1
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Chen J, Huang J, Hu Y. Photo-programmable hydrogel iontronics for electrically and chromatically rewritable circuits. Biosens Bioelectron 2024; 263:116596. [PMID: 39116632 DOI: 10.1016/j.bios.2024.116596] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/29/2024] [Revised: 07/11/2024] [Accepted: 07/18/2024] [Indexed: 08/10/2024]
Abstract
Hydrogel-based iontronics is emerging as a promising frontier in healthcare and human-machine interfacing (HMI), offering excellent compatibility with biological systems in terms of electrical, chemical, and mechanical properties. However, conventional hydrogel systems have limitations in dynamically regulating their electrical and optical properties, which restricts their use in adaptive electronics and responsive interfaces. In this study, we present a new hydrogel system with UV photochemistry-induced reversible conductivity, enabling reversible changes in conductivity. Unlike typical photo-responsive hydrogels that revert to their original states upon removal of the light source, the new hydrogel can maintain its activated states without continuous light exposure, facilitating practical applications. By leveraging the photobase triphenylmethane leucohydroxide and photoacid n-nitrobenzaldehyde, we achieve a significant increase in photo-induced conductivity compared to existing photo-ionic hydrogels. Combining the effective photo-induced conductivity and the accompanied photochromatic effect, we demonstrate a full hydrogel-based stylus pad capable of tracking motion and strokes, and a soft calculator keypad with programmable conductivity and imprinted patterns. These advancements underscore the importance of actively controlling localized conductivity and processing light inputs in hydrogels, exhibiting their potential for diverse applications in bioelectronics and HMI.
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Affiliation(s)
- Jiehao Chen
- The George W. Woodruff School of Mechanical Engineering, Georgia Institute of Technology, Atlanta, GA, 30332, USA
| | - Jiahe Huang
- The School of Chemical and Biomolecular Engineering, Georgia Institute of Technology, Atlanta, GA, 30332, USA
| | - Yuhang Hu
- The George W. Woodruff School of Mechanical Engineering, Georgia Institute of Technology, Atlanta, GA, 30332, USA; The School of Chemical and Biomolecular Engineering, Georgia Institute of Technology, Atlanta, GA, 30332, USA.
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2
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Chen J, Huang J, Hu Y. An optoionic hydrogel with UV-regulated ion conductivity for reprogrammable iontronics: Logic processing and image sensing. SCIENCE ADVANCES 2024; 10:eadn0439. [PMID: 38865467 PMCID: PMC11168472 DOI: 10.1126/sciadv.adn0439] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/06/2024] [Accepted: 05/06/2024] [Indexed: 06/14/2024]
Abstract
The development of smart hydrogels capable of actively controlling ion conductivity is of paramount importance for iontronics. Most current work in this field focuses on enhancing the hydrogels' ion conductivity. Few successes have been seen in achieving spatial regulation of ion flow through external control. Among various controls, light gives the best spatial and temporal resolution for practical iontronic applications. However, developing hydrogels that can generate drastic ion concentration change upon photoirradiation for tunable conductivity is challenging. Very few molecules can enable photoion generation, and most of them are hydrophobic and low quantum yield. Here, we present an optoionic hydrogel that uses triphenylmethane leuconitrile (TPMLN) for ultraviolet-regulated ion conductivity. Through postpolymerization TPMLN synthesizing, we can incorporate high concentration of the hydrophobic TPMLN in hydrogels without compromising the hydrogel's mechanical integrity. Upon light irradiation, the hydrogel's local conductivity can change an unprecedented 10-fold. We also demonstrated soft optoionic devices that are capable of logic processing and photo imaging.
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Affiliation(s)
- Jiehao Chen
- The George W. Woodruff School of Mechanical Engineering, Georgia Institute of Technology, Atlanta, GA 30332, USA
| | - Jiahe Huang
- The School of Chemical and Biomolecular Engineering, Georgia Institute of Technology, Atlanta, GA 30332, USA
| | - Yuhang Hu
- The George W. Woodruff School of Mechanical Engineering, Georgia Institute of Technology, Atlanta, GA 30332, USA
- The School of Chemical and Biomolecular Engineering, Georgia Institute of Technology, Atlanta, GA 30332, USA
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3
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Katrivas L, Makarovsky A, Kempinski B, Randazzo A, Improta R, Rotem D, Porath D, Kotlyar AB. Ag +-Mediated Folding of Long Polyguanine Strands to Double and Quadruple Helixes. NANOMATERIALS (BASEL, SWITZERLAND) 2024; 14:663. [PMID: 38668157 PMCID: PMC11055002 DOI: 10.3390/nano14080663] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/17/2024] [Revised: 04/03/2024] [Accepted: 04/07/2024] [Indexed: 04/29/2024]
Abstract
Metal-mediated base pairing of DNA has been a topic of extensive research spanning over more than four decades. Precise positioning of a single metal ion by predetermining the DNA sequence, as well as improved conductivity offered by the ions, make these structures interesting candidates in the context of using DNA in nanotechnology. Here, we report the formation and characterization of conjugates of long (kilo bases) homoguanine DNA strands with silver ions. We demonstrate using atomic force microscopy (AFM) and scanning tunneling microscope (STM) that binding of silver ions leads to folding of homoguanine DNA strands in a "hairpin" fashion to yield double-helical, left-handed molecules composed of G-G base pairs each stabilized by a silver ion. Further folding of the DNA-silver conjugate yields linear molecules in which the two halves of the double helix are twisted one against the other in a right-handed fashion. Quantum mechanical calculations on smaller molecular models support the helical twist directions obtained by the high resolution STM analysis. These long guanine-based nanostructures bearing a chain of silver ions have not been synthesized and studied before and are likely to possess conductive properties that will make them attractive candidates for nanoelectronics.
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Affiliation(s)
- Liat Katrivas
- Department of Biochemistry and Molecular Biology, George S. Wise Faculty of Life Sciences and Nanotechnology Center, Tel Aviv University, Ramat Aviv, Tel-Aviv 6997801, Israel; (L.K.); (B.K.)
| | - Anna Makarovsky
- Institute of Chemistry and The Center for Nanoscience and Nanotechnology, The Hebrew University of Jerusalem, Jerusalem 7610001, Israel; (A.M.); (D.R.)
| | - Benjamin Kempinski
- Department of Biochemistry and Molecular Biology, George S. Wise Faculty of Life Sciences and Nanotechnology Center, Tel Aviv University, Ramat Aviv, Tel-Aviv 6997801, Israel; (L.K.); (B.K.)
| | - Antonio Randazzo
- Department of Pharmacy, University of Naples Federico II, Via D. Montesano 49, I-80131 Napoli, Italy;
| | - Roberto Improta
- Istituto di Biostrutture e Bioimmagini-CNR (IBB-CNR), Via De Amicis 95, I-80145 Napoli, Italy;
| | - Dvir Rotem
- Institute of Chemistry and The Center for Nanoscience and Nanotechnology, The Hebrew University of Jerusalem, Jerusalem 7610001, Israel; (A.M.); (D.R.)
| | - Danny Porath
- Institute of Chemistry and The Center for Nanoscience and Nanotechnology, The Hebrew University of Jerusalem, Jerusalem 7610001, Israel; (A.M.); (D.R.)
| | - Alexander B. Kotlyar
- Department of Biochemistry and Molecular Biology, George S. Wise Faculty of Life Sciences and Nanotechnology Center, Tel Aviv University, Ramat Aviv, Tel-Aviv 6997801, Israel; (L.K.); (B.K.)
