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Lin P, Yang H, Nakata E, Morii T. Mechanistic Aspects for the Modulation of Enzyme Reactions on the DNA Scaffold. Molecules 2022; 27:molecules27196309. [PMID: 36234845 PMCID: PMC9572797 DOI: 10.3390/molecules27196309] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2022] [Revised: 09/20/2022] [Accepted: 09/21/2022] [Indexed: 12/03/2022] Open
Abstract
Cells have developed intelligent systems to implement the complex and efficient enzyme cascade reactions via the strategies of organelles, bacterial microcompartments and enzyme complexes. The scaffolds such as the membrane or protein in the cell are believed to assist the co-localization of enzymes and enhance the enzymatic reactions. Inspired by nature, enzymes have been located on a wide variety of carriers, among which DNA scaffolds attract great interest for their programmability and addressability. Integrating these properties with the versatile DNA–protein conjugation methods enables the spatial arrangement of enzymes on the DNA scaffold with precise control over the interenzyme distance and enzyme stoichiometry. In this review, we survey the reactions of a single type of enzyme on the DNA scaffold and discuss the proposed mechanisms for the catalytic enhancement of DNA-scaffolded enzymes. We also review the current progress of enzyme cascade reactions on the DNA scaffold and discuss the factors enhancing the enzyme cascade reaction efficiency. This review highlights the mechanistic aspects for the modulation of enzymatic reactions on the DNA scaffold.
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2
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Mariconti M, Morel M, Baigl D, Rudiuk S. Enzymatically Active DNA-Protein Nanogels with Tunable Cross-Linking Density. Biomacromolecules 2021; 22:3431-3439. [PMID: 34260203 DOI: 10.1021/acs.biomac.1c00501] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/30/2023]
Abstract
Hybrid DNA-protein nanogels represent potential protein vectors and enzymatic nanoreactors for modern biotechnology. Here, we describe a new, easy, and robust method for preparation of tunable DNA-protein nanogels with controllable size and density. For this purpose, polymerase chain reaction is used to prepare highly biotinylated DNA as a soft biopolymeric backbone, which can be efficiently cross-linked via streptavidin-biotin binding. This approach enables us to control both the density and size of the resulting nanogels not only by adjusting the amount of the cross-linking streptavidin but also by using different rates of DNA biotinylation. This gives DNA-streptavidin nanogels with the size ranging from 80 nm, for the most compact state, to up to 200 nm. Furthermore, using streptavidin-enzyme conjugates allows the straightforward one-pot incorporation of enzymes during the preparation of the nanogels. Monoenzymatic and multienzymatic nanogels have been obtained in this manner, and their catalytic activities have been characterized. All tested enzymes (alkaline phosphatase (AP), horseradish peroxidase (HRP), and β-galactosidase (βGal)), incorporated individually or in a coupled manner (glucose oxidase (GOx)-HRP cascade), were shown to remain functional. The activities of AP and βGal were unchanged while that of HRP was slightly improved inside the nanogels. We demonstrate that, for HRP, it is not the DNA-to-enzyme ratio but the physical density of the functionalized DNA nanogels that is responsible for the improvement of its enzymatic activity.
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Affiliation(s)
- Marina Mariconti
- PASTEUR, Department of Chemistry, PSL University, Sorbonne Université, CNRS, Ecole Normale Supérieure, Paris 75005, France
| | - Mathieu Morel
- PASTEUR, Department of Chemistry, PSL University, Sorbonne Université, CNRS, Ecole Normale Supérieure, Paris 75005, France
| | - Damien Baigl
- PASTEUR, Department of Chemistry, PSL University, Sorbonne Université, CNRS, Ecole Normale Supérieure, Paris 75005, France
| | - Sergii Rudiuk
- PASTEUR, Department of Chemistry, PSL University, Sorbonne Université, CNRS, Ecole Normale Supérieure, Paris 75005, France
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3
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Lin P, Dinh H, Nakata E, Morii T. Dynamic Shape Transformation of a DNA Scaffold Applied for an Enzyme Nanocarrier. Front Chem 2021; 9:697857. [PMID: 34249866 PMCID: PMC8263910 DOI: 10.3389/fchem.2021.697857] [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: 04/20/2021] [Accepted: 06/01/2021] [Indexed: 11/13/2022] Open
Abstract
Structural programmability and accurate addressability of DNA nanostructures are ideal characteristics for the platform of arranging enzymes with the nanoscale precision. In this study, a three-dimensional DNA scaffold was designed to enable a dynamic shape transition from an open plate-like structure to its closed state of a hexagonal prism structure. The two domains in the open state were folded together to transform into the closed state by hybridization of complementary short DNA closing keys at both of the facing edges in over 90% yield. The shape transformation of the DNA scaffold was extensively studied by means of the fluorescence energy transfer measurement, atomic force microscope images, and agarose gel electrophoretic analyses. A dimeric enzyme xylitol dehydrogenase was assembled on the DNA scaffold in its open state in a high-loading yield. The enzyme loaded on the scaffold was subsequently transformed to its closed state by the addition of short DNA closing keys. The enzyme encapsulated in the closed state displayed comparable activity to that in the open state, ensuring that the catalytic activity of the enzyme was well maintained in the DNA nanocarrier. The nanocarrier with efficient encapsulation ability is potentially applicable for drug delivery, biosensing, biocatalytic, and diagnostic tools.
