1
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Sorrentino D, Ranallo S, Ricci F, Franco E. Developmental assembly of multi-component polymer systems through interconnected synthetic gene networks in vitro. Nat Commun 2024; 15:8561. [PMID: 39362892 PMCID: PMC11452209 DOI: 10.1038/s41467-024-52986-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2024] [Accepted: 09/26/2024] [Indexed: 10/05/2024] Open
Abstract
Living cells regulate the dynamics of developmental events through interconnected signaling systems that activate and deactivate inert precursors. This suggests that similarly, synthetic biomaterials could be designed to develop over time by using chemical reaction networks to regulate the availability of assembling components. Here we demonstrate how the sequential activation or deactivation of distinct DNA building blocks can be modularly coordinated to form distinct populations of self-assembling polymers using a transcriptional signaling cascade of synthetic genes. Our building blocks are DNA tiles that polymerize into nanotubes, and whose assembly can be controlled by RNA molecules produced by synthetic genes that target the tile interaction domains. To achieve different RNA production rates, we use a strategy based on promoter "nicking" and strand displacement. By changing the way the genes are cascaded and the RNA levels, we demonstrate that we can obtain spatially and temporally different outcomes in nanotube assembly, including random DNA polymers, block polymers, and as well as distinct autonomous formation and dissolution of distinct polymer populations. Our work demonstrates a way to construct autonomous supramolecular materials whose properties depend on the timing of molecular instructions for self-assembly, and can be immediately extended to a variety of other nucleic acid circuits and assemblies.
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Affiliation(s)
- Daniela Sorrentino
- Department of Mechanical and Aerospace Engineering, University of California at Los Angeles, Los Angeles, CA, USA
- Department of Chemical Science and Technologies, University of Rome, Tor Vergata, Via della Ricerca Scientifica, Rome, Italy
| | - Simona Ranallo
- Department of Chemical Science and Technologies, University of Rome, Tor Vergata, Via della Ricerca Scientifica, Rome, Italy
| | - Francesco Ricci
- Department of Chemical Science and Technologies, University of Rome, Tor Vergata, Via della Ricerca Scientifica, Rome, Italy.
| | - Elisa Franco
- Department of Mechanical and Aerospace Engineering, University of California at Los Angeles, Los Angeles, CA, USA.
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2
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Schaffter SW, Kengmana E, Fern J, Byrne SR, Schulman R. Strategies to Reduce Promoter-Independent Transcription of DNA Nanostructures and Strand Displacement Complexes. ACS Synth Biol 2024; 13:1964-1977. [PMID: 38885464 DOI: 10.1021/acssynbio.3c00726] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/20/2024]
Abstract
Bacteriophage RNA polymerases, in particular T7 RNA polymerase (RNAP), are well-characterized and popular enzymes for many RNA applications in biotechnology both in vitro and in cellular settings. These monomeric polymerases are relatively inexpensive and have high transcription rates and processivity to quickly produce large quantities of RNA. T7 RNAP also has high promoter-specificity on double-stranded DNA (dsDNA) such that it only initiates transcription downstream of its 17-base promoter site on dsDNA templates. However, there are many promoter-independent T7 RNAP transcription reactions involving transcription initiation in regions of single-stranded DNA (ssDNA) that have been reported and characterized. These promoter-independent transcription reactions are important to consider when using T7 RNAP transcriptional systems for DNA nanotechnology and DNA computing applications, in which ssDNA domains often stabilize, organize, and functionalize DNA nanostructures and facilitate strand displacement reactions. Here we review the existing literature on promoter-independent transcription by bacteriophage RNA polymerases with a specific focus on T7 RNAP, and provide examples of how promoter-independent reactions can disrupt the functionality of DNA strand displacement circuit components and alter the stability and functionality of DNA-based materials. We then highlight design strategies for DNA nanotechnology applications that can mitigate the effects of promoter-independent T7 RNAP transcription. The design strategies we present should have an immediate impact by increasing the rate of success of using T7 RNAP for applications in DNA nanotechnology and DNA computing.
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Affiliation(s)
- Samuel W Schaffter
- Department of Chemical & Biomolecular Engineering, Johns Hopkins University, Baltimore, Maryland 21218, United States
| | - Eli Kengmana
- Department of Chemical & Biomolecular Engineering, Johns Hopkins University, Baltimore, Maryland 21218, United States
| | - Joshua Fern
- Department of Chemical & Biomolecular Engineering, Johns Hopkins University, Baltimore, Maryland 21218, United States
| | - Shane R Byrne
- Department of Chemistry, Johns Hopkins University, Baltimore, Maryland 21218, United States
| | - Rebecca Schulman
- Department of Chemical & Biomolecular Engineering, Johns Hopkins University, Baltimore, Maryland 21218, United States
- Department of Chemistry, Johns Hopkins University, Baltimore, Maryland 21218, United States
- Department of Computer Science, Johns Hopkins University, Baltimore, Maryland 21218, United States
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3
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Samanta A, Baranda Pellejero L, Masukawa M, Walther A. DNA-empowered synthetic cells as minimalistic life forms. Nat Rev Chem 2024; 8:454-470. [PMID: 38750171 DOI: 10.1038/s41570-024-00606-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 04/12/2024] [Indexed: 06/13/2024]
Abstract
Cells, the fundamental units of life, orchestrate intricate functions - motility, adaptation, replication, communication, and self-organization within tissues. Originating from spatiotemporally organized structures and machinery, coupled with information processing in signalling networks, cells embody the 'sensor-processor-actuator' paradigm. Can we glean insights from these processes to construct primitive artificial systems with life-like properties? Using de novo design approaches, what can we uncover about the evolutionary path of life? This Review discusses the strides made in crafting synthetic cells, utilizing the powerful toolbox of structural and dynamic DNA nanoscience. We describe how DNA can serve as a versatile tool for engineering entire synthetic cells or subcellular entities, and how DNA enables complex behaviour, including motility and information processing for adaptive and interactive processes. We chart future directions for DNA-empowered synthetic cells, envisioning interactive systems wherein synthetic cells communicate within communities and with living cells.
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Affiliation(s)
- Avik Samanta
- Life-Like Materials and Systems, Department of Chemistry, University of Mainz, Mainz, Germany.
- Centre for Nanotechnology, Indian Institute of Technology Roorkee, Roorkee, India.
| | | | - Marcos Masukawa
- Life-Like Materials and Systems, Department of Chemistry, University of Mainz, Mainz, Germany
| | - Andreas Walther
- Life-Like Materials and Systems, Department of Chemistry, University of Mainz, Mainz, Germany.
