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Hall-Thomsen H, Small S, Gavrilov M, Ha T, Schulman R, Moerman PG. Directing Uphill Strand Displacement with an Engineered Superhelicase. ACS Synth Biol 2023; 12:3424-3432. [PMID: 37844274 PMCID: PMC10661026 DOI: 10.1021/acssynbio.3c00452] [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: 07/24/2023] [Indexed: 10/18/2023]
Abstract
The ability to finely tune reaction rates and binding energies between components has made DNA strand displacement circuits promising candidates to replicate the complex regulatory functions of biological reaction networks. However, these circuits often lack crucial properties, such as signal turnover and the ability to transiently respond to successive input signals that require the continuous input of chemical energy. Here, we introduce a method for providing such energy to strand displacement networks in a controlled fashion: an engineered DNA helicase, Rep-X, that transiently dehybridizes specific DNA complexes, enabling the strands in the complex to participate in downstream hybridization or strand displacement reactions. We demonstrate how this process can direct the formation of specific metastable structures by design and that this dehybridization process can be controlled by DNA strand displacement reactions that effectively protect and deprotect a double-stranded complex from unwinding by Rep-X. These findings can guide the design of active DNA strand displacement regulatory networks, in which sustained dynamical behavior is fueled by helicase-regulated unwinding.
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Affiliation(s)
- Helena Hall-Thomsen
- Chemical
& Biomolecular Engineering, Johns Hopkins
University, Baltimore, Maryland 21218, United States
| | - Shavier Small
- Chemical
& Biomolecular Engineering, Johns Hopkins
University, Baltimore, Maryland 21218, United States
| | - Momcilo Gavrilov
- Biophysics
and Biophysical Chemistry, Johns Hopkins
University, Baltimore, Maryland 21218, United States
| | - Taekjip Ha
- Biophysics
and Biophysical Chemistry, Johns Hopkins
University, Baltimore, Maryland 21218, United States
- Biomedical
Engineering, Johns Hopkins University, Baltimore, Maryland 21218, United States
- Howard
Hughes Medical Institute, Chevy
Chase, Maryland 20815, United States
| | - Rebecca Schulman
- Chemical
& Biomolecular Engineering, Johns Hopkins
University, Baltimore, Maryland 21218, United States
- Computer
Science, Johns Hopkins University, Baltimore, Maryland 21218, United States
- Chemistry, Johns Hopkins University, Baltimore, Maryland 21218, United States
| | - Pepijn Gerben Moerman
- Chemical
& Biomolecular Engineering, Johns Hopkins
University, Baltimore, Maryland 21218, United States
- Chemical
Engineering and Chemistry, Eindhoven University
of Technology, Eindhoven 5612 AP, Netherlands
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2
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Sun M, Deng J, Walther A. Communication and Cross-Regulation between Chemically Fueled Sender and Receiver Reaction Networks. Angew Chem Int Ed Engl 2023; 62:e202214499. [PMID: 36354214 PMCID: PMC10107503 DOI: 10.1002/anie.202214499] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2022] [Indexed: 11/11/2022]
Abstract
Nature connects multiple fuel-driven chemical/enzymatic reaction networks (CRNs/ERNs) via cross-regulation to hierarchically control biofunctions for a tailored adaption in complex sensory landscapes. Herein, we introduce a facile example of communication and cross-regulation among two fuel-driven DNA-based ERNs regulated by a concatenated RNA transcription regulator. ERN1 ("sender") is designed for the fuel-driven promoter formation for T7 RNA polymerase, which activates RNA transcription. The produced RNA can deactivate or activate DNA in ERN2 ("receiver") by toehold-mediated strand displacement, leading to a communication between two ERNs. The RNA from ERN1 can repress or promote the fuel-driven state of ERN2; ERN2 in turn feedbacks to regulate the lifetime of ERN1. Furthermore, the incorporation of RNase H allows for RNA degradation and enables the autonomous recovery of ERN2. We believe that concatenation of multiple CRNs/ERNs provides a basis for the design of more elaborate autonomous regulatory mechanisms in systems chemistry and synthetic biology.
