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Fu J, Yang YR, Dhakal S, Zhao Z, Liu M, Zhang T, Walter NG, Yan H. Assembly of multienzyme complexes on DNA nanostructures. Nat Protoc 2016; 11:2243-2273. [DOI: 10.1038/nprot.2016.139] [Citation(s) in RCA: 81] [Impact Index Per Article: 10.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
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303
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Wang Y, Jiang LP, Zhou S, Bi S, Zhu JJ. DNA Polymerase-Directed Hairpin Assembly for Targeted Drug Delivery and Amplified Biosensing. ACS APPLIED MATERIALS & INTERFACES 2016; 8:26532-26540. [PMID: 27690212 DOI: 10.1021/acsami.6b08597] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/06/2023]
Abstract
Due to the predictable conformation and programmable Watson-Crick base-pairing interactions, DNA has proven to be an attractive material to construct various nanostructures. Herein, we demonstrate a simple model of DNA polymerase-directed hairpin assembly (PDHA) to construct DNA nanoassemblies for versatile applications in biomedicine and biosensing. The system consists of only two hairpins, an initiator and a DNA polymerase. Upon addition of aptamer-linked initiator, the inert stems of the two hairpins are activated alternately under the direction of DNA polymerase, which thus grows into aptamer-tethered DNA nanoassemblies (AptNAs). Moreover, through incorporating fluorophores and drug-loading sites into the AptNAs, we have constructed multifunctional DNA nanoassemblies for targeted cancer therapy with high drug payloads and good biocompatibility. Interestingly, using the as-prepared AptNAs as building blocks, DNA nanohydrogels are self-assembled after centrifugation driven by liquid crystallization and dense packaging of DNA duplexes. Taking advantage of easy preparation and high loading capacity, the PDHAs are readily extended to the fabrication of a label-free biosensing platform, achieving amplified electrochemical detection of microRNA-21 (miR-21) with a detection limit as low as 0.75 fM and a dynamic range of 8 orders of magnitude. This biosensor also demonstrates excellent specificity to discriminate the target miR-21 from the control microRNAs and even the one-base mismatched one and further performs well in analyzing miR-21 in MCF-7 tumor cells.
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Affiliation(s)
- Yingying Wang
- State Key Laboratory of Analytical Chemistry for Life Science and Collaborative Innovation Center of Chemistry for Life Sciences, School of Chemistry and Chemical Engineering, Nanjing University , Nanjing 210093, China
| | - Li-Ping Jiang
- State Key Laboratory of Analytical Chemistry for Life Science and Collaborative Innovation Center of Chemistry for Life Sciences, School of Chemistry and Chemical Engineering, Nanjing University , Nanjing 210093, China
| | - Shiwei Zhou
- State Key Laboratory of Analytical Chemistry for Life Science and Collaborative Innovation Center of Chemistry for Life Sciences, School of Chemistry and Chemical Engineering, Nanjing University , Nanjing 210093, China
| | - Sai Bi
- State Key Laboratory of Analytical Chemistry for Life Science and Collaborative Innovation Center of Chemistry for Life Sciences, School of Chemistry and Chemical Engineering, Nanjing University , Nanjing 210093, China
- Collaborative Innovation Center for Marine Biomass Fiber Materials and Textiles, College of Chemistry and Chemical Engineering, Shandong Sino-Japanese Center for Collaborative Research of Carbon Nanomaterials, Laboratory of Fiber Materials and Modern Textiles, the Growing Base for State Key Laboratory, Qingdao University , Qingdao 266071, China
| | - Jun-Jie Zhu
- State Key Laboratory of Analytical Chemistry for Life Science and Collaborative Innovation Center of Chemistry for Life Sciences, School of Chemistry and Chemical Engineering, Nanjing University , Nanjing 210093, China
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304
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Matek C, Šulc P, Randisi F, Doye JPK, Louis AA. Coarse-grained modelling of supercoiled RNA. J Chem Phys 2016; 143:243122. [PMID: 26723607 DOI: 10.1063/1.4933066] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/18/2023] Open
Abstract
We study the behaviour of double-stranded RNA under twist and tension using oxRNA, a recently developed coarse-grained model of RNA. Introducing explicit salt-dependence into the model allows us to directly compare our results to data from recent single-molecule experiments. The model reproduces extension curves as a function of twist and stretching force, including the buckling transition and the behaviour of plectoneme structures. For negative supercoiling, we predict denaturation bubble formation in plectoneme end-loops, suggesting preferential plectoneme localisation in weak base sequences. OxRNA exhibits a positive twist-stretch coupling constant, in agreement with recent experimental observations.
