2016

Spatially and temporally controlled hydrogels for tissue engineering journal, September 2017

DNA sequence–directed shape change of photopatterned hydrogels via high-degree swelling journal, September 2017

Installing logic-gate responses to a variety of biological substances in supramolecular hydrogel–enzyme hybrids journal, May 2014

DNAzyme crosslinked hydrogel: a new platform for visual detection of metal ions journal, January 2011

Integrating DNA-Strand-Displacement Circuitry with Self-Assembly of Spherical Nucleic Acids journal, November 2015

Preprogramming Complex Hydrogel Responses using Enzymatic Reaction Networks journal, January 2017

Reversible Modulation of DNA-Based Hydrogel Shapes by Internal Stress Interactions journal, December 2016

Engineering Target-Responsive Hydrogels Based on Aptamer−Target Interactions journal, May 2008

Catalyzed Relaxation of a Metastable DNA Fuel journal, September 2006

Stacking nonenzymatic circuits for high signal gain journal, March 2013

Programmable chemical controllers made from DNA journal, September 2013

Preparation of supramolecular hydrogel–enzyme hybrids exhibiting biomolecule-responsive gel degradation journal, August 2016

Circulating microRNAs as stable blood-based markers for cancer detection journal, July 2008

An autonomous polymerization motor powered by DNA hybridization journal, July 2007

DNA Strand-Displacement Timer Circuits journal, October 2016

Diversity in the dynamical behaviour of a compartmentalized programmable biochemical oscillator journal, February 2014

A Nonenzymatic Hairpin DNA Cascade Reaction Provides High Signal Gain of mRNA Imaging inside Live Cells journal, April 2015

Dynamic DNA Structures journal, February 2019

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Enzyme-Free Nucleic Acid Logic Circuits
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Enzyme-Triggered Folding of Hydrogels: Toward a Mimic of the Venus Flytrap
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Reversible Logic Circuits Made of DNA
journal, December 2011

Modulated degradation of hydrogels with thermo-responsive network in relation to their swelling behavior
journal, April 1998

Biomimetic Hydrogel-Based Actuating Systems
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A DNA Aptamer That Binds Adenosine and ATP
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Smart micro/nanoparticles in stimulus-responsive drug/gene delivery systems
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Supramolecular Hydrogel Exhibiting Four Basic Logic Gate Functions To Fine-Tune Substance Release
journal, April 2009

Mechanical Properties of a Reversible, DNA-Crosslinked Polyacrylamide Hydrogel
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Stimuli-responsive smart gating membranes
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A biochemical logic approach to biomarker-activated drug release
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journal, September 2013

Dynamically Reshaping Signaling Networks to Program Cell Fate via Genetic Controllers
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journal, June 1999

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Near-Infrared Light-Responsive Core–Shell Nanogels for Targeted Drug Delivery
journal, May 2011

Programming biomolecular self-assembly pathways
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Control of DNA Strand Displacement Kinetics Using Toehold Exchange
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Absolute metabolite concentrations and implied enzyme active site occupancy in Escherichia coli
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Multi-Arm Junctions for Dynamic DNA Nanotechnology
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journal, December 2011

Programming colloidal phase transitions with DNA strand displacement
journal, February 2015

NUPACK: Analysis and design of nucleic acid systems
journal, November 2010

Proteome-pI: proteome isoelectric point database
journal, October 2016

Spatially and temporally controlled hydrogels for tissue engineering
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Installing logic-gate responses to a variety of biological substances in supramolecular hydrogel–enzyme hybrids
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Preprogramming Complex Hydrogel Responses using Enzymatic Reaction Networks
journal, January 2017

Reversible Modulation of DNA-Based Hydrogel Shapes by Internal Stress Interactions
journal, December 2016

Engineering Target-Responsive Hydrogels Based on Aptamer−Target Interactions
journal, May 2008

Catalyzed Relaxation of a Metastable DNA Fuel
journal, September 2006

Stacking nonenzymatic circuits for high signal gain
journal, March 2013

Programmable chemical controllers made from DNA
journal, September 2013

Preparation of supramolecular hydrogel–enzyme hybrids exhibiting biomolecule-responsive gel degradation
journal, August 2016

Circulating microRNAs as stable blood-based markers for cancer detection
journal, July 2008

An autonomous polymerization motor powered by DNA hybridization
journal, July 2007

DNA Strand-Displacement Timer Circuits
journal, October 2016

Diversity in the dynamical behaviour of a compartmentalized programmable biochemical oscillator
journal, February 2014

A Nonenzymatic Hairpin DNA Cascade Reaction Provides High Signal Gain of mRNA Imaging inside Live Cells
journal, April 2015

Dynamic DNA Structures
journal, February 2019

Dynamic Nanostructures from DNA‐Coupled Molecules, Polymers, and Nanoparticles
journal, February 2019

Boron nitride/agarose hydrogel composites with high thermal conductivities
journal, September 2019

Aptamer-Functionalized DNA Nanostructures for Biological Applications
journal, February 2020

Building in vitro transcriptional regulatory networks by successively integrating multiple functional circuit modules
journal, August 2019

Morpholino Target Molecular Properties Affect the Swelling Process of Oligomorpholino-Functionalized Responsive Hydrogels
journal, January 2020