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Affiliation(s)
- Mo Sun
- Department of Chemistry, Fudan University, Shanghai, 200438, China.,Cluster of Excellence livMatS @ FIT - Freiburg Center for Interactive Materials and Bioinspired Technologies, University of Freiburg, Georges-Köhler-Allee 105, 79110, Freiburg, Germany
| | - Jie Deng
- Life Like Materials and Systems, Department of Chemistry, University of Mainz, Duesbergweg 10-14, 55128, Mainz, Germany.,Dana-Farber Cancer Institute, Wyss Institute for Biologically Inspired Engineering, Harvard Medical School, Boston, MA 02115, USA
| | - Andreas Walther
- Life Like Materials and Systems, Department of Chemistry, University of Mainz, Duesbergweg 10-14, 55128, Mainz, Germany.,Cluster of Excellence livMatS @ FIT - Freiburg Center for Interactive Materials and Bioinspired Technologies, University of Freiburg, Georges-Köhler-Allee 105, 79110, Freiburg, Germany
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3
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Higashi SL, Shintani Y, Ikeda M. Installing Reduction Responsiveness into Biomolecules by Introducing Nitroaryl Groups. Chemistry 2022; 28:e202201103. [DOI: 10.1002/chem.202201103] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2022] [Indexed: 11/11/2022]
Affiliation(s)
- Sayuri L. Higashi
- United Graduate School of Drug Discovery and Medical Information Sciences Gifu University 1-1 Yanagido Gifu 501-1193 Japan
- Present address: Institut für Physiologische Chemie und Pathobiochemie Universität Münster Waldeyerstraße 15 48149 Münster Germany
| | - Yuki Shintani
- Department of Life Science and Chemistry Graduate School of Natural Science and Technology Gifu University 1-1 Yanagido Gifu 501-1193 Japan
| | - Masato Ikeda
- United Graduate School of Drug Discovery and Medical Information Sciences Gifu University 1-1 Yanagido Gifu 501-1193 Japan
- Department of Life Science and Chemistry Graduate School of Natural Science and Technology Gifu University 1-1 Yanagido Gifu 501-1193 Japan
- Institute for Glyco-core Research (iGCORE) Gifu University 1-1 Yanagido Gifu 501-1193 Japan
- Institute of Nano-Life-Systems Institutes of Innovation for Future Society Nagoya University Furo-cho, Chikusa-ku Nagoya 464-8603 Japan
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4
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Farag N, Ercolani G, Del Grosso E, Ricci F. DNA Tile Self‐Assembly Guided by Base Excision Repair Enzymes. Angew Chem Int Ed Engl 2022; 61:e202208367. [DOI: 10.1002/anie.202208367] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2022] [Indexed: 12/18/2022]
Affiliation(s)
- Nada Farag
- Department of Chemical Sciences and Technologies University of Rome Tor Vergata Via della Ricerca Scientifica 00133 Rome Italy
| | - Gianfranco Ercolani
- Department of Chemical Sciences and Technologies University of Rome Tor Vergata Via della Ricerca Scientifica 00133 Rome Italy
| | - Erica Del Grosso
- Department of Chemical Sciences and Technologies University of Rome Tor Vergata Via della Ricerca Scientifica 00133 Rome Italy
| | - Francesco Ricci
- Department of Chemical Sciences and Technologies University of Rome Tor Vergata Via della Ricerca Scientifica 00133 Rome Italy
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5
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Farag N, Ercolani G, Del Grosso E, Ricci F. DNA Tile Self‐Assembly Guided by Base Excision Repair Enzymes. Angew Chem Int Ed Engl 2022. [DOI: 10.1002/ange.202208367] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
Affiliation(s)
- Nada Farag
- Universita degli Studi di Roma Tor Vergata Chemistry ITALY
| | | | | | - Francesco Ricci
- University of Rome, Tor Vergata Department of Chemistry Via della Ricerca Scientifica 00133 Rome ITALY
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6
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Del Grosso E, Irmisch P, Gentile S, Prins LJ, Seidel R, Ricci F. Dissipative Control over the Toehold-Mediated DNA Strand Displacement Reaction. Angew Chem Int Ed Engl 2022; 61:e202201929. [PMID: 35315568 PMCID: PMC9324813 DOI: 10.1002/anie.202201929] [Citation(s) in RCA: 24] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2022] [Indexed: 12/31/2022]
Abstract
Here we show a general approach to achieve dissipative control over toehold‐mediated strand‐displacement, the most widely employed reaction in the field of DNA nanotechnology. The approach relies on rationally re‐engineering the classic strand displacement reaction such that the high‐energy invader strand (fuel) is converted into a low‐energy waste product through an energy‐dissipating reaction allowing the spontaneous return to the original state over time. We show that such dissipative control over the toehold‐mediated strand displacement process is reversible (up to 10 cycles), highly controllable and enables unique temporal activation of DNA systems. We show here two possible applications of this strategy: the transient labelling of DNA structures and the additional temporal control of cascade reactions.