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4
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Gyorgy A. Competition and evolutionary selection among core regulatory motifs in gene expression control. Nat Commun 2023; 14:8266. [PMID: 38092759 PMCID: PMC10719253 DOI: 10.1038/s41467-023-43327-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/04/2023] [Accepted: 11/07/2023] [Indexed: 12/17/2023] Open
Abstract
Gene products that are beneficial in one environment may become burdensome in another, prompting the emergence of diverse regulatory schemes that carry their own bioenergetic cost. By ensuring that regulators are only expressed when needed, we demonstrate that autoregulation generally offers an advantage in an environment combining mutation and time-varying selection. Whether positive or negative feedback emerges as dominant depends primarily on the demand for the target gene product, typically to ensure that the detrimental impact of inevitable mutations is minimized. While self-repression of the regulator curbs the spread of these loss-of-function mutations, self-activation instead facilitates their propagation. By analyzing the transcription network of multiple model organisms, we reveal that reduced bioenergetic cost may contribute to the preferential selection of autoregulation among transcription factors. Our results not only uncover how seemingly equivalent regulatory motifs have fundamentally different impact on population structure, growth dynamics, and evolutionary outcomes, but they can also be leveraged to promote the design of evolutionarily robust synthetic gene circuits.
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Affiliation(s)
- Andras Gyorgy
- Division of Engineering, New York University Abu Dhabi, Abu Dhabi, UAE.
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5
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Gyorgy A, Menezes A, Arcak M. A blueprint for a synthetic genetic feedback optimizer. Nat Commun 2023; 14:2554. [PMID: 37137895 PMCID: PMC10156725 DOI: 10.1038/s41467-023-37903-0] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2022] [Accepted: 04/05/2023] [Indexed: 05/05/2023] Open
Abstract
Biomolecular control enables leveraging cells as biomanufacturing factories. Despite recent advancements, we currently lack genetically encoded modules that can be deployed to dynamically fine-tune and optimize cellular performance. Here, we address this shortcoming by presenting the blueprint of a genetic feedback module to optimize a broadly defined performance metric by adjusting the production and decay rate of a (set of) regulator species. We demonstrate that the optimizer can be implemented by combining available synthetic biology parts and components, and that it can be readily integrated with existing pathways and genetically encoded biosensors to ensure its successful deployment in a variety of settings. We further illustrate that the optimizer successfully locates and tracks the optimum in diverse contexts when relying on mass action kinetics-based dynamics and parameter values typical in Escherichia coli.
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Affiliation(s)
- Andras Gyorgy
- Division of Engineering, New York University Abu Dhabi, Abu Dhabi, UAE.
| | - Amor Menezes
- Department of Mechanical and Aerospace Engineering, University of Florida, Gainesville, FL, USA
| | - Murat Arcak
- Department of Electrical Engineering and Computer Sciences, University of California, Berkeley, CA, USA
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6
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Anastassov S, Filo M, Chang CH, Khammash M. A cybergenetic framework for engineering intein-mediated integral feedback control systems. Nat Commun 2023; 14:1337. [PMID: 36906662 PMCID: PMC10008564 DOI: 10.1038/s41467-023-36863-9] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2022] [Accepted: 02/21/2023] [Indexed: 03/13/2023] Open
Abstract
The ability of biological systems to tightly regulate targeted variables, despite external and internal disturbances, is known as Robust Perfect Adaptation (RPA). Achieved frequently through biomolecular integral feedback controllers at the cellular level, RPA has important implications for biotechnology and its various applications. In this study, we identify inteins as a versatile class of genetic components suitable for implementing these controllers and present a systematic approach for their design. We develop a theoretical foundation for screening intein-based RPA-achieving controllers and a simplified approach for modeling them. We then genetically engineer and test intein-based controllers using commonly used transcription factors in mammalian cells and demonstrate their exceptional adaptation properties over a wide dynamic range. The small size, flexibility, and applicability of inteins across life forms allow us to create a diversity of genetic RPA-achieving integral feedback control systems that can be used in various applications, including metabolic engineering and cell-based therapy.
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Affiliation(s)
- Stanislav Anastassov
- Department of Biosystems Science and Engineering, ETH Zürich, 4058, Basel, Switzerland
| | - Maurice Filo
- Department of Biosystems Science and Engineering, ETH Zürich, 4058, Basel, Switzerland
| | - Ching-Hsiang Chang
- Department of Biosystems Science and Engineering, ETH Zürich, 4058, Basel, Switzerland
| | - Mustafa Khammash
- Department of Biosystems Science and Engineering, ETH Zürich, 4058, Basel, Switzerland.
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7
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Dong J, Willner I. Dynamic Transcription Machineries Guide the Synthesis of Temporally Operating DNAzymes, Gated and Cascaded DNAzyme Catalysis. ACS NANO 2023; 17:687-696. [PMID: 36576858 PMCID: PMC9836355 DOI: 10.1021/acsnano.2c10108] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 10/11/2022] [Accepted: 12/23/2022] [Indexed: 06/17/2023]
Abstract
Transient transcription machineries play important roles in the dynamic modulation of gene expression and the sequestered regulation of cellular networks. The present study emulates such processes by designing artificial reaction modules consisting of transcription machineries that guide the transient synthesis of catalytic DNAzymes, the transient operation of gated DNAzymes, and the temporal activation of an intercommunicated DNAzyme cascade. The reaction modules rely on functional constituents that lead to the triggered activation of transcription machineries in the presence of the nucleoside triphosphates oligonucleotide fuel, yielding the transient formation and dissipative depletion of the intermediate DNAzyme(s) products. The kinetics of the transient DNAzyme networks are computationally simulated, allowing to predict and experimentally validate the performance of the systems under different auxiliary conditions. The study advances the field of systems chemistry by introducing transcription machinery-based networks for the dynamic control over transient catalysis─a primary step toward life-like cellular assemblies.
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8
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Schaffter SW, Chen KL, O'Brien J, Noble M, Murugan A, Schulman R. Standardized excitable elements for scalable engineering of far-from-equilibrium chemical networks. Nat Chem 2022; 14:1224-1232. [PMID: 35927329 DOI: 10.1038/s41557-022-01001-3] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2021] [Accepted: 06/16/2022] [Indexed: 01/01/2023]
Abstract
Engineered far-from-equilibrium synthetic chemical networks that pulse or switch states in response to environmental signals could precisely regulate the kinetics of chemical synthesis or self-assembly. Currently, such networks must be extensively tuned to compensate for the different activities of and unintended reactions between a network's various chemical components. Modular elements with standardized performance could be used to rapidly construct networks with designed functions. Here we develop standardized excitable chemical regulatory elements, termed genelets, and use them to construct complex in vitro transcriptional networks. We develop a protocol for identifying >15 interchangeable genelet elements with uniform performance and minimal crosstalk. These elements can be combined to engineer feedforward and feedback modules whose dynamics match those predicted by a simple kinetic model. Modules can then be rationally integrated and organized into networks that produce tunable temporal pulses and act as multistate switchable memories. Standardized genelet elements, and the workflow to identify more, should make engineering complex far-from-equilibrium chemical dynamics routine.
