1
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Navarrete-Miguel M, Giussani A, Rubio M, Boggio-Pasqua M, Borin AC, Roca-Sanjuán D. Quantum-Chemistry Study of the Photophysical Properties of 4-Thiouracil and Comparisons with 2-Thiouracil. J Phys Chem A 2024; 128:2273-2285. [PMID: 38504122 PMCID: PMC10982997 DOI: 10.1021/acs.jpca.3c06310] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2023] [Revised: 02/16/2024] [Accepted: 03/03/2024] [Indexed: 03/21/2024]
Abstract
DNA in living beings is constantly damaged by exogenous and endogenous agents. However, in some cases, DNA photodamage can have interesting applications, as it happens in photodynamic therapy. In this work, the current knowledge on the photophysics of 4-thiouracil has been extended by further quantum-chemistry studies to improve the agreement between theory and experiments, to better understand the differences with 2-thiouracil, and, last but not least, to verify its usefulness as a photosensitizer for photodynamic therapy. This study has been carried out by determining the most favorable deactivation paths of UV-vis photoexcited 4-thiouracil by means of the photochemical reaction path approach and an efficient combination of the complete-active-space second-order perturbation theory//complete-active-space self-consistent field (CASPT2//CASSCF), (CASPT2//CASPT2), time-dependent density functional theory (TDDFT), and spin-flip TDDFT (SF-TDDFT) methodologies. By comparing the data computed herein for both 4-thiouracil and 2-thiouracil, a rationale is provided on the relatively higher yields of intersystem crossing, triplet lifetime and singlet oxygen production of 4-thiouracil, and the relatively higher yield of phosphorescence of 2-thiouracil.
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Affiliation(s)
- Miriam Navarrete-Miguel
- Instituto
de Ciencia Molecular, Universitat de València, P.O. Box 22085, ES-46071 Valencia, Spain
| | - Angelo Giussani
- Instituto
de Ciencia Molecular, Universitat de València, P.O. Box 22085, ES-46071 Valencia, Spain
| | - Mercedes Rubio
- Departament
de Química Física, Universitat
de València, 46100 Burjassot, Spain
| | - Martial Boggio-Pasqua
- Laboratoire
de Chimie et Physique Quantiques, IRSAMC,
CNRS et Université Toulouse 3, 118 route de Narbonne, 31062 Toulouse, France
| | - Antonio Carlos Borin
- Department
of Fundamental Chemistry, Institute of Chemistry,
University of São Paulo, Av. Prof. Lineu Prestes, 748, São Paulo CEP 05508-000, Brazil
| | - Daniel Roca-Sanjuán
- Instituto
de Ciencia Molecular, Universitat de València, P.O. Box 22085, ES-46071 Valencia, Spain
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2
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Mozneb M, Mirtaheri E, Sanabria AO, Li CZ. Bioelectronic properties of DNA, protein, cells and their applications for diagnostic medical devices. Biosens Bioelectron 2020; 167:112441. [PMID: 32763825 DOI: 10.1016/j.bios.2020.112441] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2020] [Revised: 07/07/2020] [Accepted: 07/08/2020] [Indexed: 01/25/2023]
Abstract
From a couple of centuries ago, understanding physical properties of biological material, their interference with their natural host and their potential manipulation for employment as a conductor in medical devices, has gathered substantial interest in the field of bioelectronics. With the fast-emerging technologies for fabrication of diagnostic modalities, wearable biosensors and implantable devices, which electrical components are of essential importance, a need for developing novel conductors within such devices has evolved over the past decades. As the possibility of electron transport within small biological molecules, such as DNA and proteins, as well as larger elements such as cells was established, several discoveries of the modern charge characterization technologies were evolved. Development of Electrochemical Scanning Tunneling Microscopy and Nuclear Magnetic Resonance among many other techniques were of vital importance, following the discoveries made in sub-micron scales of biological material. This review covers the most recent understandings of electronic properties within different scale of biological material starting from nanometer range to millimeter-sized organs. We also discuss the state-of-the-art technology that's been made taking advantage of electronic properties of biological material for addressing diseases like Parkinson's Disease and Epilepsy.
