Design and Characterization of DNA Strand-Displacement Circuits in Serum-Supplemented Cell Medium
Abstract
The functional stability and lifetimes of synthetic molecular circuits in biological environments are important for long-term, stable sensors or controllers of cell or tissue behavior. DNA-based molecular circuits, particularly DNA strand-displacement circuits, provide simple and effective biocompatible control mechanisms and sensors, but are vulnerable to digestion by nucleases present in living tissues and serum-supplemented cell culture. The stability of double-stranded and single-stranded DNA circuit components in serum-supplemented cell medium and the corresponding effect of nuclease-mediated degradation on circuit performance were characterized to determine the major routes of degradation and DNA strand-displacement circuit failure. Simple circuit design choices, such as the use of 5' toeholds within the DNA complexes used as reactants in the strand-displacement reactions and the termination of single-stranded components with DNA hairpin domains at the 3' termini, significantly increase the functional lifetime of the circuit components in the presence of nucleases. Furthermore, simulations of multireaction circuits, guided by the experimentally measured operation of single-reaction circuits, enable predictive realization of multilayer and competitive-reaction circuit behavior. Altogether, these results provide a basic route to increased DNA circuit stability in cell culture environments.
- Authors:
-
- Johns Hopkins Univ., Baltimore, MD (United States). Chemical and Biomolecular Engineering
- Johns Hopkins Univ., Baltimore, MD (United States). Chemical and Biomolecular Engineering and Computer Science
- Publication Date:
- Research Org.:
- Johns Hopkins Univ., Baltimore, MD (United States)
- Sponsoring Org.:
- USDOE Office of Science (SC), Basic Energy Sciences (BES)
- OSTI Identifier:
- 1363867
- Grant/Contract Number:
- SC0015906
- Resource Type:
- Accepted Manuscript
- Journal Name:
- ACS Synthetic Biology
- Additional Journal Information:
- Journal Volume: 6; Journal Issue: 9; Journal ID: ISSN 2161-5063
- Publisher:
- American Chemical Society (ACS)
- Country of Publication:
- United States
- Language:
- English
- Subject:
- 77 NANOSCIENCE AND NANOTECHNOLOGY; 59 BASIC BIOLOGICAL SCIENCES; degradation; DNA strand displacement; molecular circuits; nuclease; serum
Citation Formats
Fern, Joshua, and Schulman, Rebecca. Design and Characterization of DNA Strand-Displacement Circuits in Serum-Supplemented Cell Medium. United States: N. p., 2017.
Web. doi:10.1021/acssynbio.7b00105.
Fern, Joshua, & Schulman, Rebecca. Design and Characterization of DNA Strand-Displacement Circuits in Serum-Supplemented Cell Medium. United States. https://doi.org/10.1021/acssynbio.7b00105
Fern, Joshua, and Schulman, Rebecca. Tue .
"Design and Characterization of DNA Strand-Displacement Circuits in Serum-Supplemented Cell Medium". United States. https://doi.org/10.1021/acssynbio.7b00105. https://www.osti.gov/servlets/purl/1363867.
@article{osti_1363867,
title = {Design and Characterization of DNA Strand-Displacement Circuits in Serum-Supplemented Cell Medium},
author = {Fern, Joshua and Schulman, Rebecca},
abstractNote = {The functional stability and lifetimes of synthetic molecular circuits in biological environments are important for long-term, stable sensors or controllers of cell or tissue behavior. DNA-based molecular circuits, particularly DNA strand-displacement circuits, provide simple and effective biocompatible control mechanisms and sensors, but are vulnerable to digestion by nucleases present in living tissues and serum-supplemented cell culture. The stability of double-stranded and single-stranded DNA circuit components in serum-supplemented cell medium and the corresponding effect of nuclease-mediated degradation on circuit performance were characterized to determine the major routes of degradation and DNA strand-displacement circuit failure. Simple circuit design choices, such as the use of 5' toeholds within the DNA complexes used as reactants in the strand-displacement reactions and the termination of single-stranded components with DNA hairpin domains at the 3' termini, significantly increase the functional lifetime of the circuit components in the presence of nucleases. Furthermore, simulations of multireaction circuits, guided by the experimentally measured operation of single-reaction circuits, enable predictive realization of multilayer and competitive-reaction circuit behavior. Altogether, these results provide a basic route to increased DNA circuit stability in cell culture environments.},
doi = {10.1021/acssynbio.7b00105},
journal = {ACS Synthetic Biology},
number = 9,
volume = 6,
place = {United States},
year = {Tue May 30 00:00:00 EDT 2017},
month = {Tue May 30 00:00:00 EDT 2017}
}
Web of Science
Works referenced in this record:
Enzyme-Free Nucleic Acid Logic Circuits
journal, December 2006
- Seelig, G.; Soloveichik, D.; Zhang, D. Y.