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Affiliation(s)
- Samuel W Schaffter
- Department of Chemical & Biomolecular Engineering, Johns Hopkins University, Baltimore, MD, USA
| | - Kuan-Lin Chen
- Department of Chemical & Biomolecular Engineering, Johns Hopkins University, Baltimore, MD, USA
| | - Jackson O'Brien
- Department of Physics, University of Chicago, Chicago, IL, USA
| | - Madeline Noble
- Department of Chemical & Biomolecular Engineering, Johns Hopkins University, Baltimore, MD, USA
| | - Arvind Murugan
- Department of Physics, University of Chicago, Chicago, IL, USA
| | - Rebecca Schulman
- Department of Chemical & Biomolecular Engineering, Johns Hopkins University, Baltimore, MD, USA. .,Department of Computer Science, Johns Hopkins University, Baltimore, MD, USA. .,Department of Chemistry, Johns Hopkins University, Baltimore, MD, USA.
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9
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Maeda YT. Negative autoregulation controls size scaling in confined gene expression reactions. Sci Rep 2022; 12:10516. [PMID: 35732682 PMCID: PMC9217826 DOI: 10.1038/s41598-022-14719-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2021] [Accepted: 06/10/2022] [Indexed: 11/09/2022] Open
Abstract
Gene expression via transcription-translation is the most fundamental reaction to sustain biological systems, and complex reactions occur in a small compartment of living cells. There is increasing evidence that physical effects, such as molecular crowding or excluded volume effects of transcriptional-translational machinery, affect the yield of reaction products. On the other hand, transcriptional feedback that controls gene expression during mRNA synthesis is also a vital mechanism that regulates protein synthesis in cells. However, the excluded volume effect of spatial constraints on feedback regulation is not well understood. Here, we study the confinement effect on transcriptional autoregulatory feedbacks of gene expression reactions using a theoretical model. The excluded volume effects between molecules and the membrane interface suppress the gene expression in a small cell-sized compartment. We find that negative feedback regulation at the transcription step mitigates this size-induced gene repression and alters the scaling relation of gene expression level on compartment volume, approaching the regular scaling relation without the steric effect. This recovery of regular size-scaling of gene expression does not appear in positive feedback regulation, suggesting that negative autoregulatory feedback is crucial for maintaining reaction products constant regardless of compartment size in heterogeneous cell populations.
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Affiliation(s)
- Yusuke T Maeda
- Department of Physics, Kyushu University, Motooka 744, Fukuoka, 819-0395, Japan.
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10
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Gyorgy A. Context-Dependent Stability and Robustness of Genetic Toggle Switches with Leaky Promoters. Life (Basel) 2021; 11:life11111150. [PMID: 34833026 PMCID: PMC8624834 DOI: 10.3390/life11111150] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2021] [Revised: 10/21/2021] [Accepted: 10/26/2021] [Indexed: 01/22/2023] Open
Abstract
Multistable switches are ubiquitous building blocks in both systems and synthetic biology. Given their central role, it is thus imperative to understand how their fundamental properties depend not only on the tunable biophysical properties of the switches themselves, but also on their genetic context. To this end, we reveal in this article how these factors shape the essential characteristics of toggle switches implemented using leaky promoters such as their stability and robustness to noise, both at single-cell and population levels. In particular, our results expose the roles that competition for scarce transcriptional and translational resources, promoter leakiness, and cell-to-cell heterogeneity collectively play. For instance, the interplay between protein expression from leaky promoters and the associated cost of relying on shared cellular resources can give rise to tristable dynamics even in the absence of positive feedback. Similarly, we demonstrate that while promoter leakiness always acts against multistability, resource competition can be leveraged to counteract this undesirable phenomenon. Underpinned by a mechanistic model, our results thus enable the context-aware rational design of multistable genetic switches that are directly translatable to experimental considerations, and can be further leveraged during the synthesis of large-scale genetic systems using computer-aided biodesign automation platforms.
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Affiliation(s)
- Andras Gyorgy
- Division of Engineering, New York University Abu Dhabi, Abu Dhabi P.O. Box 129188, United Arab Emirates
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11
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Design of time-delayed safety switches for CRISPR gene therapy. Sci Rep 2021; 11:16908. [PMID: 34413448 PMCID: PMC8377138 DOI: 10.1038/s41598-021-96510-5] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2021] [Accepted: 08/11/2021] [Indexed: 11/16/2022] Open
Abstract
CRISPR system is a powerful gene editing tool which has already been reported to address a variety of gene relevant diseases in different cell lines. However, off-target effect and immune response caused by Cas9 remain two fundamental problems. Inspired by previously reported Cas9 self-elimination systems, time-delayed safety switches are designed in this work. Firstly, ultrasensitive relationship is constructed between Cas9-sgRNA (enzyme) and Cas9 plasmids (substrate), which generates the artificial time delay. Then intrinsic time delay in biomolecular activities is revealed by data fitting and utilized in constructing safety switches. The time-delayed safety switches function by separating the gene editing process and self-elimination process, and the tunable delay time may ensure a good balance between gene editing efficiency and side effect minimization. By addressing gene therapy efficiency, off-target effect, immune response and drug accumulation, we hope our safety switches may offer inspiration in realizing safe and efficient gene therapy in humans.
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12
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Kim J, Quijano JF, Kim J, Yeung E, Murray RM. Synthetic logic circuits using RNA aptamer against T7 RNA polymerase. Biotechnol J 2021; 17:e2000449. [PMID: 33813787 DOI: 10.1002/biot.202000449] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2020] [Revised: 03/05/2021] [Accepted: 03/30/2021] [Indexed: 12/23/2022]
Abstract
Recent advances in nucleic acids engineering introduced several RNA-based regulatory components for synthetic gene circuits, expanding the toolsets to engineer organisms. In this work, we designed genetic circuits implementing an RNA aptamer previously described to have the capability of binding to the T7 RNA polymerase and inhibiting its activity in vitro. We first demonstrated the utility of the RNA aptamer in combination with programmable synthetic transcription networks in vitro. As a step to quickly assess the feasibility of aptamer functions in vivo, we tested the aptamer and its sequence variants in the cell-free expression system, verifying the aptamer functionality in the cell-free testbed. The expression of aptamer in E. coli demonstrated control over GFP expression driven by T7 RNA polymerase, indicating its ability to serve as building blocks for logic circuits and transcriptional cascades. This work elucidates the potential of T7 RNA polymerase aptamer as regulators for synthetic biological circuits and metabolic engineering.
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Affiliation(s)
- Jongmin Kim
- Department of Life Sciences, Pohang University of Science and Technology, Pohang, Gyeongbuk, Republic of Korea.,Department of Biology and Biological Engineering, California Institute of Technology, Pasadena, California, USA
| | - Juan F Quijano
- Department of Biological Sciences, Columbia University, New York, New York, USA
| | - Jeongwon Kim
- Department of Life Sciences, Pohang University of Science and Technology, Pohang, Gyeongbuk, Republic of Korea
| | - Enoch Yeung
- Department of Control and Dynamical Systems, California Institute of Technology, Pasadena, California, USA.,Department of Mechanical Engineering, University of California, Santa Barbara, California, USA
| | - Richard M Murray
- Department of Biology and Biological Engineering, California Institute of Technology, Pasadena, California, USA.,Department of Control and Dynamical Systems, California Institute of Technology, Pasadena, California, USA
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13
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Cuba Samaniego C, Franco E. Ultrasensitive molecular controllers for quasi-integral feedback. Cell Syst 2021; 12:272-288.e3. [PMID: 33539724 DOI: 10.1016/j.cels.2021.01.001] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2019] [Revised: 09/22/2020] [Accepted: 01/11/2021] [Indexed: 12/24/2022]
Abstract
Feedback control has enabled the success of automated technologies by mitigating the effects of variability, unknown disturbances, and noise. While it is known that biological feedback loops reduce the impact of noise and help shape kinetic responses, many questions remain about how to design molecular integral controllers. Here, we propose a modular strategy to build molecular quasi-integral feedback controllers, which involves following two design principles. The first principle is to utilize an ultrasensitive response, which determines the gain of the controller and influences the steady-state error. The second is to use a tunable threshold of the ultrasensitive response, which determines the equilibrium point of the system. We describe a reaction network, named brink controller, that satisfies these conditions by combining molecular sequestration and an activation/deactivation cycle. With computational models, we examine potential biological implementations of brink controllers, and we illustrate different example applications.