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Affiliation(s)
- Maedeh Mozneb
- Florida International University, Biomedical Engineering Department, 10555 West Flagler Street, Miami, FL, 33174, USA.
| | - Elnaz Mirtaheri
- Florida International University, Biomedical Engineering Department, 10555 West Flagler Street, Miami, FL, 33174, USA.
| | - Arianna Ortega Sanabria
- Florida International University, Biomedical Engineering Department, 10555 West Flagler Street, Miami, FL, 33174, USA.
| | - Chen-Zhong Li
- Florida International University, Biomedical Engineering Department, 10555 West Flagler Street, Miami, FL, 33174, USA.
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3
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Kimna C, Lieleg O. Engineering an orchestrated release avalanche from hydrogels using DNA-nanotechnology. J Control Release 2019; 304:19-28. [DOI: 10.1016/j.jconrel.2019.04.028] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2019] [Revised: 04/18/2019] [Accepted: 04/19/2019] [Indexed: 01/08/2023]
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4
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Liu Y, Kumar S, Taylor RE. Mix-and-match nanobiosensor design: Logical and spatial programming of biosensors using self-assembled DNA nanostructures. WILEY INTERDISCIPLINARY REVIEWS-NANOMEDICINE AND NANOBIOTECHNOLOGY 2018; 10:e1518. [PMID: 29633568 DOI: 10.1002/wnan.1518] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Received: 09/29/2017] [Revised: 01/23/2018] [Accepted: 02/14/2018] [Indexed: 01/04/2023]
Abstract
The evergrowing need to understand and engineer biological and biochemical mechanisms has led to the emergence of the field of nanobiosensing. Structural DNA nanotechnology, encompassing methods such as DNA origami and single-stranded tiles, involves the base pairing-driven knitting of DNA into discrete one-, two-, and three-dimensional shapes at nanoscale. Such nanostructures enable a versatile design and fabrication of nanobiosensors. These systems benefit from DNA's programmability, inherent biocompatibility, and the ability to incorporate and organize functional materials such as proteins and metallic nanoparticles. In this review, we present a mix-and-match taxonomy and approach to designing nanobiosensors in which the choices of bioanalyte and transduction mechanism are fully independent of each other. We also highlight opportunities for greater complexity and programmability of these systems that are built using structural DNA nanotechnology. This article is categorized under: Implantable Materials and Surgical Technologies > Nanomaterials and Implants Diagnostic Tools > Biosensing Biology-Inspired Nanomaterials > Nucleic Acid-Based Structures Nanotechnology Approaches to Biology > Nanoscale Systems in Biology.
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Affiliation(s)
- Ying Liu
- Department of Mechanical Engineering, Carnegie Mellon University, Pittsburgh, Pennsylvania
| | - Sriram Kumar
- Department of Mechanical Engineering, Carnegie Mellon University, Pittsburgh, Pennsylvania
| | - Rebecca E Taylor
- Department of Mechanical Engineering, Carnegie Mellon University, Pittsburgh, Pennsylvania.,Department of Biomedical Engineering, Carnegie Mellon University, Pittsburgh, Pennsylvania
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5
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Drobnak I, Ljubetič A, Gradišar H, Pisanski T, Jerala R. Designed Protein Origami. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2017; 940:7-27. [PMID: 27677507 DOI: 10.1007/978-3-319-39196-0_2] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/11/2023]
Abstract
Proteins are highly perfected natural molecular machines, owing their properties to the complex tertiary structures with precise spatial positioning of different functional groups that have been honed through millennia of evolutionary selection. The prospects of designing new molecular machines and structural scaffolds beyond the limits of natural proteins make design of new protein folds a very attractive prospect. However, de novo design of new protein folds based on optimization of multiple cooperative interactions is very demanding. As a new alternative approach to design new protein folds unseen in nature, folds can be designed as a mathematical graph, by the self-assembly of interacting polypeptide modules within the single chain. Orthogonal coiled-coil dimers seem like an ideal building module due to their shape, adjustable length, and above all their designability. Similar to the approach of DNA nanotechnology, where complex tertiary structures are designed from complementary nucleotide segments, a polypeptide chain composed of a precisely specified sequence of coiled-coil forming segments can be designed to self-assemble into polyhedral scaffolds. This modular approach encompasses long-range interactions that define complex tertiary structures. We envision that by expansion of the toolkit of building blocks and design strategies of the folding pathways protein origami technology will be able to construct diverse molecular machines.
