Design and Characterization of DNA Strand-Displacement Circuits in Serum-Supplemented Cell Medium

Fern, Joshua; Schulman, Rebecca

doi:10.1021/acssynbio.7b00105

Design and Characterization of DNA Strand-Displacement Circuits in Serum-Supplemented Cell Medium

Journal Article · Tue May 30 00:00:00 EDT 2017 · ACS Synthetic Biology

DOI:https://doi.org/10.1021/acssynbio.7b00105· OSTI ID:1363867

^[1]; ^[2]

Johns Hopkins Univ., Baltimore, MD (United States). Chemical and Biomolecular Engineering; The Johns Hopkins University
Johns Hopkins Univ., Baltimore, MD (United States). Chemical and Biomolecular Engineering and Computer Science

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.

View Accepted Manuscript (DOE)

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

Sponsoring Organization:: USDOE Office of Science (SC), Basic Energy Sciences (BES) (SC-22)

Grant/Contract Number:: SC0015906

OSTI ID:: 1363867

Journal Information:: ACS Synthetic Biology, Journal Name: ACS Synthetic Biology Journal Issue: 9 Vol. 6; ISSN 2161-5063

Publisher:: American Chemical Society (ACS)Copyright Statement

Country of Publication:: United States

Language:: English

References (37)