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4
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Martínez-Fernández L, Kohl FR, Zhang Y, Ghosh S, Saks AJ, Kohler B. Triplet Excimer Formation in a DNA Duplex with Silver Ion-Mediated Base Pairs. J Am Chem Soc 2024; 146:1914-1925. [PMID: 38215466 DOI: 10.1021/jacs.3c08793] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/14/2024]
Abstract
The dynamics of excited electronic states in self-assembled structures formed between silver(I) ions and cytosine-containing DNA strands or monomeric cytosine derivatives were investigated by time-resolved infrared (TRIR) spectroscopy and quantum mechanical calculations. The steady-state and time-resolved spectra depend sensitively on the underlying structures, which change with pH and the nucleobase and silver ion concentrations. At pH ∼ 4 and low dC20 strand concentration, an intramolecularly folded i-motif is observed, in which protons, and not silver ions, mediate C-C base pairing. However, at the higher strand concentrations used in the TRIR measurements, dC20 strands associate pairwise to yield duplex structures containing C-Ag+-C base pairs with a high degree of propeller twisting. UV excitation of the silver ion-mediated duplex produces a long-lived excited state, which we assign to a triplet excimer state localized on a pair of stacked cytosines. The computational results indicate that the propeller-twisted motifs induced by metal-ion binding are responsible for the enhanced intersystem crossing that populates the triplet state and not a generic heavy atom effect. Although triplet excimer states have been discussed frequently as intermediates in the formation of cyclobutane pyrimidine dimers, we find neither computational nor experimental evidence for cytosine-cytosine photoproduct formation in the systems studied. These findings provide a rare demonstration of a long-lived triplet excited state that is formed in a significant yield in a DNA duplex, demonstrating that supramolecular structural changes induced by metal ion binding profoundly affect DNA photophysics.
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Affiliation(s)
- Lara Martínez-Fernández
- Departamento de Química, Facultad de Ciencias and Institute for Advanced Research in Chemical Science (IADCHEM), Universidad Autónoma de Madrid, Campus de Excelencia UAM-CSIC, Cantoblanco, 28049 Madrid, Spain
| | - Forrest R Kohl
- Department of Chemistry and Biochemistry, 100 West 18th Avenue, Columbus, 43210 Ohio, United States
| | - Yuyuan Zhang
- Department of Chemistry and Biochemistry, 100 West 18th Avenue, Columbus, 43210 Ohio, United States
| | - Supriya Ghosh
- Department of Chemistry and Biochemistry, 100 West 18th Avenue, Columbus, 43210 Ohio, United States
| | - Andrew J Saks
- Department of Chemistry and Biochemistry, 100 West 18th Avenue, Columbus, 43210 Ohio, United States
| | - Bern Kohler
- Department of Chemistry and Biochemistry, 100 West 18th Avenue, Columbus, 43210 Ohio, United States
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5
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Jeong J, An SY, Hu X, Zhao Y, Yin R, Szczepaniak G, Murata H, Das SR, Matyjaszewski K. Biomass RNA for the Controlled Synthesis of Degradable Networks by Radical Polymerization. ACS NANO 2023; 17:21912-21922. [PMID: 37851525 PMCID: PMC10655241 DOI: 10.1021/acsnano.3c08244] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/31/2023] [Accepted: 10/12/2023] [Indexed: 10/20/2023]
Abstract
Nucleic acids extracted from biomass have emerged as sustainable and environmentally friendly building blocks for the fabrication of multifunctional materials. Until recently, the fabrication of biomass nucleic acid-based structures has been facilitated through simple crosslinking of biomass nucleic acids, which limits the possibility of material properties engineering. This study presents an approach to convert biomass RNA into an acrylic crosslinker through acyl imidazole chemistry. The number of acrylic moieties on RNA was engineered by varying the acylation conditions. The resulting RNA crosslinker can undergo radical copolymerization with various acrylic monomers, thereby offering a versatile route for creating materials with tunable properties (e.g., stiffness and hydrophobic characteristics). Further, reversible-deactivation radical polymerization methods, such as atom transfer radical polymerization (ATRP) and reversible addition-fragmentation chain transfer (RAFT), were also explored as additional approaches to engineer the hydrogel properties. The study also demonstrated the metallization of the biomass RNA-based material, thereby offering potential applications in enhancing electrical conductivity. Overall, this research expands the opportunities in biomass-based biomaterial fabrication, which allows tailored properties for diverse applications.
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Affiliation(s)
- Jaepil Jeong
- Department
of Chemistry, Carnegie Mellon University, Pittsburgh, Pennsylvania 15213, United States
- Center
for Nucleic Acids Science & Technology, Carnegie Mellon University, Pittsburgh, Pennsylvania 15213, United States
| | - So Young An
- Department
of Chemistry, Carnegie Mellon University, Pittsburgh, Pennsylvania 15213, United States
| | - Xiaolei Hu
- Department
of Chemistry, Carnegie Mellon University, Pittsburgh, Pennsylvania 15213, United States
| | - Yuqi Zhao
- Department
of Materials Science & Engineering, Carnegie Mellon University, Pittsburgh, Pennsylvania 15213, United States
| | - Rongguan Yin
- Department
of Chemistry, Carnegie Mellon University, Pittsburgh, Pennsylvania 15213, United States
| | - Grzegorz Szczepaniak
- Department
of Chemistry, Carnegie Mellon University, Pittsburgh, Pennsylvania 15213, United States
- University
of Warsaw, Faculty of Chemistry, Pasteura 1, 02-093 Warsaw, Poland
| | - Hironobu Murata
- Department
of Chemistry, Carnegie Mellon University, Pittsburgh, Pennsylvania 15213, United States
| | - Subha R. Das
- Department
of Chemistry, Carnegie Mellon University, Pittsburgh, Pennsylvania 15213, United States
- Center
for Nucleic Acids Science & Technology, Carnegie Mellon University, Pittsburgh, Pennsylvania 15213, United States
| | - Krzysztof Matyjaszewski
- Department
of Chemistry, Carnegie Mellon University, Pittsburgh, Pennsylvania 15213, United States
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6
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Lu B, Ohayon YP, Woloszyn K, Yang CF, Yoder JB, Rothschild LJ, Wind SJ, Hendrickson WA, Mao C, Seeman NC, Canary JW, Sha R, Vecchioni S. Heterobimetallic Base Pair Programming in Designer 3D DNA Crystals. J Am Chem Soc 2023; 145:17945-17953. [PMID: 37530628 DOI: 10.1021/jacs.3c05478] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 08/03/2023]
Abstract
Metal-mediated DNA (mmDNA) presents a pathway toward engineering bioinorganic and electronic behavior into DNA devices. Many chemical and biophysical forces drive the programmable chelation of metals between pyrimidine base pairs. Here, we developed a crystallographic method using the three-dimensional (3D) DNA tensegrity triangle motif to capture single- and multi-metal binding modes across granular changes to environmental pH using anomalous scattering. Leveraging this programmable crystal, we determined 28 biomolecular structures to capture mmDNA reactions. We found that silver(I) binds with increasing occupancy in T-T and U-U pairs at elevated pH levels, and we exploited this to capture silver(I) and mercury(II) within the same base pair and to isolate the titration points for homo- and heterometal base pair modes. We additionally determined the structure of a C-C pair with both silver(I) and mercury(II). Finally, we extend our paradigm to capture cadmium(II) in T-T pairs together with mercury(II) at high pH. The precision self-assembly of heterobimetallic DNA chemistry at the sub-nanometer scale will enable atomistic design frameworks for more elaborate mmDNA-based nanodevices and nanotechnologies.