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Affiliation(s)
- Igor Drobnak
- Laboratory of Biotechnology, National Institute of Chemistry, Ljubljana, Slovenia
| | - Ajasja Ljubetič
- Laboratory of Biotechnology, National Institute of Chemistry, Ljubljana, Slovenia
| | - Helena Gradišar
- Laboratory of Biotechnology, National Institute of Chemistry, Ljubljana, Slovenia.,EN-FIST Centre of Excellence, Ljubljana, Slovenia
| | - Tomaž Pisanski
- Faculty of Mathematics and Physics, University of Ljubljana, Ljubljana, Slovenia.,University of Primorska, Koper, Slovenia
| | - Roman Jerala
- Laboratory of Biotechnology, National Institute of Chemistry, Ljubljana, Slovenia. .,EN-FIST Centre of Excellence, Ljubljana, Slovenia.
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6
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Hong F, Zhang F, Liu Y, Yan H. DNA Origami: Scaffolds for Creating Higher Order Structures. Chem Rev 2017; 117:12584-12640. [DOI: 10.1021/acs.chemrev.6b00825] [Citation(s) in RCA: 645] [Impact Index Per Article: 92.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Affiliation(s)
- Fan Hong
- The Biodesign Institute and
School of Molecular Sciences, Arizona State University, Tempe, Arizona 85287, United States
| | - Fei Zhang
- The Biodesign Institute and
School of Molecular Sciences, Arizona State University, Tempe, Arizona 85287, United States
| | - Yan Liu
- The Biodesign Institute and
School of Molecular Sciences, Arizona State University, Tempe, Arizona 85287, United States
| | - Hao Yan
- The Biodesign Institute and
School of Molecular Sciences, Arizona State University, Tempe, Arizona 85287, United States
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7
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Estrich NA, Hernandez-Garcia A, de Vries R, LaBean TH. Engineered Diblock Polypeptides Improve DNA and Gold Solubility during Molecular Assembly. ACS NANO 2017; 11:831-842. [PMID: 28048935 DOI: 10.1021/acsnano.6b07291] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/06/2023]
Abstract
Programmed molecular recognition is being developed for the bionanofabrication of mixed organic/inorganic supramolecular assemblies for applications in electronics, photonics, and medicine. For example, DNA-based nanotechnology seeks to exploit the easily programmed complementary base-pairing of DNA to direct assembly of complex, designed nanostructures. Optimal solution conditions for bionanofabrication, mimicking those of biological systems, may involve high concentrations of biomacromolecules (proteins, nucleic acids, etc.) and significant concentrations of various ions (Mg2+, Na+, Cl-, etc.). Given a desire to assemble diverse inorganic components (metallic nanoparticles, quantum dots, carbon nanostructures, etc.), it will be increasingly difficult to find solution conditions simultaneously compatible with all components. Frequently, the use of chemical surfactants is undesirable, leaving a need for the development of alternative strategies. Herein, we discuss the use of artificial, diblock polypeptides in the role of solution compatibilizing agents for molecular assembly. We describe the use of two distinct diblock polypeptides with affinity for DNA in the stabilization of DNA origami and DNA-functionalized gold nanoparticles (spheres and rods) in solution, protection of DNA from enzymatic degradation, as well as two 3D tetrahedral DNA origamis. We present initial data showing that the diblock polypeptides promote the formation in the solution of desired organic/inorganic assemblies.
