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Sugawara T, Oishi M. Latent Toehold-Mediated DNA Circuits Based on a Bulge-Loop Structure for Leakage Reduction and Its Application to Signal-Amplifying DNA Logic Gates. ACS APPLIED MATERIALS & INTERFACES 2024; 16:15907-15915. [PMID: 38508218 DOI: 10.1021/acsami.3c19344] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 03/22/2024]
Abstract
DNA circuits based on successive toehold-mediated DNA displacement reactions, particularly entropy-driven DNA circuit (EDC) systems, have attracted considerable attention as powerful enzyme-free tools for dynamic DNA nanotechnology. However, background leakage (noise signal) often occurs when the circuit is executed nonspecifically, even in the absence of the appropriate catalyst DNA (input). This study designed and developed a new latent toehold-mediated DNA circuit (LDC) system that relies on a bulge-loop structure as a latent toehold toward leakage reduction. Furthermore, the number (size) of nucleotides (nt) in the bulge-loop is found to play a significant role in the performance (i.e., leakage, signal, and kinetics) of LDC systems. In fact, the signal rate for the LDC systems increased as the number of nt in the bulge-loop increased from 4 to 8, whereas the leakage rate of the LDC systems with bulge-loops of 7 nt or less was low, but the leakage rate of the LDC system with a bulge-loop of 8 nt increased significantly. Note that the LDC system with the optimal bulge-loop (7 nt) was capable of not only reducing the leakage but also accelerating the circuit speed without any signal loss, unlike methods of reducing the leakage by reducing the signal reported previously for the conventional EDC systems. These facts indicate that the 7 nt bulge-loop acts as a "latent" toehold for the DNA circuit system. By using the amplification function of output signals with an accelerated circuit and reduced leakage, our LDC system with a 7 nt bulge-loop could be applied directly and successfully to signal-amplifying DNA logic gates such as OR and AND gates, and thus, sufficient output signals could be obtained even with a small amount of input. These findings reveal that our LDC systems with a bulge-loop structure can replace the conventional EDC system and have enormous potential in the field of DNA nanotechnology.
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Affiliation(s)
- Taku Sugawara
- Department of Materials Science, Faculty of Pure and Applied Sciences, University of Tsukuba, 1-1-1 Tennoudai, Tsukuba, Ibaraki 305-8573, Japan
| | - Motoi Oishi
- Department of Materials Science, Faculty of Pure and Applied Sciences, University of Tsukuba, 1-1-1 Tennoudai, Tsukuba, Ibaraki 305-8573, Japan
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2
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Tobiason M, Yurke B, Hughes WL. Generation of DNA oligomers with similar chemical kinetics via in-silico optimization. Commun Chem 2023; 6:226. [PMID: 37853171 PMCID: PMC10584830 DOI: 10.1038/s42004-023-01026-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2023] [Accepted: 10/10/2023] [Indexed: 10/20/2023] Open
Abstract
Networks of interacting DNA oligomers are useful for applications such as biomarker detection, targeted drug delivery, information storage, and photonic information processing. However, differences in the chemical kinetics of hybridization reactions, referred to as kinetic dispersion, can be problematic for some applications. Here, it is found that limiting unnecessary stretches of Watson-Crick base pairing, referred to as unnecessary duplexes, can yield exceptionally low kinetic dispersions. Hybridization kinetics can be affected by unnecessary intra-oligomer duplexes containing only 2 base-pairs, and such duplexes explain up to 94% of previously reported kinetic dispersion. As a general design rule, it is recommended that unnecessary intra-oligomer duplexes larger than 2 base-pairs and unnecessary inter-oligomer duplexes larger than 7 base-pairs be avoided. Unnecessary duplexes typically scale exponentially with network size, and nearly all networks contain unnecessary duplexes substantial enough to affect hybridization kinetics. A new method for generating networks which utilizes in-silico optimization to mitigate unnecessary duplexes is proposed and demonstrated to reduce in-vitro kinetic dispersions as much as 96%. The limitations of the new design rule and generation method are evaluated in-silico by creating new oligomers for several designs, including three previously programmed reactions and one previously engineered structure.
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Affiliation(s)
- Michael Tobiason
- Department of Computer Science, Boise State University, Boise, ID, USA.