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Affiliation(s)
- Brandon Lu
- Department of Chemistry, New York University, New York, New York 10003, United States
| | - Yoel P Ohayon
- Department of Chemistry, New York University, New York, New York 10003, United States
| | - Karol Woloszyn
- Department of Chemistry, New York University, New York, New York 10003, United States
| | - Chu-Fan Yang
- Department of Chemistry, New York University, New York, New York 10003, United States
| | - Jesse B Yoder
- IMCA-CAT, Argonne National Lab, Argonne, Illinois 60439, United States
| | - Lynn J Rothschild
- NASA Ames Research Center, Planetary Sciences Branch, Moffett Field, California 94035, United States
| | - Shalom J Wind
- Department of Applied Physics and Applied Mathematics, Columbia University, New York, New York 10027, United States
| | - Wayne A Hendrickson
- Department of Biochemistry and Molecular Biophysics, Columbia University, New York, New York 10032, United States
| | - Chengde Mao
- Department of Chemistry, Purdue University, West Lafayette, Indiana 47907, United States
| | - Nadrian C Seeman
- Department of Chemistry, New York University, New York, New York 10003, United States
| | - James W Canary
- Department of Chemistry, New York University, New York, New York 10003, United States
| | - Ruojie Sha
- Department of Chemistry, New York University, New York, New York 10003, United States
| | - Simon Vecchioni
- Department of Chemistry, New York University, New York, New York 10003, United States
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7
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Vecchioni S, Lu B, Livernois W, Ohayon YP, Yoder JB, Yang CF, Woloszyn K, Bernfeld W, Anantram MP, Canary JW, Hendrickson WA, Rothschild LJ, Mao C, Wind SJ, Seeman NC, Sha R. Metal-Mediated DNA Nanotechnology in 3D: Structural Library by Templated Diffraction. ADVANCED MATERIALS (DEERFIELD BEACH, FLA.) 2023; 35:e2210938. [PMID: 37268326 DOI: 10.1002/adma.202210938] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/03/2022] [Revised: 03/06/2023] [Indexed: 06/04/2023]
Abstract
DNA double helices containing metal-mediated DNA (mmDNA) base pairs are constructed from Ag+ and Hg2+ ions between pyrimidine:pyrimidine pairs with the promise of nanoelectronics. Rational design of mmDNA nanomaterials is impractical without a complete lexical and structural description. Here, the programmability of structural DNA nanotechnology toward its founding mission of self-assembling a diffraction platform for biomolecular structure determination is explored. The tensegrity triangle is employed to build a comprehensive structural library of mmDNA pairs via X-ray diffraction and generalized design rules for mmDNA construction are elucidated. Two binding modes are uncovered: N3-dominant, centrosymmetric pairs and major groove binders driven by 5-position ring modifications. Energy gap calculations show additional levels in the lowest unoccupied molecular orbitals (LUMO) of mmDNA structures, rendering them attractive molecular electronic candidates.
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Affiliation(s)
- Simon Vecchioni
- Department of Chemistry, New York University, New York, NY, 10003, USA
| | - Brandon Lu
- Department of Chemistry, New York University, New York, NY, 10003, USA
| | - William Livernois
- Department of Electrical and Computer Engineering, University of Washington, Seattle, WA, 98195, USA
| | - Yoel P Ohayon
- Department of Chemistry, New York University, New York, NY, 10003, USA
| | - Jesse B Yoder
- IMCA-CAT, Argonne National Lab, Argonne, IL, 60439, USA
| | - Chu-Fan Yang
- Department of Chemistry, New York University, New York, NY, 10003, USA
| | - Karol Woloszyn
- Department of Chemistry, New York University, New York, NY, 10003, USA
| | - William Bernfeld
- Department of Chemistry, New York University, New York, NY, 10003, USA
- ASPIRE Program, King School, Stamford, CT, 06905, USA
| | - M P Anantram
- Department of Electrical and Computer Engineering, University of Washington, Seattle, WA, 98195, USA
| | - James W Canary
- Department of Chemistry, New York University, New York, NY, 10003, USA
| | - Wayne A Hendrickson
- Department of Biochemistry and Molecular Biophysics, Columbia University, New York, NY, 10032, USA
| | - Lynn J Rothschild
- NASA Ames Research Center, Planetary Sciences Branch, Moffett Field, CA, 94035, USA
| | - Chengde Mao
- Department of Chemistry, Purdue University, West Lafayette, IN, 47907, USA
| | - Shalom J Wind
- Department of Applied Physics and Applied Math, Columbia University, New York, NY, 10027, USA
| | - Nadrian C Seeman
- Department of Chemistry, New York University, New York, NY, 10003, USA
| | - Ruojie Sha
- Department of Chemistry, New York University, New York, NY, 10003, USA
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8
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Hartung J, McCann N, Doe E, Hayth H, Benkato K, Johnson MB, Viard M, Afonin KA, Khisamutdinov EF. Toehold-Mediated Shape Transition of Nucleic Acid Nanoparticles. ACS APPLIED MATERIALS & INTERFACES 2023; 15:25300-25312. [PMID: 37204867 PMCID: PMC10331730 DOI: 10.1021/acsami.3c01604] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/21/2023]
Abstract
We introduce a toehold-mediated strand displacement strategy for regulated shape-switching of nucleic acid nanoparticles (NANPs) enabling their sequential transformation from triangular to hexagonal architectures at isothermal conditions. The successful shape transitions were confirmed by electrophoretic mobility shift assays, atomic force microscopy, and dynamic light scattering. Furthermore, implementation of split fluorogenic aptamers allowed for monitoring the individual transitions in real time. Three distinct RNA aptamers─malachite green (MG), broccoli, and mango─were embedded within NANPs as reporter domains to confirm shape transitions. While MG "lights up" within the square, pentagonal, and hexagonal constructs, the broccoli is activated only upon formation of pentagon and hexagon NANPs, and mango reports only the presence of hexagons. Moreover, the designed RNA fluorogenic platform can be employed to construct a logic gate that performs an AND operation with three single-stranded RNA inputs by implementing a non-sequential polygon transformation approach. Importantly, the polygonal scaffolds displayed promising potential as drug delivery agents and biosensors. All polygons exhibited effective cellular internalization followed by specific gene silencing when decorated with fluorophores and RNAi inducers. This work offers a new perspective for the design of toehold-mediated shape-switching nanodevices to activate different light-up aptamers for the development of biosensors, logic gates, and therapeutic devices in the nucleic acid nanotechnology.