A Molecular Translator that Acts by Binding-Induced DNA Strand Displacement for a Homogeneous Protein Assay Li, Feng; Zhang, Hongquan; Lai, Chong Angewandte Chemie International Edition, Vol. 51, Issue 37 https://doi.org/10.1002/anie.201202677	journal	August 2012
Hairpin DNAzymes: a new tool for efficient cellular gene silencing Abdelgany, Amr; Wood, Matthew; Beeson, David The Journal of Gene Medicine, Vol. 9, Issue 8 https://doi.org/10.1002/jgm.1061	journal	August 2007
Operation of a DNA-Based Autocatalytic Network in Serum Graugnard, Elton; Cox, Amber; Lee, Jeunghoon Lecture Notes in Computer Science https://doi.org/10.1007/978-3-642-18305-8_8	book	January 2011
DNA nanotubes as intracellular delivery vehicles in vivo Sellner, Sabine; Kocabey, Samet; Nekolla, Katharina Biomaterials, Vol. 53 https://doi.org/10.1016/j.biomaterials.2015.02.099	journal	June 2015
EDTA-mediated inhibition of DNases protects circulating cell-free DNA from ex vivo degradation in blood samples Barra, Gustavo Barcelos; Santa Rita, Ticiane Henriques; Vasques, Júlia de Almeida Clinical Biochemistry, Vol. 48, Issue 15 https://doi.org/10.1016/j.clinbiochem.2015.02.014	journal	October 2015
Immunochemical assay for deoxyribonuclease activity in body fluids Cherepanova, Anna; Tamkovich, Svetlana; Pyshnyi, Dmitrii Journal of Immunological Methods, Vol. 325, Issue 1-2 https://doi.org/10.1016/j.jim.2007.06.004	journal	August 2007
Nature-Inspired DNA Nanosensor for Real-Time in Situ Detection of mRNA in Living Cells Tay, Chor Yong; Yuan, Liang; Leong, David Tai ACS Nano, Vol. 9, Issue 5 https://doi.org/10.1021/acsnano.5b01954	journal	April 2015
DNA Strand-Displacement Timer Circuits Fern, Joshua; Scalise, Dominic; Cangialosi, Angelo ACS Synthetic Biology, Vol. 6, Issue 2 https://doi.org/10.1021/acssynbio.6b00170	journal	October 2016
Kinetic Studies of DNA Cleavage Reactions Catalyzed by an ATP-Dependent Deoxyribonuclease on a 27-MHz Quartz-Crystal Microbalance Matsuno, Hisao; Furusawa, Hiroyuki; Okahata, Yoshio Biochemistry, Vol. 44, Issue 7 https://doi.org/10.1021/bi048486+	journal	January 2005
Predicting Stability of DNA Duplexes in Solutions Containing Magnesium and Monovalent Cations Owczarzy, Richard; Moreira, Bernardo G.; You, Yong Biochemistry, Vol. 47, Issue 19 https://doi.org/10.1021/bi702363u	journal	May 2008
Programmable Release of Multiple Protein Drugs from Aptamer-Functionalized Hydrogels via Nucleic Acid Hybridization Battig, Mark R.; Soontornworajit, Boonchoy; Wang, Yong Journal of the American Chemical Society, Vol. 134, Issue 30 https://doi.org/10.1021/ja305238a	journal	July 2012
Programmable Hydrogels for Controlled Cell Catch and Release Using Hybridized Aptamers and Complementary Sequences Zhang, Zhaoyang; Chen, Niancao; Li, Shihui Journal of the American Chemical Society, Vol. 134, Issue 38 https://doi.org/10.1021/ja307717w	journal	September 2012
DNA Computation in Mammalian Cells: MicroRNA Logic Operations Hemphill, James; Deiters, Alexander Journal of the American Chemical Society, Vol. 135, Issue 28 https://doi.org/10.1021/ja404350s	journal	May 2013
Control of DNA Strand Displacement Kinetics Using Toehold Exchange Zhang, David Yu; Winfree, Erik Journal of the American Chemical Society, Vol. 131, Issue 47 https://doi.org/10.1021/ja906987s	journal	December 2009
Stability of DNA Origami Nanoarrays in Cell Lysate Mei, Qian; Wei, Xixi; Su, Fengyu Nano Letters, Vol. 11, Issue 4 https://doi.org/10.1021/nl1040836	journal	April 2011
Addressing the Instability of DNA Nanostructures in Tissue Culture Hahn, Jaeseung; Wickham, Shelley F. J.; Shih, William M. ACS Nano, Vol. 8, Issue 9 https://doi.org/10.1021/nn503513p	journal	August 2014
Programmable in situ amplification for multiplexed imaging of mRNA expression Choi, Harry M. T.; Chang, Joann Y.; Trinh, Le A. Nature Biotechnology, Vol. 28, Issue 11 https://doi.org/10.1038/nbt.1692	journal	October 2010
Autonomous molecular cascades for evaluation of cell surfaces Rudchenko, Maria; Taylor, Steven; Pallavi, Payal Nature Nanotechnology, Vol. 8, Issue 8 https://doi.org/10.1038/nnano.2013.142	journal	July 2013
Programmable chemical controllers made from DNA Chen, Yuan-Jyue; Dalchau, Neil; Srinivas, Niranjan Nature Nanotechnology, Vol. 8, Issue 10 https://doi.org/10.1038/nnano.2013.189	journal	September 2013
Computing in mammalian cells with nucleic acid strand exchange Groves, Benjamin; Chen, Yuan-Jyue; Zurla, Chiara Nature Nanotechnology, Vol. 11, Issue 3 https://doi.org/10.1038/nnano.2015.278	journal	December 2015
DNA topology influences molecular machine lifetime in human serum Goltry, Sara; Hallstrom, Natalya; Clark, Tyler Nanoscale, Vol. 7, Issue 23 https://doi.org/10.1039/C5NR02283E	journal	January 2015
Enhanced resistance of DNA nanostructures to enzymatic digestion Keum, Jung-Won; Bermudez, Harry Chemical Communications, Issue 45 https://doi.org/10.1039/b917661f	journal	January 2009
Aptamer based reversible DNA induced hydrogel system for molecular recognition and separation He, Xiaojin; Wei, Bryan; Mi, Yongli Chemical Communications, Vol. 46, Issue 34 https://doi.org/10.1039/c0cc01392g	journal	January 2010
Controlling DNA–nanoparticle serum interactions Zagorovsky, Kyryl; Chou, Leo Y. T.; Chan, Warren C. W. Proceedings of the National Academy of Sciences, Vol. 113, Issue 48 https://doi.org/10.1073/pnas.1610028113	journal	November 2016
Actin Is the Naturally Occurring Inhibitor of Deoxyribonuclease I Lazarides, E.; Lindberg, U. Proceedings of the National Academy of Sciences, Vol. 71, Issue 12 https://doi.org/10.1073/pnas.71.12.4742	journal	December 1974
Substrate Specificity and Kinetics of Degradation of Antisense Oligonucleotides by a 3′ Exonuclease in Plasma Eder, Paul S.; DeVINE, Rene J.; Dagle, John M. Antisense Research and Development, Vol. 1, Issue 2 https://doi.org/10.1089/ard.1991.1.141	journal	January 1991
Studies on the Mechanism of Stabilization of Partially Phosphorothioated Oligonucleotides Against Nucleolytic Degradation Uhlmann, Eugen; Ryte, Antonina; Peyman, Anusch Antisense and Nucleic Acid Drug Development, Vol. 7, Issue 4 https://doi.org/10.1089/oli.1.1997.7.345	journal	August 1997
Effect of Dynamic Stiffness of the Substrates on Neurite Outgrowth by Using a DNA-Crosslinked Hydrogel Jiang, Frank Xue; Yurke, Bernard; Schloss, Rene S. Tissue Engineering Part A, Vol. 16, Issue 6 https://doi.org/10.1089/ten.tea.2009.0574	journal	June 2010
Modified deoxyoligonucleotides stable to exonuclease degradation in serum Shaw, Jeng-Pyng; Kent, Kenneth; Bird, Jeff Nucleic Acids Research, Vol. 19, Issue 4 https://doi.org/10.1093/nar/19.4.747	journal	January 1991
The Interaction of Bovine Pancreatic Deoxyribonuclease I and Skeletal Muscle Actin Mannherz, Hans Georg; Goody, Roger S.; Konrad, Manfred European Journal of Biochemistry, Vol. 104, Issue 2 https://doi.org/10.1111/j.1432-1033.1980.tb04437.x	journal	March 1980
Mechanical Properties of a Reversible, DNA-Crosslinked Polyacrylamide Hydrogel Lin, David C.; Yurke, Bernard; Langrana, Noshir A. Journal of Biomechanical Engineering, Vol. 126, Issue 1 https://doi.org/10.1115/1.1645529	journal	February 2004
Enzyme-Free Nucleic Acid Logic Circuits Seelig, G.; Soloveichik, D.; Zhang, D. Y. Science, Vol. 314, Issue 5805 https://doi.org/10.1126/science.1132493	journal	December 2006
Engineering Entropy-Driven Reactions and Networks Catalyzed by DNA Zhang, D. Y.; Turberfield, A. J.; Yurke, B. Science, Vol. 318, Issue 5853 https://doi.org/10.1126/science.1148532	journal	November 2007
Scaling Up Digital Circuit Computation with DNA Strand Displacement Cascades Qian, L.; Winfree, E. Science, Vol. 332, Issue 6034 https://doi.org/10.1126/science.1200520	journal	June 2011
The Thermodynamics of DNA Structural Motifs SantaLucia, John; Hicks, Donald Annual Review of Biophysics and Biomolecular Structure, Vol. 33, Issue 1 https://doi.org/10.1146/annurev.biophys.32.110601.141800	journal	June 2004
Antisense hairpin loop oligonucleotides as inhibitors of expression of multidrug resistance-associated protein 1: their stability in fetal calf serum and human plasma. Rebowski, G.; Wójcik, M.; Boczkowska, M. Acta Biochimica Polonica, Vol. 48, Issue 4 https://doi.org/10.18388/abp.2001_3867	journal	December 2001
Cellular Uptake of Tile-Assembled DNA Nanotubes Kocabey, Samet; Meinl, Hanna; MacPherson, Iain Nanomaterials, Vol. 5, Issue 1 https://doi.org/10.3390/nano5010047	journal	December 2014