- Micron School of Materials Science & Engineering, Boise State University, Boise, ID, USA.
| | - Bernard Yurke
- Micron School of Materials Science & Engineering, Boise State University, Boise, ID, USA
- Department of Electrical & Computer Engineering, Boise State University, Boise, ID, USA
| | - William L Hughes
- School of Engineering, University of British Columbia Okanagan Campus, Kelowna, BC, Canada.
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Lysne D, Hachigian T, Thachuk C, Lee J, Graugnard E. Leveraging Steric Moieties for Kinetic Control of DNA Strand Displacement Reactions. J Am Chem Soc 2023. [PMID: 37487322 PMCID: PMC10401717 DOI: 10.1021/jacs.3c04344] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 07/26/2023]
Abstract
DNA strand displacement networks are a critical part of dynamic DNA nanotechnology and are proven primitives for implementing chemical reaction networks. Precise kinetic control of these networks is important for their use in a range of applications. Among the better understood and widely leveraged kinetic properties of these networks are toehold sequence, length, composition, and location. While steric hindrance has been recognized as an important factor in such systems, a clear understanding of its impact and role is lacking. Here, a systematic investigation of steric hindrance within a DNA toehold-mediated strand displacement network was performed through tracking kinetic reactions of reporter complexes with incremental concatenation of steric moieties near the toehold. Two subsets of steric moieties were tested with systematic variation of structures and reaction conditions to isolate sterics from electrostatics. Thermodynamic and coarse-grained computational modeling was performed to gain further insight into the impacts of steric hindrance. Steric factors yielded up to 3 orders of magnitude decrease in the reaction rate constant. This pronounced effect demonstrates that steric moieties can be a powerful tool for kinetic control in strand displacement networks while also being more broadly informative of DNA structural assembly in both DNA-based therapeutic and diagnostic applications that possess elements of steric hindrance through DNA functionalization with an assortment of chemistries.
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Affiliation(s)
- Drew Lysne
- Micron School of Materials Science and Engineering, Boise State University, 1910 University Dr., Boise, Idaho 83725, United States
| | - Tim Hachigian
- Micron School of Materials Science and Engineering, Boise State University, 1910 University Dr., Boise, Idaho 83725, United States
| | - Chris Thachuk
- Paul G Allen School of Computer Science and Engineering, University of Washington, Paul G. Allen Center, Box 352350, 185 E Stevens Way NE, Seattle, Washington 98195-2350, United States
| | - Jeunghoon Lee
- Micron School of Materials Science and Engineering, Boise State University, 1910 University Dr., Boise, Idaho 83725, United States
- Department of Chemistry and Biochemistry, Boise State University, 1910 University Dr., Boise, Idaho 83725, United States
| | - Elton Graugnard
- Micron School of Materials Science and Engineering, Boise State University, 1910 University Dr., Boise, Idaho 83725, United States
- Center for Advanced Energy Studies, Idaho Falls, Idaho 83401, United States
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Chu Y, Xiao SJ, Zhu JJ. Rapid Signal Amplification Based on Planetary Cross-Catalytic Hairpin Assembly Reactions. Anal Chem 2023; 95:4317-4324. [PMID: 36826784 DOI: 10.1021/acs.analchem.2c04374] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/25/2023]
Abstract
Non-enzymatic nucleic acid catalytic systems based on branch migration have been developed, with applications ranging from biological sensing to molecular computation. A scalable planetary cross-catalytic (PCC) system is built up in this work by cross-cascading three planetary catalytic hairpin assembly (CHA) reactions with a central three-arm-branched CHA reaction. With the bottom-up hierarchy strategy, we designed four levels of catalytic reactions, simple CHA reactions, two-layered linear cascades, conventional one-planetary PCC reactions, and two- and three-planetary PCC reactions, and examined the reaction products and intermediates in each level via native polyacrylamide gel electrophoresis. The gel shift assay optimized the designs of hairpin strands to keep the leaking reactions at a manageable level and protect against signal attenuation during serial signal transduction in nucleic acid circuits. The reaction kinetics, measured via fluorescence, are strongly dependent on the number of planetary reactions. As a result, the three-planetary PCC system achieved an exponential amplification factor of about 3k, while the conventional one-planetary cross-catalytic system has an amplification factor of 2k (k represents the cycling number). Finally, we demonstrated the rapid detection of a cancer biomarker, microRNA141, used as the catalyst in a two-planetary PCC system. We envision that the PCC systems could be applied in biological signal transduction, biocomputing, rapid detection of single- and multi-target nucleic acid probes, etc.