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Affiliation(s)
- Jordan Hartung
- Department of Chemistry, Ball State University, Muncie, Indiana 47306, United States
| | - Nathan McCann
- Department of Chemistry, Ball State University, Muncie, Indiana 47306, United States
| | - Erwin Doe
- Department of Chemistry, Ball State University, Muncie, Indiana 47306, United States
| | - Hannah Hayth
- Department of Chemistry, Ball State University, Muncie, Indiana 47306, United States
| | - Kheiria Benkato
- Department of Chemistry, Ball State University, Muncie, Indiana 47306, United States
| | - M Brittany Johnson
- Department of Biology, University of North Carolina at Charlotte, Charlotte, North Carolina 28223, United States
| | - Mathias Viard
- Laboratory of Integrative Cancer Immunology, Center for Cancer Research, National Cancer Institute, Bethesda, Maryland 20892, United States
- Basic Science Program, Leidos Biomedical Research Inc. National Cancer Institute, National Institutes of Health, Frederick, Maryland 21702, United States
| | - Kirill A Afonin
- Department of Chemistry, University of North Carolina at Charlotte, Charlotte, North Carolina 28223, United States
| | - Emil F Khisamutdinov
- Department of Chemistry, Ball State University, Muncie, Indiana 47306, United States
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9
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Lu B, Woloszyn K, Ohayon YP, Yang B, Zhang C, Mao C, Seeman NC, Vecchioni S, Sha R. Programmable 3D Hexagonal Geometry of DNA Tensegrity Triangles. Angew Chem Int Ed Engl 2023; 62:e202213451. [PMID: 36520622 DOI: 10.1002/anie.202213451] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2022] [Revised: 12/12/2022] [Accepted: 12/13/2022] [Indexed: 12/23/2022]
Abstract
Non-canonical interactions in DNA remain under-explored in DNA nanotechnology. Recently, many structures with non-canonical motifs have been discovered, notably a hexagonal arrangement of typically rhombohedral DNA tensegrity triangles that forms through non-canonical sticky end interactions. Here, we find a series of mechanisms to program a hexagonal arrangement using: the sticky end sequence; triangle edge torsional stress; and crystallization condition. We showcase cross-talking between Watson-Crick and non-canonical sticky ends in which the ratio between the two dictates segregation by crystal forms or combination into composite crystals. Finally, we develop a method for reconfiguring the long-range geometry of formed crystals from rhombohedral to hexagonal and vice versa. These data demonstrate fine control over non-canonical motifs and their topological self-assembly. This will vastly increase the programmability, functionality, and versatility of rationally designed DNA constructs.
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Affiliation(s)
- Brandon Lu
- Department of Chemistry, New York University, New York, NY 10003, USA
| | - Karol Woloszyn
- Department of Chemistry, New York University, New York, NY 10003, USA
| | - Yoel P Ohayon
- Department of Chemistry, New York University, New York, NY 10003, USA
| | - Bena Yang
- Department of Chemistry, New York University, New York, NY 10003, USA
| | - Cuizheng Zhang
- Department of Chemistry, Purdue University, West Lafayette, IN 47907, USA
| | - Chengde Mao
- Department of Chemistry, Purdue University, West Lafayette, IN 47907, USA
| | - Nadrian C Seeman
- Department of Chemistry, New York University, New York, NY 10003, USA
| | - Simon Vecchioni
- Department of Chemistry, New York University, New York, NY 10003, USA
| | - Ruojie Sha
- Department of Chemistry, New York University, New York, NY 10003, USA
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10
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Lu B, Vecchioni S, Ohayon YP, Canary JW, Sha R. The wending rhombus: Self-assembling 3D DNA crystals. Biophys J 2022; 121:4759-4765. [PMID: 36004779 PMCID: PMC9808540 DOI: 10.1016/j.bpj.2022.08.019] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2022] [Revised: 07/11/2022] [Accepted: 08/16/2022] [Indexed: 01/07/2023] Open
Abstract
In this perspective, we provide a summary of recent developments in self-assembling three-dimensional (3D) DNA crystals. Starting from the inception of this subfield, we describe the various advancements in structure that have led to an increase in the diversity of macromolecular crystal motifs formed through self-assembly, and we further comment on the future directions of the field, which exploit noncanonical base pairing interactions beyond Watson-Crick. We then survey the current applications of self-assembling 3D DNA crystals in reversibly active nanodevices and materials engineering and provide an outlook on the direction researchers are taking these structures. Finally, we compare 3D DNA crystals with DNA origami and suggest how these distinct subfields might work together to enhance biomolecule structure solution, nanotechnological motifs, and their applications.
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Affiliation(s)
- Brandon Lu
- Department of Chemistry, New York University, New York, New York
| | - Simon Vecchioni
- Department of Chemistry, New York University, New York, New York
| | - Yoel P Ohayon
- Department of Chemistry, New York University, New York, New York
| | - James W Canary
- Department of Chemistry, New York University, New York, New York.
| | - Ruojie Sha
- Department of Chemistry, New York University, New York, New York.
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11
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Woloszyn K, Vecchioni S, Ohayon YP, Lu B, Ma Y, Huang Q, Zhu E, Chernovolenko D, Markus T, Jonoska N, Mao C, Seeman NC, Sha R. Augmented DNA Nanoarchitectures: A Structural Library of 3D Self-Assembling Tensegrity Triangle Variants. ADVANCED MATERIALS (DEERFIELD BEACH, FLA.) 2022; 34:e2206876. [PMID: 36100349 DOI: 10.1002/adma.202206876] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/28/2022] [Revised: 09/09/2022] [Indexed: 06/15/2023]
Abstract
The DNA tensegrity triangle is known to reliably self-assemble into a 3D rhombohedral crystalline lattice via sticky-end cohesion. Here, the library of accessible motifs is expanded through covalent extensions of intertriangle regions and sticky-end-coordinated linkages of adjacent triangles with double helical segments using both geometrically symmetric and asymmetric configurations. The molecular structures of 18 self-assembled architectures at resolutions of 3.32-9.32 Å are reported; the observed cell dimensions, cavity sizes, and cross-sectional areas agree with theoretical expectations. These data demonstrate that fine control over triclinic and rhombohedral crystal parameters and the customizability of more complex 3D DNA lattices are attainable via rational design. It is anticipated that augmented DNA architectures may be fine-tuned for the self-assembly of designer nanocages, guest-host complexes, and proscriptive 3D nanomaterials, as originally envisioned. Finally, designer asymmetric crystalline building blocks can be seen as a first step toward controlling and encoding information in three dimensions.
