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Fujino K, Nishio T, Fujioka K, Yoshikawa Y, Kenmotsu T, Yoshikawa K. Activation/Inhibition of Gene Expression Caused by Alcohols: Relationship with the Viscoelastic Property of a DNA Molecule. Polymers (Basel) 2022; 15:polym15010149. [PMID: 36616499 PMCID: PMC9823369 DOI: 10.3390/polym15010149] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2022] [Revised: 12/15/2022] [Accepted: 12/26/2022] [Indexed: 12/31/2022] Open
Abstract
Alcohols are used in the life sciences because they can condense and precipitate DNA. Alcohol consumption has been linked to many diseases and can alter genetic activity. In the present report, we carried out experiments to make clear how alcohols affect the efficiency of transcription-translation (TX-TL) and translation (TL) by adapting cell-free gene expression systems with plasmid DNA and RNA templates, respectively. In addition, we quantitatively analyzed intrachain fluctuations of single giant DNA molecules based on the fluctuation-dissipation theorem to gain insight into how alcohols affect the dynamical property of a DNA molecule. Ethanol (2-3%) increased gene expression levels four to five times higher than the control in the TX-TL reaction. A similar level of enhancement was observed with 2-propanol, in contrast to the inhibitory effect of 1-propanol. Similar alcohol effects were observed for the TL reaction. Intrachain fluctuation analysis through single DNA observation showed that 1-propanol markedly increased both the spring and damping constants of single DNA in contrast to the weak effects observed with ethanol, whereas 2-propanol exhibits an intermediate effect. This study indicates that the activation/inhibition effects of alcohol isomers on gene expression correlate with the changes in the viscoelastic mechanical properties of DNA molecules.
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Affiliation(s)
- Kohei Fujino
- Faculty of Life and Medical Sciences, Doshisha University, Kyoto 610-0394, Japan
| | - Takashi Nishio
- Faculty of Life and Medical Sciences, Doshisha University, Kyoto 610-0394, Japan
- Cluster of Excellence Physics of Life, Technical University of Dresden, 01307 Dresden, Germany
- Correspondence: (T.N.); (K.Y.)
| | - Keita Fujioka
- Faculty of Life and Medical Sciences, Doshisha University, Kyoto 610-0394, Japan
| | - Yuko Yoshikawa
- Faculty of Life and Medical Sciences, Doshisha University, Kyoto 610-0394, Japan
| | - Takahiro Kenmotsu
- Faculty of Life and Medical Sciences, Doshisha University, Kyoto 610-0394, Japan
| | - Kenichi Yoshikawa
- Faculty of Life and Medical Sciences, Doshisha University, Kyoto 610-0394, Japan
- Correspondence: (T.N.); (K.Y.)
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Lin P, Dinh H, Morita Y, Zhang Z, Nakata E, Kinoshita M, Morii T. Evaluation of the role of the DNA surface for enhancing the activity of scaffolded enzymes. Chem Commun (Camb) 2021; 57:3925-3928. [PMID: 33871490 DOI: 10.1039/d1cc00276g] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Abstract
The catalytic enhancements of enzymes loaded on DNA nanostructures have been attributed to the characteristics provided by highly negative charges on the surface of the DNA scaffold, such as the modulation of the local pH near enzymes. In this study, two types of enzymes with optimal activity at pH 6 and 8 equally displayed significant catalytic enhancements on the DNA scaffold surface. By using a ratiometric pH indicator, a lower local pH shift of 0.8 was observed near the DNA scaffold surface. The postulated local pH change near the DNA scaffold surface is unlikely to play a general role in enhancing the activity of the scaffolded enzymes.