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Affiliation(s)
- Nicole A Estrich
- Department of Materials Science and Engineering, North Carolina State University , Raleigh, North Carolina 27606, United States
| | - Armando Hernandez-Garcia
- Simpson Querrey Institute for Bionanotechnology, Northwestern University , Evanston, Illinois 60208, United States
- Laboratory of Physical Chemistry and Soft Matter, Wageningen University and Research Centre , Wageningen 6708 PB, The Netherlands
| | - Renko de Vries
- Laboratory of Physical Chemistry and Soft Matter, Wageningen University and Research Centre , Wageningen 6708 PB, The Netherlands
| | - Thomas H LaBean
- Department of Materials Science and Engineering, North Carolina State University , Raleigh, North Carolina 27606, United States
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8
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Nowald C, Käsdorf B, Lieleg O. Controlled nanoparticle release from a hydrogel by DNA-mediated particle disaggregation. J Control Release 2017; 246:71-78. [DOI: 10.1016/j.jconrel.2016.12.015] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2016] [Accepted: 12/09/2016] [Indexed: 10/20/2022]
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9
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Cougnon FBL. Engineering Protein Self-Assembly: A New Approach for the Design of Octahedral Cages. Chembiochem 2016; 17:2296-2298. [DOI: 10.1002/cbic.201600526] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2016] [Indexed: 11/11/2022]
Affiliation(s)
- Fabien B. L. Cougnon
- Department of Organic Chemistry; University of Geneva; 30 Quai Ernest-Ansermet 1211 Geneva 4 Switzerland
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10
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Parlea L, Puri A, Kasprzak W, Bindewald E, Zakrevsky P, Satterwhite E, Joseph K, Afonin KA, Shapiro BA. Cellular Delivery of RNA Nanoparticles. ACS COMBINATORIAL SCIENCE 2016; 18:527-47. [PMID: 27509068 PMCID: PMC6345529 DOI: 10.1021/acscombsci.6b00073] [Citation(s) in RCA: 42] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Abstract
RNA nanostructures can be programmed to exhibit defined sizes, shapes and stoichiometries from naturally occurring or de novo designed RNA motifs. These constructs can be used as scaffolds to attach functional moieties, such as ligand binding motifs or gene expression regulators, for nanobiology applications. This review is focused on four areas of importance to RNA nanotechnology: the types of RNAs of particular interest for nanobiology, the assembly of RNA nanoconstructs, the challenges of cellular delivery of RNAs in vivo, and the delivery carriers that aid in the matter. The available strategies for the design of nucleic acid nanostructures, as well as for formulation of their carriers, make RNA nanotechnology an important tool in both basic research and applied biomedical science.
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Affiliation(s)
- Lorena Parlea
- Gene Regulation and Chromosome Biology Laboratory, National Cancer Institute, Frederick, Maryland 21702, United States
| | - Anu Puri
- Gene Regulation and Chromosome Biology Laboratory, National Cancer Institute, Frederick, Maryland 21702, United States
| | - Wojciech Kasprzak
- Basic Science Program, Leidos Biomedical Research, Inc., Frederick National Laboratory for Cancer Research, Frederick, Maryland 21702, United States
| | - Eckart Bindewald
- Basic Science Program, Leidos Biomedical Research, Inc., Frederick National Laboratory for Cancer Research, Frederick, Maryland 21702, United States
| | - Paul Zakrevsky
- Gene Regulation and Chromosome Biology Laboratory, National Cancer Institute, Frederick, Maryland 21702, United States
| | - Emily Satterwhite
- Department of Chemistry, University of North Carolina at Charlotte, Charlotte, North Carolina 28223, United States
| | - Kenya Joseph
- Department of Chemistry, University of North Carolina at Charlotte, Charlotte, North Carolina 28223, United States
| | - Kirill A. Afonin
- Department of Chemistry, University of North Carolina at Charlotte, Charlotte, North Carolina 28223, United States
- Nanoscale Science Program, University of North Carolina at Charlotte, Charlotte North Carolina 28223, United States
- The Center for Biomedical Engineering and Science, University of North Carolina at Charlotte, Charlotte North Carolina 28223, United States
| | - Bruce A. Shapiro
- Gene Regulation and Chromosome Biology Laboratory, National Cancer Institute, Frederick, Maryland 21702, United States