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Affiliation(s)
- Christian Cuba Samaniego
- Mechanical and Aerospace Engineering, University of California at Los Angeles, Los Angeles, CA 90095, USA
| | - Elisa Franco
- Mechanical and Aerospace Engineering, University of California at Los Angeles, Los Angeles, CA 90095, USA; Molecular Biology Institute, University of California at Los Angeles, Los Angeles, CA 90095, USA; Bioengineering, University of California at Los Angeles, Los Angeles, CA 90095, USA; Mechanical Engineering, University of California at Riverside, Riverside, CA 92521, USA.
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14
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Schaffter SW, Scalise D, Murphy TM, Patel A, Schulman R. Feedback regulation of crystal growth by buffering monomer concentration. Nat Commun 2020; 11:6057. [PMID: 33247122 PMCID: PMC7695852 DOI: 10.1038/s41467-020-19882-8] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2020] [Accepted: 10/28/2020] [Indexed: 12/26/2022] Open
Abstract
Crystallization is a ubiquitous means of self-assembly that can organize matter over length scales orders of magnitude larger than those of the monomer units. Yet crystallization is notoriously difficult to control because it is exquisitely sensitive to monomer concentration, which changes as monomers are depleted during growth. Living cells control crystallization using chemical reaction networks that offset depletion by synthesizing or activating monomers to regulate monomer concentration, stabilizing growth conditions even as depletion rates change, and thus reliably yielding desired products. Using DNA nanotubes as a model system, here we show that coupling a generic reversible bimolecular monomer buffering reaction to a crystallization process leads to reliable growth of large, uniformly sized crystals even when crystal growth rates change over time. Buffering could be applied broadly as a simple means to regulate and sustain batch crystallization and could facilitate the self-assembly of complex, hierarchical synthetic structures.
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Affiliation(s)
- Samuel W Schaffter
- Chemical & Biomolecular Engineering, Johns Hopkins University, Baltimore, MD, 21218, USA
| | - Dominic Scalise
- Chemical & Biomolecular Engineering, Johns Hopkins University, Baltimore, MD, 21218, USA
| | | | - Anusha Patel
- Chemical & Biomolecular Engineering, Johns Hopkins University, Baltimore, MD, 21218, USA
| | - Rebecca Schulman
- Chemical & Biomolecular Engineering, Johns Hopkins University, Baltimore, MD, 21218, USA.
- Department of Computer Science, Johns Hopkins University, Baltimore, MD, 21218, USA.
- Department of Chemistry, Johns Hopkins University, Baltimore, MD, 21218, USA.
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15
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Schaffter SW, Schulman R. Building in vitro transcriptional regulatory networks by successively integrating multiple functional circuit modules. Nat Chem 2019; 11:829-838. [PMID: 31427767 DOI: 10.1038/s41557-019-0292-z] [Citation(s) in RCA: 61] [Impact Index Per Article: 12.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2018] [Accepted: 06/13/2019] [Indexed: 02/04/2023]
Abstract
The regulation of cellular dynamics and responses to stimuli by genetic regulatory networks suggests how in vitro chemical reaction networks might analogously direct the dynamics of synthetic materials or chemistries. A key step in developing genetic regulatory network analogues capable of this type of sophisticated regulation is the integration of multiple coordinated functions within a single network. Here, we demonstrate how such functional integration can be achieved using in vitro transcriptional genelet circuits that emulate essential features of cellular genetic regulatory networks. By successively incorporating functional genelet modules into a bistable circuit, we construct an integrated regulatory network that dynamically changes its state in response to upstream stimuli and coordinates the timing of downstream signal expression. We use quantitative models to guide module integration and develop strategies to mitigate undesired interactions between network components that arise as the size of the network increases. This approach could enable the construction of in vitro networks capable of multifaceted chemical and material regulation.
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Affiliation(s)
- Samuel W Schaffter
- Department of Chemical and Biomolecular Engineering, Johns Hopkins University, Baltimore, MD, USA.
| | - Rebecca Schulman
- Department of Chemical and Biomolecular Engineering, Johns Hopkins University, Baltimore, MD, USA. .,Department of Computer Science, Johns Hopkins University, Baltimore, MD, USA.
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16
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Pan L, Hu Y, Ding T, Xie C, Wang Z, Chen Z, Yang J, Zhang C. Aptamer-based regulation of transcription circuits. Chem Commun (Camb) 2019; 55:7378-7381. [PMID: 31173001 DOI: 10.1039/c9cc03141c] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
We propose synthetic DNA/RNA transcription circuits based on specific aptamer recognition. By mimicking transcription factor regulation, combined with specific enzyme/DNA aptamer binding, multiple biomolecules including DNA, RNA, polymerase, restriction enzymes and methylase were used as regulators. In addition, multi-level cascading networks and methylation-switch circuits were also established. This regulation strategy has the potential to expand the toolkit of in vitro synthetic biology.
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Affiliation(s)
- Linqiang Pan
- Key Laboratory of Image Information Processing and Intelligent Control of Education Ministry of China, School of Automation, Huazhong University of Science and Technology, Wuhan 430074, P. R. China.
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17
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Hard Limits and Performance Tradeoffs in a Class of Antithetic Integral Feedback Networks. Cell Syst 2019; 9:49-63.e16. [PMID: 31279505 DOI: 10.1016/j.cels.2019.06.001] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2018] [Revised: 02/28/2019] [Accepted: 05/30/2019] [Indexed: 12/18/2022]
Abstract
Feedback regulation is pervasive in biology at both the organismal and cellular level. In this article, we explore the properties of a particular biomolecular feedback mechanism called antithetic integral feedback, which can be implemented using the binding of two molecules. Our work develops an analytic framework for understanding the hard limits, performance tradeoffs, and architectural properties of this simple model of biological feedback control. Using tools from control theory, we show that there are simple parametric relationships that determine both the stability and the performance of these systems in terms of speed, robustness, steady-state error, and leakiness. These findings yield a holistic understanding of the behavior of antithetic integral feedback and contribute to a more general theory of biological control systems.