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Affiliation(s)
- Karol Woloszyn
- Department of Chemistry, New York University, New York, NY, 10003, USA
| | - Simon Vecchioni
- Department of Chemistry, New York University, New York, NY, 10003, USA
| | - Yoel P Ohayon
- Department of Chemistry, New York University, New York, NY, 10003, USA
| | - Brandon Lu
- Department of Chemistry, New York University, New York, NY, 10003, USA
| | - Yinglun Ma
- Department of Chemistry, New York University, New York, NY, 10003, USA
| | - Qiuyan Huang
- Department of Chemistry, New York University, New York, NY, 10003, USA
| | - Eric Zhu
- Department of Chemistry, New York University, New York, NY, 10003, USA
| | | | - Tiffany Markus
- Department of Chemistry, New York University, New York, NY, 10003, USA
| | - Nataša Jonoska
- Department of Mathematics and Statistics, University of South Florida, Tampa, FL, 33620, USA
| | - Chengde Mao
- Department of Chemistry, Purdue University, West Lafayette, IN, 47907, USA
| | - Nadrian C Seeman
- Department of Chemistry, New York University, New York, NY, 10003, USA
| | - Ruojie Sha
- Department of Chemistry, New York University, New York, NY, 10003, USA
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12
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Zhang L, Liu J, Gao M, Han L, Liu X, Xing X. Fluorescent Determination of Mercury(II) and Glutathione with Binding to Thymine–Guanine Base Pairs. ANAL LETT 2022. [DOI: 10.1080/00032719.2022.2109044] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/01/2022]
Affiliation(s)
- Liyuan Zhang
- College of Chemistry and Pharmaceutical Engineering, Nanyang Normal University, Nanyang, China
| | - Jinxiao Liu
- College of Materials Science and Engineering, Zhengzhou University, Zhengzhou, China
| | - Mengying Gao
- College of Chemistry and Pharmaceutical Engineering, Nanyang Normal University, Nanyang, China
| | - Li Han
- Henan Key Laboratory of Industrial Microbial Resources and Fermentation Technology, Department of Biology and Chemical Engineering, Nanyang Institute of Technology, Nanyang, China
| | - Xueguo Liu
- Henan Key Laboratory of Industrial Microbial Resources and Fermentation Technology, Department of Biology and Chemical Engineering, Nanyang Institute of Technology, Nanyang, China
| | - Xiaojing Xing
- College of Chemistry and Pharmaceutical Engineering, Nanyang Normal University, Nanyang, China
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13
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Mesoscopic model confirms strong base pair metal mediated bonding for T-Hg 2+-T and weaker for C-Ag +-C. Chem Phys Lett 2022. [DOI: 10.1016/j.cplett.2022.139847] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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14
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Kohn EM, Shirley DJ, Hinds NM, Fry HC, Caputo GA. Peptide‐assisted
supramolecular polymerization of the anionic porphyrin
meso‐tetra
(
4‐sulfonatophenyl
)porphine. Pept Sci (Hoboken) 2022. [DOI: 10.1002/pep2.24288] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Affiliation(s)
- Eric M. Kohn
- Department of Chemistry & Biochemistry Rowan University Glassboro New Jersey USA
- Bantivoglio Honors College Rowan University Glassboro New Jersey USA
- Department of Chemistry University of Wisconsin Madison Wisconsin USA
| | - David J. Shirley
- Department of Chemistry & Biochemistry Rowan University Glassboro New Jersey USA
- Division of Chemical Biology and Medicinal Chemistry Eshelman School of Pharmacy, University of North Carolina Chapel Hill North Carolina USA
| | - Nicole M. Hinds
- Department of Chemistry & Biochemistry Rowan University Glassboro New Jersey USA
| | - H. Christopher Fry
- Argonne National Laboratory Center for Nanoscale Materials Lemont Illinois USA
| | - Gregory A. Caputo
- Department of Chemistry & Biochemistry Rowan University Glassboro New Jersey USA
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15
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Hoog T, Pawlak M, Aufdembrink L, Bachan B, Galles M, Bense N, Adamala K, Engelhart A. Switchable DNA-based Peroxidases Controlled by a Chaotropic Ion. Chembiochem 2022; 23:e202200090. [PMID: 35245408 PMCID: PMC9310614 DOI: 10.1002/cbic.202200090] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2022] [Revised: 03/02/2022] [Indexed: 11/09/2022]
Abstract
Here we demonstrate a switchable DNA electron transfer catalyst, enabled by selective destabilization of secondary structure by a denaturant, perchlorate. The system is comprised of two strands, one of which can be selectively switched between a G-quadruplex and duplex or single-stranded conformations. In the G-quadruplex state, it binds hemin, enabling peroxidase activity. This switching ability arises from our finding that perchlorate, a chaotropic Hofmeister ion, selectively destabilizes duplex over G-quadruplex DNA. By varying perchlorate concentration, we show that the DNA structure can be switched between states that do and do not catalyze electron transfer catalysis. State switching can be achieved in three ways: thermally, by dilution, or by concentration.
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Affiliation(s)
- Tanner Hoog
- University of Minnesota Twin Cities: University of Minnesota Twin Cities, Genetics, Cell Biology, and Development, UNITED STATES
| | - Matthew Pawlak
- University of Minnesota, Genetics, Cell Biology, and Development, UNITED STATES
| | - Lauren Aufdembrink
- University of Minnesota, Genetics, Cell Biology, and Development, UNITED STATES
| | - Benjamin Bachan
- University of Minnesota, Genetics, Cell Biology, and Development, UNITED STATES
| | - Matthew Galles
- NASA Langley, Structural Acoustics Branch, UNITED STATES
| | - Nicholas Bense
- NASA John H Glenn Research Center, NASA Glenn, UNITED STATES
| | - Katarzyna Adamala
- University of Minnesota, Genetics, Cell Biology, and Development, UNITED STATES
| | - Aaron Engelhart
- University of Minnesota, Department of Genetics, Cell Biology, and Development, MCB 5-130, 420 Washington Avenue SE, 55455, Minneapolis, UNITED STATES
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16
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Fardian-Melamed N, Katrivas L, Rotem D, Kotlyar A, Porath D. Electronic Level Structure of Novel Guanine Octuplex DNA Single Molecules. NANO LETTERS 2021; 21:8987-8992. [PMID: 34694812 DOI: 10.1021/acs.nanolett.1c02269] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/13/2023]
Abstract
Throughout the past few decades, guanine quadruplex DNA structures have attracted much interest both from a fundamental material science perspective and from a technologically oriented perspective. Novel guanine octuplex DNA, formed from coiled quadruplex DNA, was recently discovered as a stable and rigid DNA-based nanostructure. A detailed electronic structure study of this new nanomaterial, performed by scanning tunneling spectroscopy on a subsingle-molecule level at cryogenic temperature, is presented herein. The electronic levels and lower energy gap of guanine octuplex DNA compared to quadruplex DNA dictate higher transverse conductivity through guanine octads than through guanine tetrads.