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Affiliation(s)
- Peng Lin
- Institute of Advanced Energy, Kyoto University, Kyoto, Japan
| | - Huyen Dinh
- Institute of Advanced Energy, Kyoto University, Kyoto, Japan
| | - Eiji Nakata
- Institute of Advanced Energy, Kyoto University, Kyoto, Japan
| | - Takashi Morii
- Institute of Advanced Energy, Kyoto University, Kyoto, Japan
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4
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Shen H, Zhou Z, He W, Chao H, Su P, Song J, Yang Y. Oligonucleotide-Functionalized Enzymes Chemisorbing on Magnetic Layered Double Hydroxides: A Multimodal Catalytic Platform with Boosted Activity for Ultrasensitive Glucose Detection. ACS APPLIED MATERIALS & INTERFACES 2021; 13:14995-15007. [PMID: 33769803 DOI: 10.1021/acsami.1c01350] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/12/2023]
Abstract
A reasonable design of multifarious chemo- and biocatalytic functions within individual nano/microunits is urgently desired for high-performance cascade reactions but has heretofore remained elusive. Herein, glucose oxidase was functionalized with oligonucleotides and steadily chemisorbed on magnetic layered double hydroxides (mLDHs) to construct a multimodal catalytic platform for realizing divergent reactions with heterogeneous and biocatalytic steps. The flowerlike mLDHs served both as an enzyme support and a peroxidase mimic cooperating with enzymes for tandem catalysis. Oligo-DNA connected the enzymes to mLDHs like a bridge, and a stepwise ligand-exchange-assisted coordination mechanism was proposed to explain the robust interaction between DNA and mLDHs. More importantly, DNA significantly improved the bioactivity of the whole system. The acceleration mechanism was attributed to the diffusion tunnels for the substrate/product and enhanced substrates binding on mLDHs. The multimodal catalytic platform was applied for colorimetric and electrochemical sensing of glucose with a low limit of detection and high selectivity. The practical analysis capability of the ultrasensitive sensor was evaluated by detecting glucose in human serum and sweat, showing reliable results, satisfactory recovery, and excellent stability. The strategy of combining mLDHs and enzymes for cascade catalysis provides a universal approach to prepare chemo-enzyme hybrids with high performance, which holds great promise for applications in biosensors and industrial catalysis.
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Affiliation(s)
- Hao Shen
- Beijing Key Laboratory of Environmentally Harmful Chemical Analysis, College of Chemistry, Beijing University of Chemical Technology, Beijing 100029, P. R. China
| | - Zixin Zhou
- Beijing Key Laboratory of Environmentally Harmful Chemical Analysis, College of Chemistry, Beijing University of Chemical Technology, Beijing 100029, P. R. China
| | - Wenting He
- Beijing Key Laboratory of Environmentally Harmful Chemical Analysis, College of Chemistry, Beijing University of Chemical Technology, Beijing 100029, P. R. China
| | - Hao Chao
- Beijing Key Laboratory of Environmentally Harmful Chemical Analysis, College of Chemistry, Beijing University of Chemical Technology, Beijing 100029, P. R. China
| | - Ping Su
- Beijing Key Laboratory of Environmentally Harmful Chemical Analysis, College of Chemistry, Beijing University of Chemical Technology, Beijing 100029, P. R. China
| | - Jiayi Song
- Beijing Key Laboratory of Environmentally Harmful Chemical Analysis, College of Chemistry, Beijing University of Chemical Technology, Beijing 100029, P. R. China
| | - Yi Yang
- Beijing Key Laboratory of Environmentally Harmful Chemical Analysis, College of Chemistry, Beijing University of Chemical Technology, Beijing 100029, P. R. China
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5
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Lim S, Kim J, Kim Y, Xu D, Clark DS. CRISPR/Cas-directed programmable assembly of multi-enzyme complexes. Chem Commun (Camb) 2020; 56:4950-4953. [PMID: 32239050 DOI: 10.1039/d0cc01174f] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
We describe a versatile CRISPR/Cas-based strategy to construct multi-enzyme complexes scaffolded on a DNA template in programmable patterns. Catalytically inactive dCas9 nuclease was used in combination with SpyCatcher-SpyTag chemistry to assemble enzymes in a highly modular fashion. Five enzymes comprising the violacein biosynthesis pathway were precisely organized in nanometer proximity; a notable increase in violacein production demonstrated the benefits of scaffolding.