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11
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Ma Y, Yang X, Wei Y, Yuan Q. Applications of DNA Nanotechnology in Synthesis and Assembly of Inorganic Nanomaterials. CHINESE J CHEM 2016. [DOI: 10.1002/cjoc.201500835] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
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12
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Brown S, Majikes J, Martínez A, Girón TM, Fennell H, Samano EC, LaBean TH. An easy-to-prepare mini-scaffold for DNA origami. NANOSCALE 2015; 7:16621-4. [PMID: 26413973 DOI: 10.1039/c5nr04921k] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/20/2023]
Abstract
The DNA origami strategy for assembling designed supramolecular complexes requires ssDNA as a scaffold strand. A system is described that was designed approximately one third the length of the M13 bacteriophage genome for ease of ssDNA production. Folding of the 2404-base ssDNA scaffold into a variety of origami shapes with high assembly yields is demonstrated.
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Affiliation(s)
- S Brown
- Niels Bohr Institute, University of Copenhagen, Blegdamsvej 17, Copenhagen 2100, Denmark.
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13
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Zakeri B, Lu TK. DNA nanotechnology: new adventures for an old warhorse. Curr Opin Chem Biol 2015; 28:9-14. [PMID: 26056949 PMCID: PMC4818966 DOI: 10.1016/j.cbpa.2015.05.020] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2015] [Revised: 05/11/2015] [Accepted: 05/14/2015] [Indexed: 10/23/2022]
Abstract
As the blueprint of life, the natural exploits of DNA are admirable. However, DNA should not only be viewed within a biological context. It is an elegantly simple yet functionally complex chemical polymer with properties that make it an ideal platform for engineering new nanotechnologies. Rapidly advancing synthesis and sequencing technologies are enabling novel unnatural applications for DNA beyond the realm of genetics. Here we explore the chemical biology of DNA nanotechnology for emerging applications in communication and digital data storage. Early studies of DNA as an alternative to magnetic and optical storage mediums have not only been promising, but have demonstrated the potential of DNA to revolutionize the way we interact with digital data in the future.
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Affiliation(s)
- Bijan Zakeri
- Department of Electrical Engineering and Computer Science, Department of Biological Engineering, Research Laboratory of Electronics, Massachusetts Institute of Technology, 77 Massachusetts Avenue, Cambridge, MA 02139, USA; MIT Synthetic Biology Center, 500 Technology Square, Cambridge, MA 02139, USA.
| | - Timothy K Lu
- Department of Electrical Engineering and Computer Science, Department of Biological Engineering, Research Laboratory of Electronics, Massachusetts Institute of Technology, 77 Massachusetts Avenue, Cambridge, MA 02139, USA; MIT Synthetic Biology Center, 500 Technology Square, Cambridge, MA 02139, USA.
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14
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Pedersen RO, Kong J, Achim C, LaBean TH. Comparative Incorporation of PNA into DNA Nanostructures. Molecules 2015; 20:17645-58. [PMID: 26404232 PMCID: PMC6331967 DOI: 10.3390/molecules200917645] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2015] [Revised: 09/13/2015] [Accepted: 09/21/2015] [Indexed: 11/16/2022] Open
Abstract
DNA has shown great promise as a building material for self-assembling nanoscale structures. To further develop the potential of this technology, more methods are needed for functionalizing DNA-based nanostructures to increase their chemical diversity. Peptide nucleic acid (PNA) holds great promise for realizing this goal, as it conveniently allows for inclusion of both amino acids and peptides in nucleic acid-based structures. In this work, we explored incorporation of a positively charged PNA within DNA nanostructures. We investigated the efficiency of annealing a lysine-containing PNA probe with complementary, single-stranded DNA sequences within nanostructures, as well as the efficiency of duplex invasion and its dependence on salt concentration. Our results show that PNA allows for toehold-free strand displacement and that incorporation yield depends critically on binding site geometry. These results provide guidance for the design of PNA binding sites on nucleic acid nanostructures with an eye towards optimizing fabrication yield.