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Affiliation(s)
- Natalie Fardian-Melamed
- Institute of Chemistry and The Center for Nanoscience and Nanotechnology, The Hebrew University of Jerusalem, Jerusalem 91904, Israel
| | - Liat Katrivas
- Department of Biochemistry and Molecular Biology, George S. Wise Faculty of Life Sciences, and The Center of Nanoscience and Nanotechnology, Tel Aviv University, Ramat Aviv, Tel Aviv 69978, Israel
| | - Dvir Rotem
- Institute of Chemistry and The Center for Nanoscience and Nanotechnology, The Hebrew University of Jerusalem, Jerusalem 91904, Israel
| | - Alexander Kotlyar
- Department of Biochemistry and Molecular Biology, George S. Wise Faculty of Life Sciences, and The Center of Nanoscience and Nanotechnology, Tel Aviv University, Ramat Aviv, Tel Aviv 69978, Israel
| | - Danny Porath
- Institute of Chemistry and The Center for Nanoscience and Nanotechnology, The Hebrew University of Jerusalem, Jerusalem 91904, Israel
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17
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Pang C, Aryal BR, Ranasinghe DR, Westover TR, Ehlert AEF, Harb JN, Davis RC, Woolley AT. Bottom-Up Fabrication of DNA-Templated Electronic Nanomaterials and Their Characterization. NANOMATERIALS (BASEL, SWITZERLAND) 2021; 11:1655. [PMID: 34201888 PMCID: PMC8306176 DOI: 10.3390/nano11071655] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/29/2021] [Revised: 06/15/2021] [Accepted: 06/16/2021] [Indexed: 11/30/2022]
Abstract
Bottom-up fabrication using DNA is a promising approach for the creation of nanoarchitectures. Accordingly, nanomaterials with specific electronic, photonic, or other functions are precisely and programmably positioned on DNA nanostructures from a disordered collection of smaller parts. These self-assembled structures offer significant potential in many domains such as sensing, drug delivery, and electronic device manufacturing. This review describes recent progress in organizing nanoscale morphologies of metals, semiconductors, and carbon nanotubes using DNA templates. We describe common substrates, DNA templates, seeding, plating, nanomaterial placement, and methods for structural and electrical characterization. Finally, our outlook for DNA-enabled bottom-up nanofabrication of materials is presented.
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Affiliation(s)
- Chao Pang
- Department of Chemistry and Biochemistry, Brigham Young University, Provo, UT 84602, USA; (C.P.); (B.R.A.); (D.R.R.); (A.E.F.E.)
| | - Basu R. Aryal
- Department of Chemistry and Biochemistry, Brigham Young University, Provo, UT 84602, USA; (C.P.); (B.R.A.); (D.R.R.); (A.E.F.E.)
| | - Dulashani R. Ranasinghe
- Department of Chemistry and Biochemistry, Brigham Young University, Provo, UT 84602, USA; (C.P.); (B.R.A.); (D.R.R.); (A.E.F.E.)
| | - Tyler R. Westover
- Department of Physics and Astronomy, Brigham Young University, Provo, UT 84602, USA; (T.R.W.); (R.C.D.)
| | - Asami E. F. Ehlert
- Department of Chemistry and Biochemistry, Brigham Young University, Provo, UT 84602, USA; (C.P.); (B.R.A.); (D.R.R.); (A.E.F.E.)
| | - John N. Harb
- Department of Chemical Engineering, Brigham Young University, Provo, UT 84602, USA;
| | - Robert C. Davis
- Department of Physics and Astronomy, Brigham Young University, Provo, UT 84602, USA; (T.R.W.); (R.C.D.)
| | - Adam T. Woolley
- Department of Chemistry and Biochemistry, Brigham Young University, Provo, UT 84602, USA; (C.P.); (B.R.A.); (D.R.R.); (A.E.F.E.)
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18
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Theoretical studies on the electronic and optoelectronic properties of DNA/RNA hybrid-metal complexes. Polyhedron 2021. [DOI: 10.1016/j.poly.2020.115015] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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19
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Flamme M, Röthlisberger P, Levi-Acobas F, Chawla M, Oliva R, Cavallo L, Gasser G, Marlière P, Herdewijn P, Hollenstein M. Enzymatic Formation of an Artificial Base Pair Using a Modified Purine Nucleoside Triphosphate. ACS Chem Biol 2020; 15:2872-2884. [PMID: 33090769 DOI: 10.1021/acschembio.0c00396] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
The expansion of the genetic alphabet with additional, unnatural base pairs (UBPs) is an important and long-standing goal in synthetic biology. Nucleotides acting as ligands for the coordination of metal cations have advanced as promising candidates for such an expansion of the genetic alphabet. However, the inclusion of artificial metal base pairs in nucleic acids mainly relies on solid-phase synthesis approaches, and very little is known about polymerase-mediated synthesis. Herein, we report the selective and high yielding enzymatic construction of a silver-mediated base pair (dImC-AgI-dPurP) as well as a two-step protocol for the synthesis of DNA duplexes containing such an artificial metal base pair. Guided by DFT calculations, we also shed light into the mechanism of formation of this artificial base pair as well as into the structural and energetic preferences. The enzymatic synthesis of the dImC-AgI-dPurP artificial metal base pair provides valuable insights for the design of future, more potent systems aiming at expanding the genetic alphabet.
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Affiliation(s)
- Marie Flamme
- Institut Pasteur, Department of Structural Biology and Chemistry, Laboratory for Bioorganic Chemistry of Nucleic Acids, CNRS UMR3523, 28, rue du Docteur Roux, 75724 Paris Cedex 15, France
- Université Paris Descartes, Sorbonne Paris Cité, 12 rue de l’École de Médecine, 75006 Paris, France
- Chimie ParisTech, PSL University, CNRS, Institute of Chemistry for Life and Health Sciences, Laboratory for Inorganic Chemical Biology, 75005 Paris, France
| | - Pascal Röthlisberger
- Institut Pasteur, Department of Structural Biology and Chemistry, Laboratory for Bioorganic Chemistry of Nucleic Acids, CNRS UMR3523, 28, rue du Docteur Roux, 75724 Paris Cedex 15, France
| | - Fabienne Levi-Acobas
- Institut Pasteur, Department of Structural Biology and Chemistry, Laboratory for Bioorganic Chemistry of Nucleic Acids, CNRS UMR3523, 28, rue du Docteur Roux, 75724 Paris Cedex 15, France
| | - Mohit Chawla
- King Abdullah University of Science and Technology (KAUST), Physical Sciences and Engineering Division, Kaust Catalysis Center, Thuwal, 23955-6900 Saudi Arabia
| | - Romina Oliva
- Department of Sciences and Technologies, University Parthenope of Naples, Centro Direzionale Isola C4, 80143, Naples, Italy
| | - Luigi Cavallo
- King Abdullah University of Science and Technology (KAUST), Physical Sciences and Engineering Division, Kaust Catalysis Center, Thuwal, 23955-6900 Saudi Arabia
| | - Gilles Gasser
- Chimie ParisTech, PSL University, CNRS, Institute of Chemistry for Life and Health Sciences, Laboratory for Inorganic Chemical Biology, 75005 Paris, France
| | - Philippe Marlière
- University of Paris Saclay, CNRS, iSSB, UEVE, Genopole, 5 Rue Henri Desbrueres, 91030 Evry, France
| | - Piet Herdewijn
- KU Leuven, Rega Institute for Medical Research, Medicinal Chemistry, Herestraat, 3000 Leuven, Belgium
| | - Marcel Hollenstein
- Institut Pasteur, Department of Structural Biology and Chemistry, Laboratory for Bioorganic Chemistry of Nucleic Acids, CNRS UMR3523, 28, rue du Docteur Roux, 75724 Paris Cedex 15, France
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20
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Flamme M, Levi-Acobas F, Hensel S, Naskar S, Röthlisberger P, Sarac I, Gasser G, Müller J, Hollenstein M. Enzymatic Construction of Artificial Base Pairs: The Effect of Metal Shielding. Chembiochem 2020; 21:3398-3409. [PMID: 32673442 DOI: 10.1002/cbic.202000402] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2020] [Revised: 07/16/2020] [Indexed: 12/12/2022]
Abstract
Th formation of metal base pairs is a versatile method for the introduction of metal cations into nucleic acids that has been used in numerous applications including the construction of metal nanowires, development of energy, charge-transfer devices and expansion of the genetic alphabet. As an alternative, enzymatic construction of metal base pairs is an alluring strategy that grants access to longer sequences and offers the possibility of using such unnatural base pairs (UBPs) in SELEX experiments for the identification of functional nucleic acids. This method remains rather underexplored, and a better understanding of the key parameters in the design of efficient nucleotides is required. We have investigated the effect of methylation of the imidazole nucleoside (dImnMe TP) on the efficiency of the enzymatic construction of metal base pairs. The presence of methyl substituents on dImTP facilitates the polymerase-driven formation of dIm4Me -AgI -dIm and dIm2Me TP-CrIII -dIm base pairs. Steric factors rather than the basicity of the imidazole nucleobase appear to govern the enzymatic formation of such metal base pairs. We also demonstrate the compatibility of other metal cations rarely considered in the construction of artificial metal bases by enzymatic DNA synthesis under both primer extension reaction and PCR conditions. These findings open up new directions for the design of nucleotide analogues for the development of metal base pairs.