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Affiliation(s)
- Samuel Lim
- Department of Chemical and Biomolecular Engineering, University of California, Berkeley, CA 94720, USA.
| | - Jiwoo Kim
- Department of Chemical and Biomolecular Engineering, University of California, Berkeley, CA 94720, USA.
| | - Yujin Kim
- Department of Chemical and Biomolecular Engineering, University of California, Berkeley, CA 94720, USA.
| | - Dawei Xu
- Department of Chemical and Biomolecular Engineering, University of California, Berkeley, CA 94720, USA.
| | - Douglas S Clark
- Department of Chemical and Biomolecular Engineering, University of California, Berkeley, CA 94720, USA. and Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, 1 Cyclotron Road, Berkeley, CA 94720, USA
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6
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Zhao D, Kong Y, Zhao S, Xing H. Engineering Functional DNA–Protein Conjugates for Biosensing, Biomedical, and Nanoassembly Applications. Top Curr Chem (Cham) 2020; 378:41. [DOI: 10.1007/s41061-020-00305-7] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2019] [Accepted: 05/05/2020] [Indexed: 12/31/2022]
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7
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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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8
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Lancaster L, Abdallah W, Banta S, Wheeldon I. Engineering enzyme microenvironments for enhanced biocatalysis. Chem Soc Rev 2018; 47:5177-5186. [PMID: 29796541 DOI: 10.1039/c8cs00085a] [Citation(s) in RCA: 93] [Impact Index Per Article: 15.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
Protein engineering provides a means to alter protein structure leading to new functions. Much work has focused on the engineering of enzyme active sites to enhance catalytic activity, however there is an increasing trend towards engineering other aspects of biocatalysts as these efforts can also lead to useful improvements. This tutorial discusses recent advances in engineering an enzyme's local chemical and physical environment, with the goal of enhancing enzyme reaction kinetics, substrate selectivity, and activity in harsh conditions (e.g., low or high pH). By introducing stimuli-responsiveness to these enzyme modifications, dynamic control of activity also becomes possible. These new biomolecular and protein engineering techniques are separate and independent from traditional active site engineering and can therefore be applied synergistically to create new biocatalyst technologies with novel functions.
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Affiliation(s)
- Louis Lancaster
- Department of Chemical and Environmental Engineering, University of California, Riverside, Riverside, CA 92521, USA.
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9
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Zhou L, Morel M, Rudiuk S, Baigl D. Intramolecularly Protein-Crosslinked DNA Gels: New Biohybrid Nanomaterials with Controllable Size and Catalytic Activity. SMALL (WEINHEIM AN DER BERGSTRASSE, GERMANY) 2017; 13:1700706. [PMID: 28561941 DOI: 10.1002/smll.201700706] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/02/2017] [Revised: 04/11/2017] [Indexed: 06/07/2023]
Abstract
DNA micro- and nanogels-small-sized hydrogels made of a crosslinked DNA backbone-constitute new promising materials, but their functions have mainly been limited to those brought by DNA. Here a new way is described to prepare sub-micrometer-sized DNA gels of controllable crosslinking density that are able to embed novel functions, such as an enzymatic activity. It consists of using proteins, instead of traditional base-pairing assembly or covalent approaches, to form crosslinks inside individual DNA molecules, resulting in structures referred to as intramolecularly protein-crosslinked DNA gels (IPDGs). It is first shown that the addition of streptavidin to biotinylated T4DNA results in the successful formation of thermally stable IPDGs with a controllable crosslinking density, forming structures ranging from elongated to raspberry-shaped and pearl-necklace-like morphologies. Using reversible DNA condensation strategies, this paper shows that the gels can be reversibly actuated at a low crosslinking density, or further stabilized when they are highly crosslinked. Finally, by using streptavidin-protein conjugates, IPDGs with various enzymes are successfully functionalized. It is demonstrated that the enzymes keep their catalytic activity upon their incorporation into the gels, opening perspectives ranging from biotechnologies (e.g., enzyme manipulation) to nanomedicine (e.g., vectorization).
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Affiliation(s)
- Li Zhou
- PASTEUR, Department of Chemistry, École normale supérieure, UPMC Univ. Paris 06, CNRS, PSL Research University, 75005, Paris, France
- Sorbonne Universités, UPMC Univ. Paris 06, Ecole normale supérieure, CNRS, PASTEUR, 75005, Paris, France
| | - Mathieu Morel
- PASTEUR, Department of Chemistry, École normale supérieure, UPMC Univ. Paris 06, CNRS, PSL Research University, 75005, Paris, France
- Sorbonne Universités, UPMC Univ. Paris 06, Ecole normale supérieure, CNRS, PASTEUR, 75005, Paris, France
| | - Sergii Rudiuk
- PASTEUR, Department of Chemistry, École normale supérieure, UPMC Univ. Paris 06, CNRS, PSL Research University, 75005, Paris, France
- Sorbonne Universités, UPMC Univ. Paris 06, Ecole normale supérieure, CNRS, PASTEUR, 75005, Paris, France
| | - Damien Baigl
- PASTEUR, Department of Chemistry, École normale supérieure, UPMC Univ. Paris 06, CNRS, PSL Research University, 75005, Paris, France
- Sorbonne Universités, UPMC Univ. Paris 06, Ecole normale supérieure, CNRS, PASTEUR, 75005, Paris, France
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10
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Marth G, Hartley AM, Reddington SC, Sargisson LL, Parcollet M, Dunn KE, Jones DD, Stulz E. Precision Templated Bottom-Up Multiprotein Nanoassembly through Defined Click Chemistry Linkage to DNA. ACS NANO 2017; 11:5003-5010. [PMID: 28414900 DOI: 10.1021/acsnano.7b01711] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/07/2023]
Abstract
We demonstrate an approach that allows attachment of single-stranded DNA (ssDNA) to a defined residue in a protein of interest (POI) so as to provide optimal and well-defined multicomponent assemblies. Using an expanded genetic code system, azido-phenylalanine (azF) was incorporated at defined residue positions in each POI; copper-free click chemistry was used to attach exactly one ssDNA at precisely defined residues. By choosing an appropriate residue, ssDNA conjugation had minimal impact on protein function, even when attached close to active sites. The protein-ssDNA conjugates were used to (i) assemble double-stranded DNA systems with optimal communication (energy transfer) between normally separate groups and (ii) generate multicomponent systems on DNA origami tiles, including those with enhanced enzyme activity when bound to the tile. Our approach allows any potential protein to be simply engineered to attach ssDNA or related biomolecules, creating conjugates for designed and highly precise multiprotein nanoscale assembly with tailored functionality.