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Affiliation(s)
- Peng Lin
- Institute of Advanced Energy, Kyoto University, Uji, Kyoto 611-0011, Japan.
| | - Huyen Dinh
- Institute of Advanced Energy, Kyoto University, Uji, Kyoto 611-0011, Japan.
| | - Yuki Morita
- Institute of Advanced Energy, Kyoto University, Uji, Kyoto 611-0011, Japan.
| | - Zhengxiao Zhang
- Institute of Advanced Energy, Kyoto University, Uji, Kyoto 611-0011, Japan.
| | - Eiji Nakata
- Institute of Advanced Energy, Kyoto University, Uji, Kyoto 611-0011, Japan.
| | - Masahiro Kinoshita
- Institute of Advanced Energy, Kyoto University, Uji, Kyoto 611-0011, Japan.
| | - Takashi Morii
- Institute of Advanced Energy, Kyoto University, Uji, Kyoto 611-0011, Japan.
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Fu J, Wang Z, Liang XH, Oh SW, St Iago-McRae E, Zhang T. DNA-Scaffolded Proximity Assembly and Confinement of Multienzyme Reactions. Top Curr Chem (Cham) 2020; 378:38. [PMID: 32248317 PMCID: PMC7127875 DOI: 10.1007/s41061-020-0299-3] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2019] [Accepted: 03/07/2020] [Indexed: 12/14/2022]
Abstract
Cellular functions rely on a series of organized and regulated multienzyme cascade reactions. The catalytic efficiencies of these cascades depend on the precise spatial organization of the constituent enzymes, which is optimized to facilitate substrate transport and regulate activities. Mimicry of this organization in a non-living, artificial system would be very useful in a broad range of applications—with impacts on both the scientific community and society at large. Self-assembled DNA nanostructures are promising applications to organize biomolecular components into prescribed, multidimensional patterns. In this review, we focus on recent progress in the field of DNA-scaffolded assembly and confinement of multienzyme reactions. DNA self-assembly is exploited to build spatially organized multienzyme cascades with control over their relative distance, substrate diffusion paths, compartmentalization and activity actuation. The combination of addressable DNA assembly and multienzyme cascades can deliver breakthroughs toward the engineering of novel synthetic and biomimetic reactors.
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Affiliation(s)
- Jinglin Fu
- Department of Chemistry, Rutgers University-Camden, Camden, NJ, 08102, USA. .,Center for Computational and Integrative Biology, Rutgers University-Camden, Camden, NJ, 08102, USA.
| | - Zhicheng Wang
- Department of Chemistry, Rutgers University-Camden, Camden, NJ, 08102, USA.,Center for Computational and Integrative Biology, Rutgers University-Camden, Camden, NJ, 08102, USA
| | - Xiao Hua Liang
- Department of Chemistry, Rutgers University-Camden, Camden, NJ, 08102, USA
| | - Sung Won Oh
- Center for Computational and Integrative Biology, Rutgers University-Camden, Camden, NJ, 08102, USA
| | - Ezry St Iago-McRae
- Center for Computational and Integrative Biology, Rutgers University-Camden, Camden, NJ, 08102, USA
| | - Ting Zhang
- Department of Chemistry, Rutgers University-Camden, Camden, NJ, 08102, USA
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Fu J, Oh SW, Monckton K, Arbuckle-Keil G, Ke Y, Zhang T. Biomimetic Compartments Scaffolded by Nucleic Acid Nanostructures. SMALL (WEINHEIM AN DER BERGSTRASSE, GERMANY) 2019; 15:e1900256. [PMID: 30884139 DOI: 10.1002/smll.201900256] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/15/2019] [Revised: 02/19/2019] [Indexed: 05/28/2023]
Abstract
The behaviors of living cells are governed by a series of regulated and confined biochemical reactions. The design and successful construction of synthetic cellular reactors can be useful in a broad range of applications that will bring significant scientific and economic impact. Over the past few decades, DNA self-assembly has enabled the design and fabrication of sophisticated 1D, 2D, and 3D nanostructures, and is applied to organizing a variety of biomolecular components into prescribed 2D and 3D patterns. In this Concept, the recent and exciting progress in DNA-scaffolded compartmentalizations and their applications in enzyme encapsulation, lipid membrane assembly, artificial transmembrane nanopores, and smart drug delivery are in focus. Taking advantage of these features promises to deliver breakthroughs toward the attainment of new synthetic and biomimetic reactors.