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Affiliation(s)
- Marie Flamme
- Institut Pasteur, Department of Structural Biology and Chemistry, Laboratory for Bioorganic Chemistry of Nucleic Acids, CNRS UMR3523, 28, rue du Docteur Roux, 75724, Paris Cedex 15, France.,Université Paris Descartes, Sorbonne Paris Cité, 12 rue de l'École de Médecine, 75006, Paris, France.,Chimie ParisTech, PSL University, CNRS, Institute of Chemistry for Life and Health Sciences, Laboratory for Inorganic Chemical Biology, 11, rue Pierre et Marie Curie, 75005, Paris, France
| | - Fabienne Levi-Acobas
- Institut Pasteur, Department of Structural Biology and Chemistry, Laboratory for Bioorganic Chemistry of Nucleic Acids, CNRS UMR3523, 28, rue du Docteur Roux, 75724, Paris Cedex 15, France
| | - Susanne Hensel
- Westfälische Wilhelms-Universität Münster, Institut für Anorganische und Analytische Chemie, Corrensstrasse 30, 48149, Münster, Germany
| | - Shuvankar Naskar
- Westfälische Wilhelms-Universität Münster, Institut für Anorganische und Analytische Chemie, Corrensstrasse 30, 48149, Münster, Germany
| | - Pascal Röthlisberger
- Institut Pasteur, Department of Structural Biology and Chemistry, Laboratory for Bioorganic Chemistry of Nucleic Acids, CNRS UMR3523, 28, rue du Docteur Roux, 75724, Paris Cedex 15, France
| | - Ivo Sarac
- Institut Pasteur, Department of Structural Biology and Chemistry, Laboratory for Bioorganic Chemistry of Nucleic Acids, CNRS UMR3523, 28, rue du Docteur Roux, 75724, Paris Cedex 15, France
| | - Gilles Gasser
- Chimie ParisTech, PSL University, CNRS, Institute of Chemistry for Life and Health Sciences, Laboratory for Inorganic Chemical Biology, 11, rue Pierre et Marie Curie, 75005, Paris, France
| | - Jens Müller
- Westfälische Wilhelms-Universität Münster, Institut für Anorganische und Analytische Chemie, Corrensstrasse 30, 48149, Münster, Germany
| | - Marcel Hollenstein
- Institut Pasteur, Department of Structural Biology and Chemistry, Laboratory for Bioorganic Chemistry of Nucleic Acids, CNRS UMR3523, 28, rue du Docteur Roux, 75724, Paris Cedex 15, France
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21
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Fardian-Melamed N, Katrivas L, Eidelshtein G, Rotem D, Kotlyar A, Porath D. Electronic Level Structure of Silver-Intercalated Cytosine Nanowires. NANO LETTERS 2020; 20:4505-4511. [PMID: 32412760 DOI: 10.1021/acs.nanolett.0c01292] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/11/2023]
Abstract
Metal-mediated base-paired DNA has long been investigated for basic scientific pursuit and for nanoelectronics purposes. Particularly attractive in these domains is the Ag+-intercalated polycytosine DNA duplex. Extensive studies of this molecule have led to our current understanding of its self-assembly properties, high thermodynamic and structural stability, and high longitudinal conductivity. However, a high-resolution morphological characterization of long Ag+-intercalated polycytosine DNA has hitherto not been carried out. Furthermore, the electronic level structure of this molecule has not been studied before. Here we present a scanning tunneling microscopy and spectroscopy study of this intriguing nanowire. Its temperature-independent morphological and electronic properties suggest substantial stability, while its emergent electronic levels and energy gap provide the basis for its high conductivity.
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Affiliation(s)
- Natalie Fardian-Melamed
- Institute of Chemistry and Center for Nanoscience and Nanotechnology, The Hebrew University of Jerusalem, Jerusalem 91904, Israel
| | - Liat Katrivas
- Department of Biochemistry and Molecular Biology, George S. Wise Faculty of Life Sciences, and The Center of Nanoscience and Nanotechnology, Tel Aviv University, Ramat Aviv, Tel Aviv 69978, Israel
| | - Gennady Eidelshtein
- Department of Biochemistry and Molecular Biology, George S. Wise Faculty of Life Sciences, and The Center of Nanoscience and Nanotechnology, Tel Aviv University, Ramat Aviv, Tel Aviv 69978, Israel
| | - Dvir Rotem
- Institute of Chemistry and Center for Nanoscience and Nanotechnology, The Hebrew University of Jerusalem, Jerusalem 91904, Israel
| | - Alexander Kotlyar
- Department of Biochemistry and Molecular Biology, George S. Wise Faculty of Life Sciences, and The Center of Nanoscience and Nanotechnology, Tel Aviv University, Ramat Aviv, Tel Aviv 69978, Israel
| | - Danny Porath
- Institute of Chemistry and Center for Nanoscience and Nanotechnology, The Hebrew University of Jerusalem, Jerusalem 91904, Israel
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22
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Tavassoli A, Soleymani S, Haghparast A, Hashemi Tabar G, Bassami MR, Dehghani H. Reverse Genetics Assembly of Newcastle Disease Virus Genome Template Using Asis-Sal-Pac BioBrick Strategy. Biol Proced Online 2020; 22:9. [PMID: 32377174 PMCID: PMC7193399 DOI: 10.1186/s12575-020-00119-3] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2019] [Accepted: 03/18/2020] [Indexed: 11/25/2022] Open
Abstract
Background The BioBrick construction as an approach in synthetic biology provides the ability to assemble various gene fragments. To date, different BioBrick strategies have been exploited for assembly and cloning of a variety of gene fragments. We present a new BioBrick strategy, here referred as Asis-Sal-Pac BioBrick, which we used for the assembly of NDV as a candidate for single-stranded non-segmented, negative-sense RNA genome viruses. Results In the present study, we isolated three NDVs from clinical samples which were classified into the VIId genotype based on their pathogenicity and phylogenetic analyses. Then, SalI, AsisI, and PacI enzymes were used to design and develop a novel BioBrick strategy, which enabled us to assemble the NDV genome, adopting the “rule of six”. In this method, in each assembly step, the restriction sites in the newly formed destination plasmid are reproduced, which will be used for the next insertion. In this study using two overlapping PCRs, the cleavage site of the F gene was also modified from 112RRQKRF117to 112GRQGRL117 in order to generate the attenuated recombinant NDV. Finally, in order to construct the recombinant NDV viruses, the plasmids harboring the assembled full-length genome of the NDV and the helper plasmids were co-transfected into T7-BHK cells. The rescue of the recombinant NDVwas confirmed by RT-PCR and HA tests. Conclusions These findings suggest that the combination of reverse genetic technology and BioBrick assembly have the potential to be applied for the development of novel vaccine candidates. This promising strategy provides an effective and reliable approach to make genotype-matched vaccines against specific NDV strains or any other virus.