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Affiliation(s)
- Gabriella Marth
- School of Chemistry and Institute for Life Sciences, University of Southampton , Highfield, Southampton SO17 1BJ, United Kingdom
| | - Andrew M Hartley
- School of Biosciences, Cardiff University , Cardiff CF10 3AT, United Kingdom
| | - Samuel C Reddington
- School of Biosciences, Cardiff University , Cardiff CF10 3AT, United Kingdom
| | - Lauren L Sargisson
- School of Chemistry and Institute for Life Sciences, University of Southampton , Highfield, Southampton SO17 1BJ, United Kingdom
| | - Marlène Parcollet
- School of Chemistry and Institute for Life Sciences, University of Southampton , Highfield, Southampton SO17 1BJ, United Kingdom
| | - Katherine E Dunn
- Department of Electronics, University of York , Heslington, York YO10 5DD, United Kingdom
| | - D Dafydd Jones
- School of Biosciences, Cardiff University , Cardiff CF10 3AT, United Kingdom
| | - Eugen Stulz
- School of Chemistry and Institute for Life Sciences, University of Southampton , Highfield, Southampton SO17 1BJ, United Kingdom
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11
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Gao Y, Or S, Toop A, Wheeldon I. DNA Nanostructure Sequence-Dependent Binding of Organophosphates. LANGMUIR : THE ACS JOURNAL OF SURFACES AND COLLOIDS 2017; 33:2033-2040. [PMID: 28165751 DOI: 10.1021/acs.langmuir.6b03131] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/06/2023]
Abstract
Understanding the molecular interactions between small molecules and double-stranded DNA has important implications on the design and development of DNA and DNA-protein nanomaterials. Such materials can be assembled into a vast array of 1-, 2-, and 3D structures that contain a range of chemical and physical features where small molecules can bind via intercalation, groove binding, and electrostatics. In this work, we use a series of simulation-guided binding assays and spectroscopy techniques to investigate the binding of selected organophosphtates, methyl parathion, paraoxon, their common enzyme hydrolysis product p-nitrophenol, and double-stranded DNA fragments and DNA DX tiles, a basic building block of DNA-based materials. Docking simulations suggested that the binding strength of each compound was DNA sequence-dependent, with dissociation constants in the micromolar range. Microscale thermophoresis and fluorescence binding assays confirmed sequence-dependent binding and that paraoxon bound to DNA with Kd's between ∼10 and 300 μM, while methyl parathion bound with Kd's between ∼10 and 100 μM. p-Nitrophenol also bound to DNA but with affinities up to 650 μM. Changes in biding affinity were due to changes in binding mode as revealed by circular dichroism spectroscopy. Based on these results, two DNA DX tiles were constructed and analyzed, revealing tighter binding to the studied compounds. Taken together, the results presented here add to our fundamental understanding of the molecular interactions of these compounds with biological materials and opens new possibilities in DNA-based sensors, DNA-based matrices for organophosphate extraction, and enzyme-DNA technologies for organophosphate hydrolysis.
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Affiliation(s)
- Yingning Gao
- Department of Chemical and Environmental Engineering, University of California , Riverside, California 92521, United States
| | - Samson Or
- Department of Chemical and Environmental Engineering, University of California , Riverside, California 92521, United States
| | - Aaron Toop
- Department of Chemical and Environmental Engineering, University of California , Riverside, California 92521, United States
| | - Ian Wheeldon
- Department of Chemical and Environmental Engineering, University of California , Riverside, California 92521, United States
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12
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Collins J, Zhang T, Oh SW, Maloney R, Fu J. DNA-crowded enzyme complexes with enhanced activities and stabilities. Chem Commun (Camb) 2017; 53:13059-13062. [DOI: 10.1039/c7cc07361e] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/03/2023]
Abstract
We present a robust and simple method to prepare DNA-crowded enzyme complexes by directly assembling long DNA duplexes on the enzyme surface.