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Affiliation(s)
- Erica Del Grosso
- Department of Chemistry, University of Rome Tor Vergata, Via della Ricerca Scientifica, 00133, Rome, Italy
| | - Patrick Irmisch
- Molecular Biophysics Group, Peter Debye Institute for Soft Matter Physics, Universität Leipzig, 04103, Leipzig, Germany
| | - Serena Gentile
- Department of Chemistry, University of Rome Tor Vergata, Via della Ricerca Scientifica, 00133, Rome, Italy
| | - Leonard J Prins
- Department of Chemical fSciences, University of Padua, Via Marzolo 1, 35131, Padua, Italy
| | - Ralf Seidel
- Molecular Biophysics Group, Peter Debye Institute for Soft Matter Physics, Universität Leipzig, 04103, Leipzig, Germany
| | - Francesco Ricci
- Department of Chemistry, University of Rome Tor Vergata, Via della Ricerca Scientifica, 00133, Rome, Italy
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7
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Del Grosso E, Irmisch P, Gentile S, Prins LJ, Seidel R, Ricci F. Dissipative Control over the Toehold‐Mediated DNA Strand Displacement Reaction. Angew Chem Int Ed Engl 2022. [DOI: 10.1002/ange.202201929] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Affiliation(s)
- Erica Del Grosso
- Department of Chemistry University of Rome Tor Vergata Via della Ricerca Scientifica 00133 Rome Italy
| | - Patrick Irmisch
- Molecular Biophysics Group Peter Debye Institute for Soft Matter Physics Universität Leipzig 04103 Leipzig Germany
| | - Serena Gentile
- Department of Chemistry University of Rome Tor Vergata Via della Ricerca Scientifica 00133 Rome Italy
| | - Leonard J. Prins
- Department of Chemical fSciences University of Padua Via Marzolo 1 35131 Padua Italy
| | - Ralf Seidel
- Molecular Biophysics Group Peter Debye Institute for Soft Matter Physics Universität Leipzig 04103 Leipzig Germany
| | - Francesco Ricci
- Department of Chemistry University of Rome Tor Vergata Via della Ricerca Scientifica 00133 Rome Italy
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8
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Sun J, Vogel J, Chen L, Schleper AL, Bergner T, Kuehne AJC, von Delius M. Carbodiimide-Driven Dimerization and Self-Assembly of Artificial, Ribose-Based Amphiphiles. Chemistry 2022; 28:e202104116. [PMID: 35038189 PMCID: PMC9303926 DOI: 10.1002/chem.202104116] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2021] [Indexed: 12/20/2022]
Abstract
The aqueous self‐assembly of amphiphiles into aggregates such as micelles and vesicles has been widely investigated over the past decades with applications ranging from materials science to drug delivery. The combination of characteristic properties of nucleic acids and amphiphiles is of substantial interest to mimic biological self‐organization and compartmentalization. Herein, we present ribose‐ and ribonucleotide‐based amphiphiles and investigate their self‐assembly as well as their fundamental reactivity. We found that various types of aggregates are formed, ranging in size from nanometers to micrometers and all amphiphiles exhibit aggregation‐induced emission (AIE) in solution as well as in the solid state. We also observed that the addition of 1‐ethyl‐3‐(3‐dimethylaminopropyl)carbodiimide (EDC) leads to rapid and selective dimerization of the amphiphiles into pyrophosphates, which decreases the critical aggregation concentration (CAC) by a factor of 25 when compared to the monomers. Since the propensity for amphiphile dimerization is correlated with their tendency to self‐assemble, our results may be relevant for the formation of rudimentary compartments under prebiotic conditions.
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Affiliation(s)
- Jing Sun
- Institute of Organic Chemistry, Ulm University, Albert-Einstein-Allee 11, 89081, Ulm, Germany
| | - Julian Vogel
- Institute of Organic Chemistry, Ulm University, Albert-Einstein-Allee 11, 89081, Ulm, Germany
| | - Lisa Chen
- Institute of Macromolecular and Organic Chemistry, Ulm University, Albert-Einstein-Allee 11, 89081, Ulm, Germany
| | - A Lennart Schleper
- Institute of Macromolecular and Organic Chemistry, Ulm University, Albert-Einstein-Allee 11, 89081, Ulm, Germany
| | - Tim Bergner
- Central Facility for Electron Microscopy, Ulm University, Albert-Einstein-Allee 11, 89081, Ulm, Germany
| | - Alexander J C Kuehne
- Institute of Macromolecular and Organic Chemistry, Ulm University, Albert-Einstein-Allee 11, 89081, Ulm, Germany.,DWI - Leibniz-Institute for Interactive Materials, Forckenbeckstraße 50, 52074, Aachen, Germany
| | - Max von Delius
- Institute of Organic Chemistry, Ulm University, Albert-Einstein-Allee 11, 89081, Ulm, Germany
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9
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Henry SJ, Stephanopoulos N. Functionalizing DNA nanostructures for therapeutic applications. WILEY INTERDISCIPLINARY REVIEWS. NANOMEDICINE AND NANOBIOTECHNOLOGY 2021; 13:e1729. [PMID: 34008347 PMCID: PMC8526372 DOI: 10.1002/wnan.1729] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/22/2020] [Revised: 03/29/2021] [Accepted: 04/26/2021] [Indexed: 12/29/2022]
Abstract
Recent advances in nanotechnology have enabled rapid progress in many areas of biomedical research, including drug delivery, targeted therapies, imaging, and sensing. The emerging field of DNA nanotechnology, in which oligonucleotides are designed to self-assemble into programmable 2D and 3D nanostructures, offers great promise for further advancements in biomedicine. DNA nanostructures present highly addressable and functionally diverse platforms for biological applications due to their ease of construction, controllable architecture and size/shape, and multiple avenues for chemical modification. Both supramolecular and covalent modification with small molecules and polymers have been shown to expand or enhance the functions of DNA nanostructures in biological contexts. These alterations include the addition of small molecule, protein, or nucleic acid moieties that enable structural stability under physiological conditions, more efficient cellular uptake and targeting, delivery of various molecular cargos, stimulus-responsive behaviors, or modulation of a host immune response. Herein, various types of DNA nanostructure modifications and their functional consequences are examined, followed by a brief discussion of the future opportunities for functionalized DNA nanostructures as well as the barriers that must be overcome before their translational use. This article is categorized under: Nanotechnology Approaches to Biology > Nanoscale Systems in Biology Therapeutic Approaches and Drug Discovery > Emerging Technologies Biology-Inspired Nanomaterials > Nucleic Acid-Based Structures.