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18
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Jeong D, Klocke M, Agarwal S, Kim J, Choi S, Franco E, Kim J. Cell-Free Synthetic Biology Platform for Engineering Synthetic Biological Circuits and Systems. Methods Protoc 2019; 2:E39. [PMID: 31164618 PMCID: PMC6632179 DOI: 10.3390/mps2020039] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2019] [Revised: 04/12/2019] [Accepted: 05/08/2019] [Indexed: 01/07/2023] Open
Abstract
Synthetic biology brings engineering disciplines to create novel biological systems for biomedical and technological applications. The substantial growth of the synthetic biology field in the past decade is poised to transform biotechnology and medicine. To streamline design processes and facilitate debugging of complex synthetic circuits, cell-free synthetic biology approaches has reached broad research communities both in academia and industry. By recapitulating gene expression systems in vitro, cell-free expression systems offer flexibility to explore beyond the confines of living cells and allow networking of synthetic and natural systems. Here, we review the capabilities of the current cell-free platforms, focusing on nucleic acid-based molecular programs and circuit construction. We survey the recent developments including cell-free transcription-translation platforms, DNA nanostructures and circuits, and novel classes of riboregulators. The links to mathematical models and the prospects of cell-free synthetic biology platforms will also be discussed.
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Affiliation(s)
- Dohyun Jeong
- Division of Integrative Biosciences and Biotechnology, Pohang University of Science and Technology, 77 Cheongam-ro, Pohang, Gyeongbuk 37673, Korea.
| | - Melissa Klocke
- Department of Mechanical Engineering, University of California at Riverside, 900 University Ave, Riverside, CA 92521, USA.
| | - Siddharth Agarwal
- Department of Mechanical Engineering, University of California at Riverside, 900 University Ave, Riverside, CA 92521, USA.
| | - Jeongwon Kim
- Division of Integrative Biosciences and Biotechnology, Pohang University of Science and Technology, 77 Cheongam-ro, Pohang, Gyeongbuk 37673, Korea.
| | - Seungdo Choi
- Division of Integrative Biosciences and Biotechnology, Pohang University of Science and Technology, 77 Cheongam-ro, Pohang, Gyeongbuk 37673, Korea.
| | - Elisa Franco
- Department of Mechanical and Aerospace Engineering, University of California at Los Angeles, 420 Westwood Plaza, Los Angeles, CA 90095, USA.
| | - Jongmin Kim
- Division of Integrative Biosciences and Biotechnology, Pohang University of Science and Technology, 77 Cheongam-ro, Pohang, Gyeongbuk 37673, Korea.
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19
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Olsman N, Xiao F, Doyle JC. Architectural Principles for Characterizing the Performance of Antithetic Integral Feedback Networks. iScience 2019; 14:277-291. [PMID: 31015073 PMCID: PMC6479019 DOI: 10.1016/j.isci.2019.04.004] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2018] [Revised: 03/14/2019] [Accepted: 04/01/2019] [Indexed: 02/06/2023] Open
Abstract
As we begin to design increasingly complex synthetic biomolecular systems, it is essential to develop rational design methodologies that yield predictable circuit performance. Here we apply mathematical tools from the theory of control and dynamical systems to yield practical insights into the architecture and function of a particular class of biological feedback circuit. Specifically, we show that it is possible to analytically characterize both the operating regime and performance tradeoffs of an antithetic integral feedback circuit architecture. Furthermore, we demonstrate how these principles can be applied to inform the design process of a particular synthetic feedback circuit.
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Affiliation(s)
- Noah Olsman
- Department of Control and Dynamical Systems, California Institute of Technology, 1200 E. California Boulevard, Pasadena, CA 91125, USA; Department of Systems Biology, Harvard Medical School, 200 Longwood Avenue, Boston, MA 02215, USA.
| | - Fangzhou Xiao
- Division of Biology and Biological Engineering, California Institute of Technology, 1200 E. California Boulevard, Pasadena, CA 91125, USA
| | - John C Doyle
- Department of Control and Dynamical Systems, California Institute of Technology, 1200 E. California Boulevard, Pasadena, CA 91125, USA; Division of Biology and Biological Engineering, California Institute of Technology, 1200 E. California Boulevard, Pasadena, CA 91125, USA
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20
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Baetica AA, Westbrook A, El-Samad H. Control theoretical concepts for synthetic and systems biology. ACTA ACUST UNITED AC 2019. [DOI: 10.1016/j.coisb.2019.02.010] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
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21
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Pasotti L, Bellato M, Politi N, Casanova M, Zucca S, Cusella De Angelis MG, Magni P. A Synthetic Close-Loop Controller Circuit for the Regulation of an Extracellular Molecule by Engineered Bacteria. IEEE TRANSACTIONS ON BIOMEDICAL CIRCUITS AND SYSTEMS 2019; 13:248-258. [PMID: 30489274 DOI: 10.1109/tbcas.2018.2883350] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/09/2023]
Abstract
Feedback control is ubiquitous in biological systems. It can also play a crucial role in the design of synthetic circuits implementing novel functions in living systems, to achieve self-regulation of gene expression, noise reduction, rise time decrease, or adaptive pathway control. Despite in vitro, in vivo, and ex vivo implementations have been successfully reported, the design of biological close-loop systems with quantitatively predictable behavior is still a major challenge. In this work, we tested a model-based bottom-up design of a synthetic close-loop controller in engineered Escherichia coli, aimed to automatically regulate the concentration of an extracellular molecule, N-(3-oxohexanoyl)-L-homoserine lactone (HSL), by rewiring the elements of heterologous quorum sensing/quenching networks. The synthetic controller was successfully constructed and experimentally validated. Relying on mathematical model and experimental characterization of individual regulatory parts and enzymes, we evaluated the predictability of the interconnected system behavior in vivo. The culture was able to reach an HSL steady-state level of 72 nM, accurately predicted by the model, and showed superior capabilities in terms of robustness against cell density variation and disturbance rejection, compared with a corresponding open-loop circuit. This engineering-inspired design approach may be adopted for the implementation of other close-loop circuits for different applications and contribute to decreasing trial-and-error steps.
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22
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Agrawal DK, Tang X, Westbrook A, Marshall R, Maxwell CS, Lucks J, Noireaux V, Beisel CL, Dunlop MJ, Franco E. Mathematical Modeling of RNA-Based Architectures for Closed Loop Control of Gene Expression. ACS Synth Biol 2018; 7:1219-1228. [PMID: 29709170 DOI: 10.1021/acssynbio.8b00040] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
Abstract
Feedback allows biological systems to control gene expression precisely and reliably, even in the presence of uncertainty, by sensing and processing environmental changes. Taking inspiration from natural architectures, synthetic biologists have engineered feedback loops to tune the dynamics and improve the robustness and predictability of gene expression. However, experimental implementations of biomolecular control systems are still far from satisfying performance specifications typically achieved by electrical or mechanical control systems. To address this gap, we present mathematical models of biomolecular controllers that enable reference tracking, disturbance rejection, and tuning of the temporal response of gene expression. These controllers employ RNA transcriptional regulators to achieve closed loop control where feedback is introduced via molecular sequestration. Sensitivity analysis of the models allows us to identify which parameters influence the transient and steady state response of a target gene expression process, as well as which biologically plausible parameter values enable perfect reference tracking. We quantify performance using typical control theory metrics to characterize response properties and provide clear selection guidelines for practical applications. Our results indicate that RNA regulators are well-suited for building robust and precise feedback controllers for gene expression. Additionally, our approach illustrates several quantitative methods useful for assessing the performance of biomolecular feedback control systems.