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Affiliation(s)
- John Collins
- Department of Chemistry
- Rutgers University – Camden
- Camden
- USA
| | - Ting Zhang
- Department of Chemistry
- Rutgers University – Camden
- Camden
- USA
| | - Sung Won Oh
- Center for Computational and Integrative Biology
- Rutgers University – Camden
- Camden
- USA
| | - Robert Maloney
- Department of Chemistry
- Rutgers University – Camden
- Camden
- USA
| | - Jinglin Fu
- Department of Chemistry
- Rutgers University – Camden
- Camden
- USA
- Center for Computational and Integrative Biology
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13
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Deiana M, Pokladek Z, Olesiak-Banska J, Młynarz P, Samoc M, Matczyszyn K. Photochromic switching of the DNA helicity induced by azobenzene derivatives. Sci Rep 2016; 6:28605. [PMID: 27339811 PMCID: PMC4919647 DOI: 10.1038/srep28605] [Citation(s) in RCA: 33] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2016] [Accepted: 06/03/2016] [Indexed: 01/08/2023] Open
Abstract
The photochromic properties of azobenzene, involving conformational changes occurring upon interaction with light, provide an excellent tool to establish new ways of selective regulation applied to biosystems. We report here on the binding of two water-soluble 4-(phenylazo)benzoic acid derivatives (Azo-2N and Azo-3N) with double stranded DNA and demonstrate that the photoisomerization of Azo-3N leads to changes in DNA structure. In particular, we show that stabilization and destabilization of the B-DNA secondary structure can be photochemically induced in situ by light. This photo-triggered process is fully reversible and could be an alternative pathway to control a broad range of biological processes. Moreover, we found that the bicationic Azo-3N exhibited a higher DNA-binding constant than the monocationic Azo-2N pointing out that the number of positive charges along the photosensitive polyamines chain plays a pivotal role in stabilizing the photochrome-DNA complex.
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Affiliation(s)
- Marco Deiana
- Advanced Materials Engineering and Modelling Group, Faculty of Chemistry, Wroclaw University of Science and Technology, Wyb. Wyspianskiego 27, 50-370 Wroclaw, Poland
| | - Ziemowit Pokladek
- Department of Bioorganic Chemistry, Faculty of Chemistry, Wroclaw University of Science and Technology, Wyb. Wyspianskiego 27, 50-370 Wroclaw, Poland
| | - Joanna Olesiak-Banska
- Advanced Materials Engineering and Modelling Group, Faculty of Chemistry, Wroclaw University of Science and Technology, Wyb. Wyspianskiego 27, 50-370 Wroclaw, Poland
| | - Piotr Młynarz
- Department of Bioorganic Chemistry, Faculty of Chemistry, Wroclaw University of Science and Technology, Wyb. Wyspianskiego 27, 50-370 Wroclaw, Poland
| | - Marek Samoc
- Advanced Materials Engineering and Modelling Group, Faculty of Chemistry, Wroclaw University of Science and Technology, Wyb. Wyspianskiego 27, 50-370 Wroclaw, Poland
| | - Katarzyna Matczyszyn
- Advanced Materials Engineering and Modelling Group, Faculty of Chemistry, Wroclaw University of Science and Technology, Wyb. Wyspianskiego 27, 50-370 Wroclaw, Poland
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14
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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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15
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Li W, Li Y, Yin X, Liang Y, Li J, Wang C, Lan Y, Wang H, Ju Y, Li G. Azobenzene-bridged bile acid dimers: an interesting class of conjugates with conformation-controlled bioactivity. Tetrahedron Lett 2016. [DOI: 10.1016/j.tetlet.2016.04.107] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/21/2022]
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16
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Chang CY, Lin HJ, Li BR, Li YK. A Novel Metallo-β-Lactamase Involved in the Ampicillin Resistance of Streptococcus pneumoniae ATCC 49136 Strain. PLoS One 2016; 11:e0155905. [PMID: 27214294 PMCID: PMC4877090 DOI: 10.1371/journal.pone.0155905] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2016] [Accepted: 05/08/2016] [Indexed: 12/28/2022] Open
Abstract
Streptococcus pneumoniae, a penicillin-sensitive bacterium, is recognized as a major cause of pneumonia and is treated clinically with penicillin-based antibiotics. The rapid increase in resistance to penicillin and other antibiotics affects 450 million people globally and results in 4 million deaths every year. To unveil the mechanism of resistance of S. pneumoniae is thus an important issue to treat streptococcal disease that might consequently save millions of lives around the world. In this work, we isolated a streptococci-conserved L-ascorbate 6-phosphate lactonase, from S. pneumoniae ATCC 49136. This protein reveals a metallo-β-lactamase activity in vitro, which is able to deactivate an ampicillin-based antibiotic by hydrolyzing the amide bond of the β-lactam ring. The Michaelis parameter (Km) = 25 μM and turnover number (kcat) = 2 s(-1) were obtained when nitrocefin was utilized as an optically measurable substrate. Through confocal images and western blot analyses with a specific antibody, the indigenous protein was recognized in S. pneumoniae ATCC 49136. The protein-overexpressed S. pneumonia exhibits a high ampicillin-tolerance ability in vivo. In contrast, the protein-knockout S. pneumonia reveals the ampicillin-sensitive feature relative to the wild type strain. Based on these results, we propose that this protein is a membrane-associated metallo-β-lactamase (MBL) involved in the antibiotic-resistant property of S. pneumoniae.