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Affiliation(s)
- Skylar J.W. Henry
- School of Molecular Sciences, Biodesign Center for Molecular Design and Biomimetics, Arizona State University, Tempe AZ
| | - Nicholas Stephanopoulos
- School of Molecular Sciences, Biodesign Center for Molecular Design and Biomimetics, Arizona State University, Tempe AZ
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10
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Gentile S, Del Grosso E, Prins LJ, Ricci F. Reorganization of Self‐Assembled DNA‐Based Polymers using Orthogonally Addressable Building Blocks**. Angew Chem Int Ed Engl 2021. [DOI: 10.1002/ange.202101378] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Affiliation(s)
- Serena Gentile
- 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
| | - Leonard J. Prins
- Department of Chemical Sciences University of Padua Via Marzolo 1 35131 Padua Italy
| | - Francesco Ricci
- Department of Chemistry University of Rome, Tor Vergata Via della Ricerca Scientifica 00133 Rome Italy
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11
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Gentile S, Del Grosso E, Prins LJ, Ricci F. Reorganization of Self‐Assembled DNA‐Based Polymers using Orthogonally Addressable Building Blocks**. Angew Chem Int Ed Engl 2021; 60:12911-12917. [DOI: 10.1002/anie.202101378] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2021] [Revised: 03/11/2021] [Indexed: 01/20/2023]
Affiliation(s)
- Serena Gentile
- 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
| | - Leonard J. Prins
- Department of Chemical Sciences University of Padua Via Marzolo 1 35131 Padua Italy
| | - Francesco Ricci
- Department of Chemistry University of Rome, Tor Vergata Via della Ricerca Scientifica 00133 Rome Italy
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12
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Kariyawasam LS, Hossain MM, Hartley CS. The Transient Covalent Bond in Abiotic Nonequilibrium Systems. Angew Chem Int Ed Engl 2021. [DOI: 10.1002/ange.202014678] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Affiliation(s)
| | | | - C. Scott Hartley
- Department of Chemistry & Biochemistry Miami University Oxford OH 45056 USA
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13
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Kariyawasam LS, Hossain MM, Hartley CS. The Transient Covalent Bond in Abiotic Nonequilibrium Systems. Angew Chem Int Ed Engl 2021; 60:12648-12658. [PMID: 33264456 DOI: 10.1002/anie.202014678] [Citation(s) in RCA: 45] [Impact Index Per Article: 15.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2020] [Indexed: 12/20/2022]
Abstract
Biochemical systems accomplish many critical functions with by operating out-of-equilibrium using the energy of chemical fuels. The formation of a transient covalent bond is a simple but very effective tool in designing analogous reaction networks. This Minireview focuses on the fuel chemistries that have been used to generate transient bonds in recent demonstrations of abiotic nonequilibrium systems (i.e., systems that do not make use of biological components). Fuel reactions are divided into two fundamental classifications depending on whether the fuel contributes structural elements to the activated state, a distinction that dictates how they can be used. Reported systems are further categorized by overall fuel reaction (e.g., hydrolysis of alkylating agents, carbodiimide hydration) and illustrate how similar chemistry can be used to effect a wide range of nonequilibrium behavior, ranging from self-assembly to the operation of molecular machines.
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Affiliation(s)
- Lasith S Kariyawasam
- Department of Chemistry & Biochemistry, Miami University, Oxford, OH, 45056, USA
| | | | - C Scott Hartley
- Department of Chemistry & Biochemistry, Miami University, Oxford, OH, 45056, USA
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