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Affiliation(s)
- Ronnie O Pedersen
- Department of Chemistry, Duke University, 124 Science Drive, Durham, NC 27708-0354, USA.
| | - Jing Kong
- Department of Chemistry, Carnegie Mellon University, Pittsburgh, PA 15213, USA.
| | - Catalina Achim
- Department of Chemistry, Carnegie Mellon University, Pittsburgh, PA 15213, USA.
| | - Thomas H LaBean
- Department of Materials Science and Engineering, North Carolina State University, 911 Partners Way, Raleigh, NC 27695-7907, USA.
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15
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Abstract
Protein-protein interactions are fundamental to many biological processes. Yet, the weak and transient noncovalent bonds that characterize most protein-protein interactions found in nature impose limits on many bioengineering experiments. Here, a new class of genetically encodable peptide-protein pairs--isopeptag-N/pilin-N, isopeptag/pilin-C, and SpyTag/SpyCatcher--that interact through autocatalytic intermolecular isopeptide bond formation is described. Reactions between peptide-protein pairs are specific, robust, orthogonal, and able to proceed under most biologically relevant conditions both in vitro and in vivo. As fusion constructs, they provide a handle on molecules of interest, both organic and inorganic, that can be grasped with an iron grip. Such stable interactions provide robust post-translational control over biological processes and open new opportunities in synthetic biology for engineering programmable and self-assembling protein nanoarchitectures.
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Affiliation(s)
- Bijan Zakeri
- Department of Electrical Engineering and Computer Science, Department of Biological Engineering, Research Laboratory of Electronics, Massachusetts Institute of Technology, 77 Massachusetts Avenue, Cambridge, MA, 02139, USA. .,MIT Synthetic Biology Center, 500 Technology Square, Cambridge, MA, 02139, USA.
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16
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Qi H, Huang G, Han Y, Zhang X, Li Y, Pingguan-Murphy B, Lu TJ, Xu F, Wang L. Engineering artificial machines from designable DNA materials for biomedical applications. TISSUE ENGINEERING PART B-REVIEWS 2015; 21:288-97. [PMID: 25547514 DOI: 10.1089/ten.teb.2014.0494] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/13/2022]
Abstract
Deoxyribonucleic acid (DNA) emerges as building bricks for the fabrication of nanostructure with complete artificial architecture and geometry. The amazing ability of DNA in building two- and three-dimensional structures raises the possibility of developing smart nanomachines with versatile controllability for various applications. Here, we overviewed the recent progresses in engineering DNA machines for specific bioengineering and biomedical applications.