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Affiliation(s)
- Chia-Yu Chang
- Department of Applied Chemistry, National Chiao Tung University, 1001 University Road, Hsinchu, Taiwan
| | - Hui-Jen Lin
- Department of Applied Chemistry, National Chiao Tung University, 1001 University Road, Hsinchu, Taiwan
| | - Bor-Ran Li
- Institute of Biomedical Engineering, National Chiao Tung University, 1001 University Road, Hsinchu, Taiwan
- Center for Interdisciplinary Science, National Chiao Tung University, 1001 University Road, Hsinchu, Taiwan
| | - Yaw-Kuen Li
- Department of Applied Chemistry, National Chiao Tung University, 1001 University Road, Hsinchu, Taiwan
- Center for Interdisciplinary Science, National Chiao Tung University, 1001 University Road, Hsinchu, Taiwan
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17
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Schimka S, Santer S, Mujkić-Ninnemann NM, Bléger D, Hartmann L, Wehle M, Lipowsky R, Santer M. Photosensitive Peptidomimetic for Light-Controlled, Reversible DNA Compaction. Biomacromolecules 2016; 17:1959-68. [DOI: 10.1021/acs.biomac.6b00052] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/03/2023]
Affiliation(s)
- Selina Schimka
- Institute
of Physics and Astronomy, University of Potsdam, 14476 Potsdam, Germany
- Max Planck Institute
of Colloids and Interfaces, 14424 Potsdam, Germany
| | - Svetlana Santer
- Institute
of Physics and Astronomy, University of Potsdam, 14476 Potsdam, Germany
| | | | - David Bléger
- Humboldt-Universität
zu Berlin, 12489 Berlin, Germany
| | - Laura Hartmann
- Max Planck Institute
of Colloids and Interfaces, 14424 Potsdam, Germany
| | - Marko Wehle
- Theory
and Bio-Systems Group, Max Planck Institute of Colloids and Interfaces, 14424 Potsdam, Germany
| | - Reinhard Lipowsky
- Theory
and Bio-Systems Group, Max Planck Institute of Colloids and Interfaces, 14424 Potsdam, Germany
| | - Mark Santer
- Theory
and Bio-Systems Group, Max Planck Institute of Colloids and Interfaces, 14424 Potsdam, Germany
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18
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Takahara M, Hayashi K, Goto M, Kamiya N. Enzymatic conjugation of multiple proteins on a DNA aptamer in a tail-specific manner. Biotechnol J 2016; 11:814-23. [PMID: 27119459 DOI: 10.1002/biot.201500560] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2015] [Revised: 02/09/2016] [Accepted: 04/22/2016] [Indexed: 12/19/2022]
Abstract
Conjugation of single-strand DNA aptamers and enzymes has been of great significance in bioanalytical and biomedical applications because of the unlimited functions provided by DNA aptamer direction. Therefore, we developed efficient tailing of a DNA aptamer, with end-specific conjugation of multiple enzymes, through enzymatic catalysis. Terminal deoxynucleotidyl transferase (TdT) added multiple Z-Gln-Gly (Z-QG) moieties to the 3'-end of a DNA aptamer via the addition of Z-QG-modified deoxyuridine triphosphate (Z-QG-dUTP) and deoxynucleoside triphosphates (dNTPs). The resultant (Z-QG)m -(dN)l-aptamer, whose Z-QGs with dN spacers served as stickers for microbial transglutaminase (MTG), were crosslinked between the Z-QGs on the DNA and a substrate peptide sequence containing lysine (K), fused to a recombinant enzyme (i.e. bacterial alkaline phosphatase; BAP) by MTG. The incorporation efficiency of Z-QG moieties on the aptamer tail and the subsequent conjugation efficiency with multiple enzyme molecules were dramatically altered by the presence of dNTPs, revealing that a combination of Z-QG-dUTP/dTTP comprised the best labeling efficiency and corresponding properties during analytical performance. Thus, a novel optimized platform for designing (BAP)n -(dT)l-DNA aptamers was demonstrated for the first time in this article, offering unique opportunities for tailoring new types of covalent protein-nucleic acid conjugates in a controllable way.
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Affiliation(s)
- Mari Takahara
- Department of Applied Chemistry, Graduate School of Engineering, Kyushu University, Fukuoka, Motooka, Japan
| | - Kounosuke Hayashi
- Department of Applied Chemistry, Graduate School of Engineering, Kyushu University, Fukuoka, Motooka, Japan.,Hitachi Aloka Medical, Ltd, Tokyo, Mure, Japan
| | - Masahiro Goto
- Department of Applied Chemistry, Graduate School of Engineering, Kyushu University, Fukuoka, Motooka, Japan.,Center for Future Chemistry, Kyushu University, Fukuoka, Motooka, Japan
| | - Noriho Kamiya
- Department of Applied Chemistry, Graduate School of Engineering, Kyushu University, Fukuoka, Motooka, Japan. .,Center for Future Chemistry, Kyushu University, Fukuoka, Motooka, Japan.