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Affiliation(s)
- Yanxin Chu
- State Key Laboratory of Analytical Chemistry for Life Science, School of Chemistry and Chemical Engineering, Nanjing University, Nanjing, Jiangsu 210023, China
| | - Shou-Jun Xiao
- State Key Laboratory of Coordination Chemistry, School of Chemistry and Chemical Engineering, Nanjing University, Nanjing 210023, China
| | - Jun-Jie Zhu
- State Key Laboratory of Analytical Chemistry for Life Science, School of Chemistry and Chemical Engineering, Nanjing University, Nanjing, Jiangsu 210023, China
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Dorsey PJ, Scalise D, Schulman R. A model of spatio-temporal regulation within biomaterials using DNA reaction-diffusion waveguides. ROYAL SOCIETY OPEN SCIENCE 2022; 9:220200. [PMID: 36016917 PMCID: PMC9399693 DOI: 10.1098/rsos.220200] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 02/17/2022] [Accepted: 08/03/2022] [Indexed: 06/15/2023]
Abstract
In multi-cellular organisms, cells and tissues coordinate biochemical signal propagation across length scales spanning micrometres to metres. Designing synthetic materials with similar capacities for coordinated signal propagation could allow these systems to adaptively regulate themselves across space and over time. Here, we combine ideas from cell signalling and electronic circuitry to propose a biochemical waveguide that transmits information in the form of a concentration of a DNA species on a directed path. The waveguide could be seamlessly integrated into a soft material because there is virtually no difference between the chemical or physical properties of the waveguide and the material it is embedded within. We propose the design of DNA strand displacement reactions to construct the system and, using reaction-diffusion models, identify kinetic and diffusive parameters that enable super-diffusive transport of DNA species via autocatalysis. Finally, to support experimental waveguide implementation, we propose a sink reaction and spatially inhomogeneous DNA concentrations that could mitigate the spurious amplification of an autocatalyst within the waveguide, allowing for controlled waveguide triggering. Chemical waveguides could facilitate the design of synthetic biomaterials with distributed sensing machinery integrated throughout their structure and enable coordinated self-regulating programmes triggered by changing environmental conditions.
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Affiliation(s)
- Phillip J. Dorsey
- Department of Chemical and Biomolecular Engineering, Johns Hopkins University, 3400 North Charles Street, Baltimore, MD 21218, USA
| | - Dominic Scalise
- Department of Chemical and Biomolecular Engineering, Johns Hopkins University, 3400 North Charles Street, Baltimore, MD 21218, USA
| | - Rebecca Schulman
- Department of Chemical and Biomolecular Engineering, Johns Hopkins University, 3400 North Charles Street, Baltimore, MD 21218, USA
- Department of Computer Science, Johns Hopkins University, 3400 North Charles Street, Baltimore, MD 21218, USA
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Hachigian T, Lysne D, Graugnard E, Lee J. Customizable Aptamer Transducer Network Designed for Feed-Forward Coupling. ACS OMEGA 2021; 6:26888-26896. [PMID: 34693110 PMCID: PMC8529589 DOI: 10.1021/acsomega.1c03146] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/15/2021] [Accepted: 09/24/2021] [Indexed: 05/28/2023]
Abstract
Solution-based biosensors that utilize aptamers have been engineered in a variety of formats to detect a range of analytes for both medical and environmental applications. However, since aptamers have fixed base sequences, incorporation of aptamers into DNA strand displacement networks for feed-forward signal amplification and processing requires significant redesign of downstream DNA reaction networks. We designed a novel aptamer transduction network that releases customizable output domains, which can then be used to initiate downstream strand displacement reaction networks without any sequence redesign of the downstream reaction networks. In our aptamer transducer (AT), aptamer input domains are independent of output domains within the same DNA complex and are reacted with a fuel strand after aptamer-ligand binding. ATs were designed to react with two fluorescent dye-labeled reporter complexes to show the customizability of the output domains, as well as being used as feed-forward inputs to two previously studied catalytic reaction networks, which can be used as amplifiers. Through our study, we show both successful customizability and feed-forward capability of our ATs.