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Affiliation(s)
- Deepak K. Agrawal
- Biomedical Engineering Department, Boston University, Boston, Massachusetts 02215, United States
| | - Xun Tang
- Department of Mechanical Engineering, University of California at Riverside, Riverside, California 92521, United States
| | - Alexandra Westbrook
- Robert F. Smith School of Chemical and Biomolecular Engineering, Cornell University, Ithaca, New York 14853, United States
| | - Ryan Marshall
- School of Physics and Astronomy, University of Minnesota, Minneapolis, Minnesota 55455, United States
| | - Colin S. Maxwell
- Department of Chemical and Biomolecular Engineering, North Carolina State University, Raleigh, North Carolina 27695, United States
| | - Julius Lucks
- Department of Chemical and Biological Engineering, Northwestern University, Evanston, Illinois 60208, United States
| | - Vincent Noireaux
- School of Physics and Astronomy, University of Minnesota, Minneapolis, Minnesota 55455, United States
| | - Chase L. Beisel
- Department of Chemical and Biomolecular Engineering, North Carolina State University, Raleigh, North Carolina 27695, United States
- Helmholtz Institute for RNA-Based Infection Research (HIRI), Josef-Schneider-Str. 2/D15, D-97080 Würzburg, Germany
| | - Mary J. Dunlop
- Biomedical Engineering Department, Boston University, Boston, Massachusetts 02215, United States
| | - Elisa Franco
- Department of Mechanical Engineering, University of California at Riverside, Riverside, California 92521, United States
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23
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Briat C, Khammash M. Perfect Adaptation and Optimal Equilibrium Productivity in a Simple Microbial Biofuel Metabolic Pathway Using Dynamic Integral Control. ACS Synth Biol 2018; 7:419-431. [PMID: 29343065 DOI: 10.1021/acssynbio.7b00188] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
The production of complex biomolecules by genetically engineered organisms is one of the most promising applications of metabolic engineering and synthetic biology. To obtain processes with high productivity, it is therefore crucial to design and implement efficient dynamic in vivo regulation strategies. We consider here the microbial biofuel production model of Dunlop et al. (2010) for which we demonstrate that an antithetic dynamic integral control strategy can achieve robust perfect adaptation for the intracellular biofuel concentration in the presence of poorly known network parameters and implementation errors in certain rate parameters of the controller. We also show that the maximum equilibrium extracellular biofuel productivity is fully defined by some of the network parameters and, in this respect, it can only be achieved when all the corresponding parameters are perfectly known. Since this optimum is a network property, it cannot be improved by the use of any controller that measures the intracellular biofuel concentration and acts on the production of pump proteins. Additional intrinsic fundamental properties for the process are also unveiled, the most important ones being the existence of a conservation relation between the productivity and the toxicity, a low sensitivity of the optimal productivity with respect to a poor implementation of the set-point for the intracellular biofuel, and a strong intrinsic robustness property of the optimal productivity with respect to poorly known parameters. Taken together, these results demonstrate that a high and robust equilibrium rate of production for the extracellular biofuel can be achieved when the parameters of the model are poorly known and those of the controllers are poorly implemented. Finally, several advantages of the proposed dynamic strategy over a static one are also emphasized.
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Affiliation(s)
- Corentin Briat
- Department of Biosystems
Science and Engineering, ETH Zürich, Basel, 4058 Switzerland
| | - Mustafa Khammash
- Department of Biosystems
Science and Engineering, ETH Zürich, Basel, 4058 Switzerland
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24
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Lloyd J, Tran CH, Wadhwani K, Cuba Samaniego C, Subramanian HKK, Franco E. Dynamic Control of Aptamer-Ligand Activity Using Strand Displacement Reactions. ACS Synth Biol 2018; 7:30-37. [PMID: 29028334 DOI: 10.1021/acssynbio.7b00277] [Citation(s) in RCA: 32] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
Nucleic acid aptamers are an expandable toolkit of sensors and regulators. To employ aptamer regulators within nonequilibrium molecular networks, the aptamer-ligand interactions should be tunable over time, so that functions within a given system can be activated or suppressed on demand. This is accomplished through complementary sequences to aptamers, which achieve programmable aptamer-ligand dissociation by displacing the aptamer from the ligand. We demonstrate the effectiveness of our simple approach on light-up aptamers as well as on aptamers inhibiting viral RNA polymerases, dynamically controlling the functionality of the aptamer-ligand complex. Mathematical models allow us to obtain estimates for the aptamer displacement kinetics. Our results suggest that aptamers, paired with their complement, could be used to build dynamic nucleic acid networks with direct control over a variety of aptamer-controllable enzymes and their downstream pathways.
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Affiliation(s)
- Jonathan Lloyd
- Bioengineering, University of California at Riverside, Riverside, California 92521, United States
| | - Claire H. Tran
- Bioengineering, University of California at Riverside, Riverside, California 92521, United States
| | - Krishen Wadhwani
- Bioengineering, University of California at Riverside, Riverside, California 92521, United States
| | - Christian Cuba Samaniego
- Mechanical
Engineering, University of California at Riverside, Riverside, California 92521, United States
| | - Hari K. K. Subramanian
- Mechanical
Engineering, University of California at Riverside, Riverside, California 92521, United States
| | - Elisa Franco
- Mechanical
Engineering, University of California at Riverside, Riverside, California 92521, United States
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25
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Stewart JM, Subramanian HKK, Franco E. Self-assembly of multi-stranded RNA motifs into lattices and tubular structures. Nucleic Acids Res 2017; 45:5449-5457. [PMID: 28204562 PMCID: PMC5435959 DOI: 10.1093/nar/gkx063] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2016] [Accepted: 01/31/2017] [Indexed: 01/20/2023] Open
Abstract
Rational design of nucleic acid molecules yields self-assembling scaffolds with increasing complexity, size and functionality. It is an open question whether design methods tailored to build DNA nanostructures can be adapted to build RNA nanostructures with comparable features. Here we demonstrate the formation of RNA lattices and tubular assemblies from double crossover (DX) tiles, a canonical motif in DNA nanotechnology. Tubular structures can exceed 1 μm in length, suggesting that this DX motif can produce very robust lattices. Some of these tubes spontaneously form with left-handed chirality. We obtain assemblies by using two methods: a protocol where gel-extracted RNA strands are slowly annealed, and a one-pot transcription and anneal procedure. We identify the tile nick position as a structural requirement for lattice formation. Our results demonstrate that stable RNA structures can be obtained with design tools imported from DNA nanotechnology. These large assemblies could be potentially integrated with a variety of functional RNA motifs for drug or nanoparticle delivery, or for colocalization of cellular components.