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Affiliation(s)
- Hao Qi
- 1Key Laboratory of Systems Bioengineering, Ministry of Education, Tianjin, P.R. China.,2School of Chemical Engineering and Technology, Tianjin University, Tianjin, P.R. China
| | - Guoyou Huang
- 3MOE Key Laboratory of Biomedical Information Engineering, School of Life Science and Technology, Xi'an Jiaotong University, Xi'an, P.R. China.,4Bioinspired Engineering and Biomechanics Center, Xi'an Jiaotong University, Xi'an, P.R. China
| | - Yulong Han
- 3MOE Key Laboratory of Biomedical Information Engineering, School of Life Science and Technology, Xi'an Jiaotong University, Xi'an, P.R. China.,4Bioinspired Engineering and Biomechanics Center, Xi'an Jiaotong University, Xi'an, P.R. China
| | - Xiaohui Zhang
- 3MOE Key Laboratory of Biomedical Information Engineering, School of Life Science and Technology, Xi'an Jiaotong University, Xi'an, P.R. China.,4Bioinspired Engineering and Biomechanics Center, Xi'an Jiaotong University, Xi'an, P.R. China
| | - Yuhui Li
- 3MOE Key Laboratory of Biomedical Information Engineering, School of Life Science and Technology, Xi'an Jiaotong University, Xi'an, P.R. China.,4Bioinspired Engineering and Biomechanics Center, Xi'an Jiaotong University, Xi'an, P.R. China
| | - Belinda Pingguan-Murphy
- 5Department of Biomedical Engineering, Faculty of Engineering, University of Malaya, Kuala Lumpur, Malaysia
| | - Tian Jian Lu
- 4Bioinspired Engineering and Biomechanics Center, Xi'an Jiaotong University, Xi'an, P.R. China
| | - Feng Xu
- 3MOE Key Laboratory of Biomedical Information Engineering, School of Life Science and Technology, Xi'an Jiaotong University, Xi'an, P.R. China.,4Bioinspired Engineering and Biomechanics Center, Xi'an Jiaotong University, Xi'an, P.R. China
| | - Lin Wang
- 3MOE Key Laboratory of Biomedical Information Engineering, School of Life Science and Technology, Xi'an Jiaotong University, Xi'an, P.R. China.,4Bioinspired Engineering and Biomechanics Center, Xi'an Jiaotong University, Xi'an, P.R. China
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17
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Kočar V, Božič Abram S, Doles T, Bašić N, Gradišar H, Pisanski T, Jerala R. TOPOFOLD, the designed modular biomolecular folds: polypeptide-based molecular origami nanostructures following the footsteps of DNA. WILEY INTERDISCIPLINARY REVIEWS-NANOMEDICINE AND NANOBIOTECHNOLOGY 2014; 7:218-37. [PMID: 25196147 DOI: 10.1002/wnan.1289] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/06/2014] [Revised: 07/08/2014] [Accepted: 07/20/2014] [Indexed: 12/14/2022]
Abstract
Biopolymers, the essential components of life, are able to form many complex nanostructures, and proteins in particular are the material of choice for most cellular processes. Owing to numerous cooperative interactions, rational design of new protein folds remains extremely challenging. An alternative strategy is to design topofolds-nanostructures built from polypeptide arrays of interacting modules that define their topology. Over the course of the last several decades DNA has successfully been repurposed from its native role of information storage to a smart nanomaterial used for nanostructure self-assembly of almost any shape, which is largely because of its programmable nature. Unfortunately, polypeptides do not possess the straightforward complementarity as do nucleic acids. However, a modular approach can nevertheless be used to assemble polypeptide nanostructures, as was recently demonstrated on a single-chain polypeptide tetrahedron. This review focuses on the current state-of-the-art in the field of topological polypeptide folds. It starts with a brief overview of the field of structural DNA and RNA nanotechnology, from which it draws parallels and possible directions of development for the emerging field of polypeptide-based nanotechnology. The principles of topofold strategy and unique properties of such polypeptide nanostructures in comparison to native protein folds are discussed. Reasons for the apparent absence of such folds in nature are also examined. Physicochemical versatility of amino acid residues and cost-effective production makes polypeptides an attractive platform for designed functional bionanomaterials.
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Affiliation(s)
- Vid Kočar
- Department of Biotechnology, National Institute of Chemistry, Ljubljana, Slovenia
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18
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Affiliation(s)
- Avni Jain
- McKetta Dept. of Chemical Engineering; The University of Texas at Austin; Austin TX 78712
| | - Jonathan A. Bollinger
- McKetta Dept. of Chemical Engineering; The University of Texas at Austin; Austin TX 78712
| | - Thomas M. Truskett
- McKetta Dept. of Chemical Engineering; The University of Texas at Austin; Austin TX 78712
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19
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Pedersen RO, Loboa EG, LaBean TH. Sensitization of transforming growth factor-β signaling by multiple peptides patterned on DNA nanostructures. Biomacromolecules 2013; 14:4157-60. [PMID: 24206086 DOI: 10.1021/bm4011722] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2023]
Abstract
We report sensitization of a cellular signaling pathway by addition of functionalized DNA nanostructures. Signaling by transforming growth factor β (TGFβ) has been shown to be dependent on receptor clustering. By patterning a DNA nanostructure with closely spaced peptides that bind to TGFβ receptor, we observe increased sensitivity of NMuMG cells to TGFβ ligand. This is evidenced by translocation of secondary messenger proteins to the nucleus and stimulation of an inducible luciferase reporter at lower concentrations of TGFβ ligand. We believe this represents an important initial step toward realization of DNA as a self-assembling and biologically compatible material for use in tissue engineering and drug delivery.