- Science, Vol. 314, Issue 5805
Cellular Uptake of Tile-Assembled DNA Nanotubes
journal, December 2014
- Kocabey, Samet; Meinl, Hanna; MacPherson, Iain
- Nanomaterials, Vol. 5, Issue 1
Nature-Inspired DNA Nanosensor for Real-Time in Situ Detection of mRNA in Living Cells
journal, April 2015
- Tay, Chor Yong; Yuan, Liang; Leong, David Tai
- ACS Nano, Vol. 9, Issue 5
Modified deoxyoligonucleotides stable to exonuclease degradation in serum
journal, January 1991
- Shaw, Jeng-Pyng; Kent, Kenneth; Bird, Jeff
- Nucleic Acids Research, Vol. 19, Issue 4
Stability of DNA Origami Nanoarrays in Cell Lysate
journal, April 2011
- Mei, Qian; Wei, Xixi; Su, Fengyu
- Nano Letters, Vol. 11, Issue 4
Addressing the Instability of DNA Nanostructures in Tissue Culture
journal, August 2014
- Hahn, Jaeseung; Wickham, Shelley F. J.; Shih, William M.
- ACS Nano, Vol. 8, Issue 9
Antisense hairpin loop oligonucleotides as inhibitors of expression of multidrug resistance-associated protein 1: their stability in fetal calf serum and human plasma.
journal, December 2001
- Rebowski, G.; Wójcik, M.; Boczkowska, M.
- Acta Biochimica Polonica, Vol. 48, Issue 4
A Molecular Translator that Acts by Binding-Induced DNA Strand Displacement for a Homogeneous Protein Assay
journal, August 2012
- Li, Feng; Zhang, Hongquan; Lai, Chong
- Angewandte Chemie International Edition, Vol. 51, Issue 37
The Thermodynamics of DNA Structural Motifs
journal, June 2004
- SantaLucia, John; Hicks, Donald
- Annual Review of Biophysics and Biomolecular Structure, Vol. 33, Issue 1
EDTA-mediated inhibition of DNases protects circulating cell-free DNA from ex vivo degradation in blood samples
journal, October 2015
- Barra, Gustavo Barcelos; Santa Rita, Ticiane Henriques; Vasques, Júlia de Almeida
- Clinical Biochemistry, Vol. 48, Issue 15
Programmable in situ amplification for multiplexed imaging of mRNA expression
journal, October 2010
- Choi, Harry M. T.; Chang, Joann Y.; Trinh, Le A.
- Nature Biotechnology, Vol. 28, Issue 11
DNA topology influences molecular machine lifetime in human serum
journal, January 2015
- Goltry, Sara; Hallstrom, Natalya; Clark, Tyler
- Nanoscale, Vol. 7, Issue 23
Computing in mammalian cells with nucleic acid strand exchange
journal, December 2015
- Groves, Benjamin; Chen, Yuan-Jyue; Zurla, Chiara
- Nature Nanotechnology, Vol. 11, Issue 3
Programmable Release of Multiple Protein Drugs from Aptamer-Functionalized Hydrogels via Nucleic Acid Hybridization
journal, July 2012
- Battig, Mark R.; Soontornworajit, Boonchoy; Wang, Yong
- Journal of the American Chemical Society, Vol. 134, Issue 30
Predicting Stability of DNA Duplexes in Solutions Containing Magnesium and Monovalent Cations
journal, May 2008
- Owczarzy, Richard; Moreira, Bernardo G.; You, Yong
- Biochemistry, Vol. 47, Issue 19
DNA nanotubes as intracellular delivery vehicles in vivo
journal, June 2015
- Sellner, Sabine; Kocabey, Samet; Nekolla, Katharina
- Biomaterials, Vol. 53
Substrate Specificity and Kinetics of Degradation of Antisense Oligonucleotides by a 3′ Exonuclease in Plasma
journal, January 1991
- Eder, Paul S.; DeVINE, Rene J.; Dagle, John M.