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Affiliation(s)
- Jaimie Marie Stewart
- Department of Bioengineering, University of California, 900 University Avenue, Riverside, CA 92521, USA
| | - Hari K K Subramanian
- Department of Mechanical Engineering, University of California, 900 University Avenue, Riverside, CA 92521, USA
| | - Elisa Franco
- Department of Mechanical Engineering, University of California, 900 University Avenue, Riverside, CA 92521, USA
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26
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Cuba Samaniego C, Franco E. An ultrasensitive biomolecular network for robust feedback control. ACTA ACUST UNITED AC 2017. [DOI: 10.1016/j.ifacol.2017.08.2466] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
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27
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Wolfe BR, Porubsky NJ, Zadeh JN, Dirks RM, Pierce NA. Constrained Multistate Sequence Design for Nucleic Acid Reaction Pathway Engineering. J Am Chem Soc 2017; 139:3134-3144. [DOI: 10.1021/jacs.6b12693] [Citation(s) in RCA: 72] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/14/2023]
Affiliation(s)
- Brian R. Wolfe
- Division of Biology & Biological Engineering, California Institute of Technology, Pasadena, California 91125, United States
| | - Nicholas J. Porubsky
- Division of Chemistry & Chemical Engineering, California Institute of Technology, Pasadena, California 91125, United States
| | - Joseph N. Zadeh
- Division of Biology & Biological Engineering, California Institute of Technology, Pasadena, California 91125, United States
| | - Robert M. Dirks
- Division of Biology & Biological Engineering, California Institute of Technology, Pasadena, California 91125, United States
| | - Niles A. Pierce
- Division of Biology & Biological Engineering, California Institute of Technology, Pasadena, California 91125, United States
- Division of Engineering & Applied Science, California Institute of Technology, Pasadena, California 91125, United States
- Weatherall
Institute of Molecular Medicine, University of Oxford, Oxford OX3 9DS, United Kingdom
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28
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Agrawal DK, Franco E, Schulman R. A self-regulating biomolecular comparator for processing oscillatory signals. J R Soc Interface 2016; 12:20150586. [PMID: 26378119 DOI: 10.1098/rsif.2015.0586] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023] Open
Abstract
While many cellular processes are driven by biomolecular oscillators, precise control of a downstream on/off process by a biochemical oscillator signal can be difficult: over an oscillator's period, its output signal varies continuously between its amplitude limits and spends a significant fraction of the time at intermediate values between these limits. Further, the oscillator's output is often noisy, with particularly large variations in the amplitude. In electronic systems, an oscillating signal is generally processed by a downstream device such as a comparator that converts a potentially noisy oscillatory input into a square wave output that is predominantly in one of two well-defined on and off states. The comparator's output then controls downstream processes. We describe a method for constructing a synthetic biochemical device that likewise produces a square-wave-type biomolecular output for a variety of oscillatory inputs. The method relies on a separation of time scales between the slow rate of production of an oscillatory signal molecule and the fast rates of intermolecular binding and conformational changes. We show how to control the characteristics of the output by varying the concentrations of the species and the reaction rates. We then use this control to show how our approach could be applied to process different in vitro and in vivo biomolecular oscillators, including the p53-Mdm2 transcriptional oscillator and two types of in vitro transcriptional oscillators. These results demonstrate how modular biomolecular circuits could, in principle, be combined to build complex dynamical systems. The simplicity of our approach also suggests that natural molecular circuits may process some biomolecular oscillator outputs before they are applied downstream.
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Affiliation(s)
- Deepak K Agrawal
- Department of Chemical and Biomolecular Engineering, Johns Hopkins University, Baltimore, MD 21218, USA
| | - Elisa Franco
- Department of Mechanical Engineering, University of California at Riverside, 900 University Avenue, Riverside, CA 92521, USA
| | - Rebecca Schulman
- Department of Chemical and Biomolecular Engineering, Johns Hopkins University, Baltimore, MD 21218, USA Department of Computer Science, Johns Hopkins University, Baltimore, MD 21218, USA
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29
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Cuba Samaniego C, Giordano G, Kim J, Blanchini F, Franco E. Molecular Titration Promotes Oscillations and Bistability in Minimal Network Models with Monomeric Regulators. ACS Synth Biol 2016; 5:321-33. [PMID: 26797494 DOI: 10.1021/acssynbio.5b00176] [Citation(s) in RCA: 38] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
Abstract
Molecular titration is emerging as an important biochemical interaction mechanism within synthetic devices built with nucleic acids and the CRISPR/Cas system. We show that molecular titration in the context of feedback circuits is a suitable mechanism to enhance the emergence of oscillations and bistable behaviors. We consider biomolecular modules that can be inhibited or activated by input monomeric regulators; the regulators compete with constitutive titrating species to determine the activity of their target. By tuning the titration rate and the concentration of titrating species, it is possible to modulate the delay and convergence speed of the transient response, and the steepness and dead zone of the stationary response of the modules. These phenomena favor the occurrence of oscillations when modules are interconnected to create a negative feedback loop; bistability is favored in a positive feedback interconnection. Numerical simulations are supported by mathematical analysis showing that the capacity of the closed loop systems to exhibit oscillations or bistability is structural.