Cited By (8)

Computing with biological switches and clocks Dalchau, Neil; Szép, Gregory; Hernansaiz-Ballesteros, Rosa Natural Computing, Vol. 17, Issue 4 https://doi.org/10.1007/s11047-018-9686-x	journal	June 2018
Synthetic Gene Expression Circuits for Designing Precision Tools in Oncology Re, Angela Frontiers in Cell and Developmental Biology, Vol. 5 https://doi.org/10.3389/fcell.2017.00077	journal	August 2017
Cell-Free Synthetic Biology Platform for Engineering Synthetic Biological Circuits and Systems Jeong, Dohyun; Klocke, Melissa; Agarwal, Siddharth Methods and Protocols, Vol. 2, Issue 2 https://doi.org/10.3390/mps2020039	journal	May 2019
A Molecular Hero Suit for In Vitro and In Vivo DNA Nanostructures Kizer, Megan E.; Linhardt, Robert J.; Chandrasekaran, Arun Richard Small, Vol. 15, Issue 26 https://doi.org/10.1002/smll.201805386	journal	February 2019
DNA-based communication in populations of synthetic protocells Joesaar, Alex; Yang, Shuo; Bögels, Bas Nature Nanotechnology, Vol. 14, Issue 4 https://doi.org/10.1038/s41565-019-0399-9	journal	March 2019
A supramolecular five-component relay switch that exposes the mechanistic competition of dissociative versus associative binding to cucurbiturils by ratiometric fluorescence monitoring Liu, Yan-Cen; Nau, Werner M.; Hennig, Andreas Chemical Communications, Vol. 55, Issue 94 https://doi.org/10.1039/c9cc07165b	journal	January 2019
Heterochiral nucleic acid circuits Kabza, Adam M.; Young, Brian E.; Kundu, Nandini Emerging Topics in Life Sciences, Vol. 3, Issue 5 https://doi.org/10.1042/etls20190102	journal	August 2019
Five Inputs Code Lock Circuit Design Based on DNA Strand Displacement Mechanism Li, Jixiang; Li, Yurong; Sun, Junwei Nano, Vol. 14, Issue 11 https://doi.org/10.1142/s1793292019501479	journal	November 2019

Similar Records

Swelling characteristics of DNA polymerization gels

Journal Article · Wed Aug 09 00:00:00 EDT 2023 · Soft Matter · OSTI ID:2420427

Effect of differentiation on the repair of DNA single strand breaks in neuroblastoma cells

Journal Article · Mon Apr 07 00:00:00 EDT 1975 · Biochem. Biophys. Res. Commun.; (United States) · OSTI ID:7187556

Related Subjects

59 BASIC BIOLOGICAL SCIENCES
77 NANOSCIENCE AND NANOTECHNOLOGY
DNA strand displacement
degradation
molecular circuits
nuclease
serum

Design and Characterization of DNA Strand-Displacement Circuits in Serum-Supplemented Cell Medium

Citation Formats

References (37)

Cited By (8)

Similar Records

Related Subjects