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19
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Zhao Z, Fu J, Dhakal S, Johnson-Buck A, Liu M, Zhang T, Woodbury NW, Liu Y, Walter NG, Yan H. Nanocaged enzymes with enhanced catalytic activity and increased stability against protease digestion. Nat Commun 2016; 7:10619. [PMID: 26861509 PMCID: PMC4749968 DOI: 10.1038/ncomms10619] [Citation(s) in RCA: 287] [Impact Index Per Article: 35.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2015] [Accepted: 01/05/2016] [Indexed: 01/06/2023] Open
Abstract
Cells routinely compartmentalize enzymes for enhanced efficiency of their metabolic pathways. Here we report a general approach to construct DNA nanocaged enzymes for enhancing catalytic activity and stability. Nanocaged enzymes are realized by self-assembly into DNA nanocages with well-controlled stoichiometry and architecture that enabled a systematic study of the impact of both encapsulation and proximal polyanionic surfaces on a set of common metabolic enzymes. Activity assays at both bulk and single-molecule levels demonstrate increased substrate turnover numbers for DNA nanocage-encapsulated enzymes. Unexpectedly, we observe a significant inverse correlation between the size of a protein and its activity enhancement. This effect is consistent with a model wherein distal polyanionic surfaces of the nanocage enhance the stability of active enzyme conformations through the action of a strongly bound hydration layer. We further show that DNA nanocages protect encapsulated enzymes against proteases, demonstrating their practical utility in functional biomaterials and biotechnology.
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Affiliation(s)
- Zhao Zhao
- Center for Molecular Design and Biomimetics, the Biodesign Institute at Arizona State University, Tempe, Arizona 85287, USA
- School of Molecular Sciences, Arizona State University, Tempe, Arizona 85287, USA
| | - Jinglin Fu
- Department of Chemistry, Center for Computational and Integrative Biology, Rutgers University-Camden, Camden, New Jersey 08102, USA
| | - Soma Dhakal
- Department of Chemistry, Single Molecule Analysis Group, University of Michigan, Ann Arbor, Michigan 48109, USA
| | - Alexander Johnson-Buck
- Department of Chemistry, Single Molecule Analysis Group, University of Michigan, Ann Arbor, Michigan 48109, USA
| | - Minghui Liu
- Center for Molecular Design and Biomimetics, the Biodesign Institute at Arizona State University, Tempe, Arizona 85287, USA
| | - Ting Zhang
- Department of Chemistry, Center for Computational and Integrative Biology, Rutgers University-Camden, Camden, New Jersey 08102, USA
| | - Neal W. Woodbury
- School of Molecular Sciences, Arizona State University, Tempe, Arizona 85287, USA
- Center for Innovations in Medicine, the Biodesign Institute at Arizona State University, Tempe, Arizona 85287, USA
| | - Yan Liu
- Center for Molecular Design and Biomimetics, the Biodesign Institute at Arizona State University, Tempe, Arizona 85287, USA
- School of Molecular Sciences, Arizona State University, Tempe, Arizona 85287, USA
| | - Nils G. Walter
- Department of Chemistry, Single Molecule Analysis Group, University of Michigan, Ann Arbor, Michigan 48109, USA
| | - Hao Yan
- Center for Molecular Design and Biomimetics, the Biodesign Institute at Arizona State University, Tempe, Arizona 85287, USA
- School of Molecular Sciences, Arizona State University, Tempe, Arizona 85287, USA
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20
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Dozier JK, Khatwani SL, Wollack JW, Wang YC, Schmidt-Dannert C, Distefano MD. Engineering protein farnesyltransferase for enzymatic protein labeling applications. Bioconjug Chem 2014; 25:1203-12. [PMID: 24946229 PMCID: PMC4103756 DOI: 10.1021/bc500240p] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
Abstract
Creating covalent protein conjugates is an active area of research due to the wide range of uses for protein conjugates spanning everything from biological studies to protein therapeutics. Protein Farnesyltransferase (PFTase) has been used for the creation of site-specific protein conjugates, and a number of PFTase substrates have been developed to facilitate that work. PFTase is an effective catalyst for protein modification because it transfers Farnesyl diphosphate (FPP) analogues to protein substrates on a cysteine four residues from the C-terminus. While much work has been done to synthesize various FPP analogues, there are few reports investigating how mutations in PFTase alter the kinetics with these unnatural analogues. Herein we examined how different mutations within the PFTase active site alter the kinetics of the PFTase reaction with a series of large FPP analogues. We found that mutating either a single tryptophan or tyrosine residue to alanine results in greatly improved catalytic parameters, particularly in kcat. Mutation of tryptophan 102β to alanine caused a 4-fold increase in kcat and a 10-fold decrease in KM for a benzaldehyde-containing FPP analogue resulting in an overall 40-fold increase in catalytic efficiency. Similarly, mutation of tyrosine 205β to alanine caused a 25-fold increase in kcat and a 10-fold decrease in KM for a coumarin-containing analogue leading to a 300-fold increase in catalytic efficiency. Smaller but significant changes in catalytic parameters were also obtained for cyclo-octene- and NBD-containing FPP analogues. The latter compound was used to create a fluorescently labeled form of Ciliary Neurotrophic Factor (CNTF), a protein of therapeutic importance. Additionally, computational modeling was performed to study how the large non-natural isoprenoid analogues can fit into the active sites enlarged via mutagenesis. Overall, these results demonstrate that PFTase can be improved via mutagenesis in ways that will be useful for protein engineering and the creation of site-specific protein conjugates.