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Affiliation(s)
- Tim Hachigian
- Micron
School of Materials Science and Engineering, Boise State University, 1910 University Dr., Boise, Idaho 83725, United
States
| | - Drew Lysne
- Micron
School of Materials Science and Engineering, Boise State University, 1910 University Dr., Boise, Idaho 83725, United
States
| | - Elton Graugnard
- Micron
School of Materials Science and Engineering, Boise State University, 1910 University Dr., Boise, Idaho 83725, United
States
| | - Jeunghoon Lee
- Micron
School of Materials Science and Engineering, Boise State University, 1910 University Dr., Boise, Idaho 83725, United
States
- Department
of Chemistry and Biochemistry, Boise State
University, 1910 University
Dr., Boise, Idaho 83725, United States
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Bertucci A, Porchetta A, Del Grosso E, Patiño T, Idili A, Ricci F. Protein‐Controlled Actuation of Dynamic Nucleic Acid Networks by Using Synthetic DNA Translators**. Angew Chem Int Ed Engl 2020. [DOI: 10.1002/ange.202008553] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
Affiliation(s)
- Alessandro Bertucci
- Department of Chemistry University of Rome Tor Vergata Via della Ricerca Scientifica 00133 Rome Italy
| | - Alessandro Porchetta
- Department of Chemistry University of Rome Tor Vergata Via della Ricerca Scientifica 00133 Rome Italy
| | - Erica Del Grosso
- Department of Chemistry University of Rome Tor Vergata Via della Ricerca Scientifica 00133 Rome Italy
| | - Tania Patiño
- Department of Chemistry University of Rome Tor Vergata Via della Ricerca Scientifica 00133 Rome Italy
| | - Andrea Idili
- Catalan Institute of Nanoscience and Nanotechnology (ICN2) Campus UAB Bellaterra 08193 Barcelona Spain
| | - Francesco Ricci
- Department of Chemistry University of Rome Tor Vergata Via della Ricerca Scientifica 00133 Rome Italy
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Bertucci A, Porchetta A, Del Grosso E, Patiño T, Idili A, Ricci F. Protein-Controlled Actuation of Dynamic Nucleic Acid Networks by Using Synthetic DNA Translators*. Angew Chem Int Ed Engl 2020; 59:20577-20581. [PMID: 32737920 DOI: 10.1002/anie.202008553] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2020] [Revised: 07/22/2020] [Indexed: 12/20/2022]
Abstract
Integrating dynamic DNA nanotechnology with protein-controlled actuation will expand our ability to process molecular information. We have developed a strategy to actuate strand displacement reactions using DNA-binding proteins by engineering synthetic DNA translators that convert specific protein-binding events into trigger inputs through a programmed conformational change. We have constructed synthetic DNA networks responsive to two different DNA-binding proteins, TATA-binding protein and Myc-Max, and demonstrated multi-input activation of strand displacement reactions. We achieved protein-controlled regulation of a synthetic RNA and of an enzyme through artificial DNA-based communication, showing the potential of our molecular system in performing further programmable tasks.
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Affiliation(s)
- Alessandro Bertucci
- Department of Chemistry, University of Rome Tor Vergata, Via della Ricerca Scientifica, 00133, Rome, Italy
| | - Alessandro Porchetta
- Department of Chemistry, University of Rome Tor Vergata, Via della Ricerca Scientifica, 00133, Rome, Italy
| | - Erica Del Grosso
- Department of Chemistry, University of Rome Tor Vergata, Via della Ricerca Scientifica, 00133, Rome, Italy
| | - Tania Patiño
- Department of Chemistry, University of Rome Tor Vergata, Via della Ricerca Scientifica, 00133, Rome, Italy
| | - Andrea Idili
- Catalan Institute of Nanoscience and Nanotechnology (ICN2), Campus UAB, Bellaterra, 08193, Barcelona, Spain
| | - Francesco Ricci
- Department of Chemistry, University of Rome Tor Vergata, Via della Ricerca Scientifica, 00133, Rome, Italy
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