- Antisense Research and Development, Vol. 1, Issue 2
Mechanical Properties of a Reversible, DNA-Crosslinked Polyacrylamide Hydrogel
journal, February 2004
- Lin, David C.; Yurke, Bernard; Langrana, Noshir A.
- Journal of Biomechanical Engineering, Vol. 126, Issue 1
Kinetic Studies of DNA Cleavage Reactions Catalyzed by an ATP-Dependent Deoxyribonuclease on a 27-MHz Quartz-Crystal Microbalance
journal, January 2005
- Matsuno, Hisao; Furusawa, Hiroyuki; Okahata, Yoshio
- Biochemistry, Vol. 44, Issue 7
Hairpin DNAzymes: a new tool for efficient cellular gene silencing
journal, August 2007
- Abdelgany, Amr; Wood, Matthew; Beeson, David
- The Journal of Gene Medicine, Vol. 9, Issue 8
The Interaction of Bovine Pancreatic Deoxyribonuclease I and Skeletal Muscle Actin
journal, March 1980
- Mannherz, Hans Georg; Goody, Roger S.; Konrad, Manfred
- European Journal of Biochemistry, Vol. 104, Issue 2
Effect of Dynamic Stiffness of the Substrates on Neurite Outgrowth by Using a DNA-Crosslinked Hydrogel
journal, June 2010
- Jiang, Frank Xue; Yurke, Bernard; Schloss, Rene S.
- Tissue Engineering Part A, Vol. 16, Issue 6
Programmable Hydrogels for Controlled Cell Catch and Release Using Hybridized Aptamers and Complementary Sequences
journal, September 2012
- Zhang, Zhaoyang; Chen, Niancao; Li, Shihui
- Journal of the American Chemical Society, Vol. 134, Issue 38
Controlling DNA–nanoparticle serum interactions
journal, November 2016
- Zagorovsky, Kyryl; Chou, Leo Y. T.; Chan, Warren C. W.
- Proceedings of the National Academy of Sciences, Vol. 113, Issue 48
Aptamer based reversible DNA induced hydrogel system for molecular recognition and separation
journal, January 2010
- He, Xiaojin; Wei, Bryan; Mi, Yongli
- Chemical Communications, Vol. 46, Issue 34
Autonomous molecular cascades for evaluation of cell surfaces
journal, July 2013
- Rudchenko, Maria; Taylor, Steven; Pallavi, Payal
- Nature Nanotechnology, Vol. 8, Issue 8
Programmable chemical controllers made from DNA
journal, September 2013
- Chen, Yuan-Jyue; Dalchau, Neil; Srinivas, Niranjan
- Nature Nanotechnology, Vol. 8, Issue 10
Engineering Entropy-Driven Reactions and Networks Catalyzed by DNA
journal, November 2007
- Zhang, D. Y.; Turberfield, A. J.; Yurke, B.
- Science, Vol. 318, Issue 5853
Immunochemical assay for deoxyribonuclease activity in body fluids
journal, August 2007
- Cherepanova, Anna; Tamkovich, Svetlana; Pyshnyi, Dmitrii
- Journal of Immunological Methods, Vol. 325, Issue 1-2
Enhanced resistance of DNA nanostructures to enzymatic digestion
journal, January 2009
- Keum, Jung-Won; Bermudez, Harry
- Chemical Communications, Issue 45
Actin Is the Naturally Occurring Inhibitor of Deoxyribonuclease I
journal, December 1974
- Lazarides, E.; Lindberg, U.