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Affiliation(s)
- Ronnie O Pedersen
- Department of Chemistry, Duke University , 124 Science Drive, Durham, North Carolina 27708-0354, United States
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20
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Klein W, Schmidt CN, Rapp B, Takabayashi S, Knowlton WB, Lee J, Yurke B, Hughes W, Graugnard E, Kuang W. Multiscaffold DNA origami nanoparticle waveguides. NANO LETTERS 2013; 13:3850-6. [PMID: 23841957 PMCID: PMC3744838 DOI: 10.1021/nl401879r] [Citation(s) in RCA: 41] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/22/2013] [Revised: 06/27/2013] [Indexed: 05/18/2023]
Abstract
DNA origami templated self-assembly has shown its potential in creating rationally designed nanophotonic devices in a parallel and repeatable manner. In this investigation, we employ a multiscaffold DNA origami approach to fabricate linear waveguides of 10 nm diameter gold nanoparticles. This approach provides independent control over nanoparticle separation and spatial arrangement. The waveguides were characterized using atomic force microscopy and far-field polarization spectroscopy. This work provides a path toward large-scale plasmonic circuitry.
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Affiliation(s)
- William
P. Klein
- Department
of Materials Science and Engineering, Department of Electrical and Computer Engineering, and Department of Chemistry
and Biochemistry, Boise State University, Boise, Idaho 83725 United States
| | - Charles N. Schmidt
- Department
of Materials Science and Engineering, Department of Electrical and Computer Engineering, and Department of Chemistry
and Biochemistry, Boise State University, Boise, Idaho 83725 United States
| | - Blake Rapp
- Department
of Materials Science and Engineering, Department of Electrical and Computer Engineering, and Department of Chemistry
and Biochemistry, Boise State University, Boise, Idaho 83725 United States
| | - Sadao Takabayashi
- Department
of Materials Science and Engineering, Department of Electrical and Computer Engineering, and Department of Chemistry
and Biochemistry, Boise State University, Boise, Idaho 83725 United States
| | - William B. Knowlton
- Department
of Materials Science and Engineering, Department of Electrical and Computer Engineering, and Department of Chemistry
and Biochemistry, Boise State University, Boise, Idaho 83725 United States
| | - Jeunghoon Lee
- Department
of Materials Science and Engineering, Department of Electrical and Computer Engineering, and Department of Chemistry
and Biochemistry, Boise State University, Boise, Idaho 83725 United States
| | - Bernard Yurke
- Department
of Materials Science and Engineering, Department of Electrical and Computer Engineering, and Department of Chemistry
and Biochemistry, Boise State University, Boise, Idaho 83725 United States
| | - William
L. Hughes
- Department
of Materials Science and Engineering, Department of Electrical and Computer Engineering, and Department of Chemistry
and Biochemistry, Boise State University, Boise, Idaho 83725 United States
| | - Elton Graugnard
- Department
of Materials Science and Engineering, Department of Electrical and Computer Engineering, and Department of Chemistry
and Biochemistry, Boise State University, Boise, Idaho 83725 United States
| | - Wan Kuang
- Department
of Materials Science and Engineering, Department of Electrical and Computer Engineering, and Department of Chemistry
and Biochemistry, Boise State University, Boise, Idaho 83725 United States
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