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Affiliation(s)
- Christian Cuba Samaniego
- Mechanical Engineering, University of California at Riverside, Riverside, California 92521, United States
| | - Giulia Giordano
- Mathematics and Computer Science, University of Udine, 33100 Udine, Italy
| | - Jongmin Kim
- Wyss Institute for Biologically Inspired Engineering, Harvard University, 3 Blackfan Circle, Boston, Massachusetts 02115, United States
| | - Franco Blanchini
- Mathematics and Computer Science, University of Udine, 33100 Udine, Italy
| | - Elisa Franco
- Mechanical Engineering, University of California at Riverside, Riverside, California 92521, United States
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30
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Boada Y, Reynoso-Meza G, Picó J, Vignoni A. Multi-objective optimization framework to obtain model-based guidelines for tuning biological synthetic devices: an adaptive network case. BMC SYSTEMS BIOLOGY 2016; 10:27. [PMID: 26968941 PMCID: PMC4788947 DOI: 10.1186/s12918-016-0269-0] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/13/2015] [Accepted: 02/16/2016] [Indexed: 12/22/2022]
Abstract
Background Model based design plays a fundamental role in synthetic biology. Exploiting modularity, i.e. using biological parts and interconnecting them to build new and more complex biological circuits is one of the key issues. In this context, mathematical models have been used to generate predictions of the behavior of the designed device. Designers not only want the ability to predict the circuit behavior once all its components have been determined, but also to help on the design and selection of its biological parts, i.e. to provide guidelines for the experimental implementation. This is tantamount to obtaining proper values of the model parameters, for the circuit behavior results from the interplay between model structure and parameters tuning. However, determining crisp values for parameters of the involved parts is not a realistic approach. Uncertainty is ubiquitous to biology, and the characterization of biological parts is not exempt from it. Moreover, the desired dynamical behavior for the designed circuit usually results from a trade-off among several goals to be optimized. Results We propose the use of a multi-objective optimization tuning framework to get a model-based set of guidelines for the selection of the kinetic parameters required to build a biological device with desired behavior. The design criteria are encoded in the formulation of the objectives and optimization problem itself. As a result, on the one hand the designer obtains qualitative regions/intervals of values of the circuit parameters giving rise to the predefined circuit behavior; on the other hand, he obtains useful information for its guidance in the implementation process. These parameters are chosen so that they can effectively be tuned at the wet-lab, i.e. they are effective biological tuning knobs. To show the proposed approach, the methodology is applied to the design of a well known biological circuit: a genetic incoherent feed-forward circuit showing adaptive behavior. Conclusion The proposed multi-objective optimization design framework is able to provide effective guidelines to tune biological parameters so as to achieve a desired circuit behavior. Moreover, it is easy to analyze the impact of the context on the synthetic device to be designed. That is, one can analyze how the presence of a downstream load influences the performance of the designed circuit, and take it into account. Electronic supplementary material The online version of this article (doi:10.1186/s12918-016-0269-0) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Yadira Boada
- Institut d'Automàtica i Informàtica Industrial, Universitat Politècnica de València, Valencia, Spain
| | - Gilberto Reynoso-Meza
- Industrial and Systems Engineering Graduate Program (PPGEPS), Pontificial Catholic University of Parana (PUCPR), Curitiba, Brazil
| | - Jesús Picó
- Institut d'Automàtica i Informàtica Industrial, Universitat Politècnica de València, Valencia, Spain
| | - Alejandro Vignoni
- Institut d'Automàtica i Informàtica Industrial, Universitat Politècnica de València, Valencia, Spain. .,Present Address: Center for Systems Biology Dresden (CSBD), Max Planck Institute of Molecular Cell Biology and Genetics, Dresden, Germany.
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31
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Computing the structural influence matrix for biological systems. J Math Biol 2015; 72:1927-58. [PMID: 26395779 DOI: 10.1007/s00285-015-0933-9] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2014] [Revised: 08/26/2015] [Indexed: 12/20/2022]
Abstract
We consider the problem of identifying structural influences of external inputs on steady-state outputs in a biological network model. We speak of a structural influence if, upon a perturbation due to a constant input, the ensuing variation of the steady-state output value has the same sign as the input (positive influence), the opposite sign (negative influence), or is zero (perfect adaptation), for any feasible choice of the model parameters. All these signs and zeros can constitute a structural influence matrix, whose (i, j) entry indicates the sign of steady-state influence of the jth system variable on the ith variable (the output caused by an external persistent input applied to the jth variable). Each entry is structurally determinate if the sign does not depend on the choice of the parameters, but is indeterminate otherwise. In principle, determining the influence matrix requires exhaustive testing of the system steady-state behaviour in the widest range of parameter values. Here we show that, in a broad class of biological networks, the influence matrix can be evaluated with an algorithm that tests the system steady-state behaviour only at a finite number of points. This algorithm also allows us to assess the structural effect of any perturbation, such as variations of relevant parameters. Our method is applied to nontrivial models of biochemical reaction networks and population dynamics drawn from the literature, providing a parameter-free insight into the system dynamics.
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32
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van Roekel HWH, Meijer LHH, Masroor S, Félix Garza ZC, Estévez-Torres A, Rondelez Y, Zagaris A, Peletier MA, Hilbers PAJ, de Greef TFA. Automated design of programmable enzyme-driven DNA circuits. ACS Synth Biol 2015; 4:735-45. [PMID: 25365785 DOI: 10.1021/sb500300d] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/18/2023]
Abstract
Molecular programming allows for the bottom-up engineering of biochemical reaction networks in a controlled in vitro setting. These engineered biochemical reaction networks yield important insight in the design principles of biological systems and can potentially enrich molecular diagnostic systems. The DNA polymerase-nickase-exonuclease (PEN) toolbox has recently been used to program oscillatory and bistable biochemical networks using a minimal number of components. Previous work has reported the automatic construction of in silico descriptions of biochemical networks derived from the PEN toolbox, paving the way for generating networks of arbitrary size and complexity in vitro. Here, we report an automated approach that further bridges the gap between an in silico description and in vitro realization. A biochemical network of arbitrary complexity can be globally screened for parameter values that display the desired function and combining this approach with robustness analysis further increases the chance of successful in vitro implementation. Moreover, we present an automated design procedure for generating optimal DNA sequences, exhibiting key characteristics deduced from the in silico analysis. Our in silico method has been tested on a previously reported network, the Oligator, and has also been applied to the design of a reaction network capable of displaying adaptation in one of its components. Finally, we experimentally characterize unproductive sequestration of the exonuclease to phosphorothioate protected ssDNA strands. The strong nonlinearities in the degradation of active components caused by this unintended cross-coupling are shown computationally to have a positive effect on adaptation quality.
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Affiliation(s)
| | | | | | | | - André Estévez-Torres
- Laboratoire
de Photonique et de Nanostructures, CNRS, route de Nozay, 91460 Marcoussis, France
| | - Yannick Rondelez
- LIMMS/CNRS-IIS,
Institute of Industrial Science, University of Tokyo, Komaba 4-6-1
Meguro-ku, Tokyo 153-8505, Japan
| | - Antonios Zagaris
- Department
of Applied Mathematics, University of Twente, P.O. Box 217, 7500 AE Enschede, The Netherlands
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33
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Yordanov B, Kim J, Petersen RL, Shudy A, Kulkarni VV, Phillips A. Computational design of nucleic acid feedback control circuits. ACS Synth Biol 2014; 3:600-16. [PMID: 25061797 DOI: 10.1021/sb400169s] [Citation(s) in RCA: 47] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
The design of synthetic circuits for controlling molecular-scale processes is an important goal of synthetic biology, with potential applications in future in vitro and in vivo biotechnology. In this paper, we present a computational approach for designing feedback control circuits constructed from nucleic acids. Our approach relies on an existing methodology for expressing signal processing and control circuits as biomolecular reactions. We first extend the methodology so that circuits can be expressed using just two classes of reactions: catalysis and annihilation. We then propose implementations of these reactions in three distinct classes of nucleic acid circuits, which rely on DNA strand displacement, DNA enzyme and RNA enzyme mechanisms, respectively. We use these implementations to design a Proportional Integral controller, capable of regulating the output of a system according to a given reference signal, and discuss the trade-offs between the different approaches. As a proof of principle, we implement our methodology as an extension to a DNA strand displacement software tool, thus allowing a broad range of nucleic acid circuits to be designed and analyzed within a common modeling framework.
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Affiliation(s)
| | - Jongmin Kim
- Division
of Biology and Biological Engineering, California Institute of Technology, Pasadena, California 91125, United States
| | | | - Angelina Shudy
- Department
of Electrical Engineering, University of Minnesota, Minneapolis, Minnesota 55455, United States
| | - Vishwesh V. Kulkarni
- Department
of Electrical Engineering, University of Minnesota, Minneapolis, Minnesota 55455, United States
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