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Affiliation(s)
- Jonathan K Dozier
- Department of Chemistry, University of Minnesota , Minneapolis, Minnesota 55455, United States
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21
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Flory JD, Simmons CR, Lin S, Johnson T, Andreoni A, Zook J, Ghirlanda G, Liu Y, Yan H, Fromme P. Low temperature assembly of functional 3D DNA-PNA-protein complexes. J Am Chem Soc 2014; 136:8283-95. [PMID: 24871902 DOI: 10.1021/ja501228c] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
Proteins have evolved to carry out nearly all the work required of living organisms within complex inter- and intracellular environments. However, systematically investigating the range of interactions experienced by a protein that influence its function remains challenging. DNA nanostructures are emerging as a convenient method to arrange a broad range of guest molecules. However, flexible methods are needed for arranging proteins in more biologically relevant 3D geometries under mild conditions that preserve protein function. Here we demonstrate how peptide nucleic acid (PNA) can be used to control the assembly of cytochrome c (12.5 kDa, pI 10.5) and azurin (13.9 kDa, pI 5.7) proteins into separate 3D DNA nanocages, in a process that maintains protein function. Toehold-mediated DNA strand displacement is introduced as a method to purify PNA-protein conjugates. The PNA-proteins were assembled within 2 min at room temperature and within 4 min at 11 °C, and hybridize with even greater efficiency than PNA conjugated to a short peptide. Gel electrophoresis and steady state and time-resolved fluorescence spectroscopy were used to investigate the effect of protein surface charge on its interaction with the negatively charged DNA nanocage. These data were used to generate a model of the DNA-PNA-protein complexes that show the negatively charged azurin protein repelled away from the DNA nanocage while the positively charged cytochrome c protein remains within and closely interacts with the DNA nanocage. When conjugated to PNA and incorporated into the DNA nanocage, the cytochrome c secondary structure and catalytic activity were maintained, and its redox potential was reduced modestly by 20 mV possibly due to neutralization of some positive surface charges. This work demonstrates a flexible new approach for using 3D nucleic acid (PNA-DNA) nanostructures to control the assembly of functional proteins, and facilitates further investigation of protein interactions as well as engineer more elaborate 3D protein complexes.
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Affiliation(s)
- Justin D Flory
- Department of Chemistry and Biochemistry, ‡Center for Bio-Inspired Solar Fuel Production, and §Biodesign Institute, Arizona State University , Tempe, Arizona 85287, United States
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22
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Venancio-Marques A, Bergen A, Rossi-Gendron C, Rudiuk S, Baigl D. Photosensitive polyamines for high-performance photocontrol of DNA higher-order structure. ACS NANO 2014; 8:3654-3663. [PMID: 24580129 DOI: 10.1021/nn500266b] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/03/2023]
Abstract
Polyamines are small, ubiquitous, positively charged molecules that play an essential role in numerous biological processes such as DNA packaging, gene regulation, neuron activity, and cell proliferation. Here, we synthesize the first series of photosensitive polyamines (PPAs) and demonstrate their ability to photoreversibly control nanoscale DNA higher-order structure with high efficiency. We show with fluorescence microscopy imaging that the efficiency of the PPAs as DNA-compacting agents is directly correlated to their molecular charge. Micromolar concentration of the most efficient molecule described here, a PPA containing three charges at neutral pH, compacts DNA molecules from a few kilobase pairs to a few hundred kilobase pairs, while subsequent 3 min UV illuminations at 365 nm triggers complete unfolding of DNA molecules. Additional application of blue light (440 nm for 3 min) induces the refolding of DNA into the compact state. Atomic force microscopy reveals that the compaction involves a global folding of the whole DNA molecule, whereas UV-induced unfolding is a modification initiated from the periphery of the compacted DNA, resulting in the occurrence of intermediate flower-like structures prior to the fully unfolded state.
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Affiliation(s)
- Anna Venancio-Marques
- Ecole Normale Supérieure-PSL Research University , Department of Chemistry, 24 Rue Lhomond, F-75005, Paris, France
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23
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Idan O, Hess H. Origins of activity enhancement in enzyme cascades on scaffolds. ACS NANO 2013; 7:8658-65. [PMID: 24007359 DOI: 10.1021/nn402823k] [Citation(s) in RCA: 110] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/22/2023]
Abstract
The concept of "metabolic channeling" as a result of rapid transfer of freely diffusing intermediate substrates between two enzymes on nanoscale scaffolds is examined using simulations and mathematical models. The increase in direct substrate transfer due to the proximity of the two enzymes provides an initial but temporary boost to the throughput of the cascade and loses importance as product molecules of enzyme 1 (substrate molecules of enzyme 2) accumulate in the surrounding container. The characteristic time scale at which this boost is significant is given by the ratio of container volume to the product of substrate diffusion constant and interenzyme distance and is on the order of milliseconds to seconds in some experimental systems. However, the attachment of a large number of enzyme pairs to a scaffold provides an increased number of local "targets", extending the characteristic time. If substrate molecules for enzyme 2 are sequestered by an alternative reaction in the container, a scaffold can result in a permanent boost to cascade throughput with a magnitude given by the ratio of the above-defined time scale to the lifetime of the substrate molecule in the container. Finally, a weak attractive interaction between substrate molecules and the scaffold creates a "virtual compartment" and substantially accelerates initial throughput. If intermediate substrates can diffuse freely, placing individual enzyme pairs on scaffolds is only beneficial in large cells, unconfined extracellular spaces or in systems with sequestering reactions.
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Affiliation(s)
- Ofer Idan
- Department of Biomedical Engineering, Columbia University , New York, New York 10027, United States
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