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Affiliation(s)
- Jinglin Fu
- Department of Chemistry and Center for Computational and Integrative Biology, Rutgers University-Camden, 315 Penn Street, Camden, NJ, 08102, USA
| | - Sung Won Oh
- Department of Chemistry and Center for Computational and Integrative Biology, Rutgers University-Camden, 315 Penn Street, Camden, NJ, 08102, USA
| | - Kristin Monckton
- Department of Chemistry and Center for Computational and Integrative Biology, Rutgers University-Camden, 315 Penn Street, Camden, NJ, 08102, USA
| | - Georgia Arbuckle-Keil
- Department of Chemistry and Center for Computational and Integrative Biology, Rutgers University-Camden, 315 Penn Street, Camden, NJ, 08102, USA
| | - Yonggang Ke
- Wallace H. Coulter Department of Biomedical Engineering, Emory University and Georgia Institute of Technology, Atlanta, GA, 30322, USA
| | - Ting Zhang
- Department of Chemistry and Center for Computational and Integrative Biology, Rutgers University-Camden, 315 Penn Street, Camden, NJ, 08102, USA
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Gao Y, Roberts CC, Toop A, Chang CEA, Wheeldon I. Mechanisms of Enhanced Catalysis in Enzyme-DNA Nanostructures Revealed through Molecular Simulations and Experimental Analysis. Chembiochem 2016; 17:1430-6. [PMID: 27173175 DOI: 10.1002/cbic.201600224] [Citation(s) in RCA: 29] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2016] [Indexed: 12/12/2022]
Abstract
Understanding and controlling the molecular interactions between enzyme substrates and DNA nanostructures has important implications in the advancement of enzyme-DNA technologies as solutions in biocatalysis. Such hybrid nanostructures can be used to create enzyme systems with enhanced catalysis by controlling the local chemical and physical environments and the spatial organization of enzymes. Here we have used molecular simulations with corresponding experiments to describe a mechanism of enhanced catalysis due to locally increased substrate concentrations. With a series of DNA nanostructures conjugated to horseradish peroxidase, we show that binding interactions between substrates and the DNA structures can increase local substrate concentrations. Increased local substrate concentrations in HRP(DNA) nanostructures resulted in 2.9- and 2.4-fold decreases in the apparent Michaelis constants of tetramethylbenzidine and 4-aminophenol, substrates of HRP with tunable binding interactions to DNA nanostructures with dissociation constants in the micromolar range. Molecular simulations and kinetic analysis also revealed that increased local substrate concentrations enhanced the rates of substrate association. Identification of the mechanism of increased local concentration of substrates in close proximity to enzymes and their active sites adds to our understanding of nanostructured biocatalysis from which we can develop guidelines for enhancing catalysis in rationally designed systems.
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Affiliation(s)
- Yingning Gao
- The Department of Chemical and Environmental Engineering, University of California-Riverside, 900 University Avenue, Riverside, CA, 92521, USA
| | - Christopher C Roberts
- The Department of Chemistry, University of Californi-Riverside, 501 Big Springs Road, Riverside, CA, 92521, USA
| | - Aaron Toop
- The Department of Chemical and Environmental Engineering, University of California-Riverside, 900 University Avenue, Riverside, CA, 92521, USA
| | - Chia-En A Chang
- The Department of Chemistry, University of Californi-Riverside, 501 Big Springs Road, Riverside, CA, 92521, USA
| | - Ian Wheeldon
- The Department of Chemical and Environmental Engineering, University of California-Riverside, 900 University Avenue, Riverside, CA, 92521, USA.
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