- Proceedings of the National Academy of Sciences, Vol. 71, Issue 12
Scaling Up Digital Circuit Computation with DNA Strand Displacement Cascades
journal, June 2011
- Qian, L.; Winfree, E.
- Science, Vol. 332, Issue 6034
DNA Strand-Displacement Timer Circuits
journal, October 2016
- Fern, Joshua; Scalise, Dominic; Cangialosi, Angelo
- ACS Synthetic Biology, Vol. 6, Issue 2
Control of DNA Strand Displacement Kinetics Using Toehold Exchange
journal, December 2009
- Zhang, David Yu; Winfree, Erik
- Journal of the American Chemical Society, Vol. 131, Issue 47
DNA Computation in Mammalian Cells: MicroRNA Logic Operations
journal, May 2013
- Hemphill, James; Deiters, Alexander
- Journal of the American Chemical Society, Vol. 135, Issue 28
Studies on the Mechanism of Stabilization of Partially Phosphorothioated Oligonucleotides Against Nucleolytic Degradation
journal, August 1997
- Uhlmann, Eugen; Ryte, Antonina; Peyman, Anusch
- Antisense and Nucleic Acid Drug Development, Vol. 7, Issue 4
Operation of a DNA-Based Autocatalytic Network in Serum
book, January 2011
- Graugnard, Elton; Cox, Amber; Lee, Jeunghoon
- Lecture Notes in Computer Science
Works referencing / citing this record:
Five Inputs Code Lock Circuit Design Based on DNA Strand Displacement Mechanism
journal, November 2019
- Li, Jixiang; Li, Yurong; Sun, Junwei
- Nano, Vol. 14, Issue 11
Synthetic Gene Expression Circuits for Designing Precision Tools in Oncology
journal, August 2017
- Re, Angela
- Frontiers in Cell and Developmental Biology, Vol. 5
Computing with biological switches and clocks
journal, June 2018
- Dalchau, Neil; Szép, Gregory; Hernansaiz-Ballesteros, Rosa
- Natural Computing, Vol. 17, Issue 4
Heterochiral nucleic acid circuits
journal, August 2019
- Kabza, Adam M.; Young, Brian E.; Kundu, Nandini
- Emerging Topics in Life Sciences, Vol. 3, Issue 5
Cell-Free Synthetic Biology Platform for Engineering Synthetic Biological Circuits and Systems
journal, May 2019
- Jeong, Dohyun; Klocke, Melissa; Agarwal, Siddharth
- Methods and Protocols, Vol. 2, Issue 2
Synthetic Gene Expression Circuits for Designing Precision Tools in Oncology
journal, August 2017
- Re, Angela
- Frontiers in Cell and Developmental Biology, Vol. 5
DNA-based communication in populations of synthetic protocells
journal, March 2019
- Joesaar, Alex; Yang, Shuo; Bögels, Bas
- Nature Nanotechnology, Vol. 14, Issue 4
A supramolecular five-component relay switch that exposes the mechanistic competition of dissociative versus associative binding to cucurbiturils by ratiometric fluorescence monitoring
journal, January 2019
- Liu, Yan-Cen; Nau, Werner M.; Hennig, Andreas
- Chemical Communications, Vol. 55, Issue 94
Computing with biological switches and clocks
journal, June 2018
- Dalchau, Neil; Szép, Gregory; Hernansaiz-Ballesteros, Rosa
- Natural Computing, Vol. 17, Issue 4
A Molecular Hero Suit for In Vitro and In Vivo DNA Nanostructures
journal, February 2019
- Kizer, Megan E.; Linhardt, Robert J.; Chandrasekaran, Arun Richard
- Small, Vol. 15, Issue 26
Cell-Free Synthetic Biology Platform for Engineering Synthetic Biological Circuits and Systems
journal, May 2019
- Jeong, Dohyun; Klocke, Melissa; Agarwal, Siddharth
- Methods and Protocols, Vol. 2, Issue 2