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Affiliation(s)
- Amin Tavassoli
- 1Division of Biotechnology, Faculty of Veterinary Medicine, Ferdowsi University of Mashhad, Azadi Square, Mashhad, Iran
| | - Safoura Soleymani
- 1Division of Biotechnology, Faculty of Veterinary Medicine, Ferdowsi University of Mashhad, Azadi Square, Mashhad, Iran
| | - Alireza Haghparast
- 1Division of Biotechnology, Faculty of Veterinary Medicine, Ferdowsi University of Mashhad, Azadi Square, Mashhad, Iran.,2Immunology Section, Department of Pathobiology , Faculty of Veterinary Medicine, Ferdowsi University of Mashhad, Mashhad, Iran
| | - Gholamreza Hashemi Tabar
- 1Division of Biotechnology, Faculty of Veterinary Medicine, Ferdowsi University of Mashhad, Azadi Square, Mashhad, Iran
| | - Mohammad Reza Bassami
- 1Division of Biotechnology, Faculty of Veterinary Medicine, Ferdowsi University of Mashhad, Azadi Square, Mashhad, Iran
| | - Hesam Dehghani
- 1Division of Biotechnology, Faculty of Veterinary Medicine, Ferdowsi University of Mashhad, Azadi Square, Mashhad, Iran.,3Department of Basic Sciences, Faculty of Veterinary Medicine, Ferdowsi University of Mashhad, Mashhad, Iran.,4Stem Cell Biology and Regenerative Medicine Research Group, Research Institute of Biotechnology, Ferdowsi University of Mashhad, Azadi Square, Mashhad, Iran
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23
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Funai T, Tagawa C, Nakagawa O, Wada SI, Ono A, Urata H. Enzymatic formation of consecutive thymine–HgII–thymine base pairs by DNA polymerases. Chem Commun (Camb) 2020; 56:12025-12028. [DOI: 10.1039/d0cc04423g] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
Ten consecutive T–HgII–T base pairs were successfully formed by DNA polymerase-catalyzed primer extension reactions.
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Affiliation(s)
- Tatsuya Funai
- Department of Bioorganic Chemistry
- Osaka University of Pharmaceutical Sciences
- 4-20-1 Nasahara
- Takatsuki
- Japan
| | - Chizuko Tagawa
- Department of Bioorganic Chemistry
- Osaka University of Pharmaceutical Sciences
- 4-20-1 Nasahara
- Takatsuki
- Japan
| | - Osamu Nakagawa
- Department of Bioorganic Chemistry
- Osaka University of Pharmaceutical Sciences
- 4-20-1 Nasahara
- Takatsuki
- Japan
| | - Shun-ichi Wada
- Department of Bioorganic Chemistry
- Osaka University of Pharmaceutical Sciences
- 4-20-1 Nasahara
- Takatsuki
- Japan
| | - Akira Ono
- Department of Material & Life Chemistry
- Faculty of Engineering, Kanagawa University
- 3-27-1 Rokkakubashi
- Kanagawa-ku
- Japan
| | - Hidehito Urata
- Department of Bioorganic Chemistry
- Osaka University of Pharmaceutical Sciences
- 4-20-1 Nasahara
- Takatsuki
- Japan
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24
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Mistry L, Waddell PG, Wright NG, Horrocks BR, Houlton A. transoid and cisoid Conformations in Silver-Mediated Cytosine Base Pairs: Hydrogen Bonding Dictates Argentophilic Interactions in the Solid State. Inorg Chem 2019; 58:13346-13352. [DOI: 10.1021/acs.inorgchem.9b02228] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023]
Affiliation(s)
- Liam Mistry
- Chemical Nanoscience Laboratory, Chemistry, School of Natural & Environmental Sciences, Newcastle University, Newcastle upon Tyne, NE1 7RU, U.K
| | - Paul G. Waddell
- Chemical Nanoscience Laboratory, Chemistry, School of Natural & Environmental Sciences, Newcastle University, Newcastle upon Tyne, NE1 7RU, U.K
| | - Nick G. Wright
- School of Engineering, Newcastle University, Newcastle upon Tyne, NE1 7RU, U.K
| | - Benjamin R. Horrocks
- Chemical Nanoscience Laboratory, Chemistry, School of Natural & Environmental Sciences, Newcastle University, Newcastle upon Tyne, NE1 7RU, U.K
| | - Andrew Houlton
- Chemical Nanoscience Laboratory, Chemistry, School of Natural & Environmental Sciences, Newcastle University, Newcastle upon Tyne, NE1 7RU, U.K
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25
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Funai T, Adachi N, Aotani M, Wada SI, Urata H. Effects of metal ions on thermal stabilities of DNA duplexes containing homo- and heterochiral mismatched base pairs: comparison of internal and terminal substitutions. NUCLEOSIDES NUCLEOTIDES & NUCLEIC ACIDS 2019; 39:310-321. [PMID: 31514571 DOI: 10.1080/15257770.2019.1658116] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
The effects of metal ions on the stabilities of duplexes containing a D-homochiral and heterochiral mismatched base pairs were studied. In some duplexes containing an internal mismatched base pair, significant stabilization by HgII and AgI ions was observed. While, in duplexes containing a terminal mismatched base pair, only the duplexes containing T-T and LT-T mispairs were significantly stabilized by HgII ions, and the stabilities of the duplexes containing T-T and LT-T mispairs exceeded those of the corresponding homochiral matched duplex. The results suggest that the formation of homo- and heterochiral T-HgII-T base pairs at duplex termini would be useful for the thermal and enzymatic stabilization of DNA-based nanodevice.
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Affiliation(s)
- Tatsuya Funai
- Department of Bioorganic Chemistry, Osaka University of Pharmaceutical Sciences, Takatsuki, Osaka, Japan
| | - Nahomi Adachi
- Department of Bioorganic Chemistry, Osaka University of Pharmaceutical Sciences, Takatsuki, Osaka, Japan
| | - Megumi Aotani
- Department of Bioorganic Chemistry, Osaka University of Pharmaceutical Sciences, Takatsuki, Osaka, Japan
| | - Shun-Ichi Wada
- Department of Bioorganic Chemistry, Osaka University of Pharmaceutical Sciences, Takatsuki, Osaka, Japan
| | - Hidehito Urata
- Department of Bioorganic Chemistry, Osaka University of Pharmaceutical Sciences, Takatsuki, Osaka, Japan
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