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Affiliation(s)
- Christian Matek
- Rudolf Peierls Centre for Theoretical Physics, University of Oxford, 1 Keble Road, Oxford OX1 3NP, United Kingdom
| | - Petr Šulc
- Center for Studies in Physics and Biology, The Rockefeller University, 1230 York Avenue, New York, New York 10065, USA
| | - Ferdinando Randisi
- Rudolf Peierls Centre for Theoretical Physics, University of Oxford, 1 Keble Road, Oxford OX1 3NP, United Kingdom
| | - Jonathan P K Doye
- Physical and Theoretical Chemistry Laboratory, Department of Chemistry, University of Oxford, South Parks Road, Oxford OX1 3QZ, United Kingdom
| | - Ard A Louis
- Rudolf Peierls Centre for Theoretical Physics, University of Oxford, 1 Keble Road, Oxford OX1 3NP, United Kingdom
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305
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Ma X, Huh J, Park W, Lee LP, Kwon YJ, Sim SJ. Gold nanocrystals with DNA-directed morphologies. Nat Commun 2016; 7:12873. [PMID: 27633935 PMCID: PMC5028415 DOI: 10.1038/ncomms12873] [Citation(s) in RCA: 36] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2016] [Accepted: 08/09/2016] [Indexed: 12/29/2022] Open
Abstract
Precise control over the structure of metal nanomaterials is important for developing advanced nanobiotechnology. Assembly methods of nanoparticles into structured blocks have been widely demonstrated recently. However, synthesis of nanocrystals with controlled, three-dimensional structures remains challenging. Here we show a directed crystallization of gold by a single DNA molecular regulator in a sequence-independent manner and its applications in three-dimensional topological controls of crystalline nanostructures. We anchor DNA onto gold nanoseed with various alignments to form gold nanocrystals with defined topologies. Some topologies are asymmetric including pushpin-, star- and biconcave disk-like structures, as well as more complex jellyfish- and flower-like structures. The approach of employing DNA enables the solution-based synthesis of nanocrystals with controlled, three-dimensional structures in a desired direction, and expands the current tools available for designing and synthesizing feature-rich nanomaterials for future translational biotechnology. Bottom-up synthesis of colloidal metallic nanomaterials with a designable structure is challenging. Here, the authors report the directed crystallisation of gold by a single DNA molecular regulator, using it to synthesise gold nanocrystals with defined complex morphologies.
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Affiliation(s)
- Xingyi Ma
- Department of Chemical &Biological Engineering, Korea University, Seoul 136713, Republic of Korea
| | - June Huh
- Department of Chemical &Biological Engineering, Korea University, Seoul 136713, Republic of Korea
| | - Wounjhang Park
- Department of Electrical, Computer &Energy Engineering, Materials Science &Engineering Program, University of Colorado, Boulder, Colorado 80309, USA
| | - Luke P Lee
- Institute of Quantitative Biosciences &Biophysics, Departments of Bioengineering, Electrical Engineering &Computer Science, University of California Berkeley, Berkeley, California 94720, USA
| | - Young Jik Kwon
- Departments of Pharmaceutical Sciences, and Chemical Engineering &Materials Science, University of California Irvine, Irvine, California 92697, USA
| | - Sang Jun Sim
- Department of Chemical &Biological Engineering, Korea University, Seoul 136713, Republic of Korea.,Green School, Korea University, Seoul 136713, Republic of Korea
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306
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The coming of age of de novo protein design. Nature 2016; 537:320-7. [DOI: 10.1038/nature19946] [Citation(s) in RCA: 803] [Impact Index Per Article: 100.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2016] [Accepted: 07/20/2016] [Indexed: 12/24/2022]
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307
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Li H, Zhang K, Pi F, Guo S, Shlyakhtenko L, Chiu W, Shu D, Guo P. Controllable Self-Assembly of RNA Tetrahedrons with Precise Shape and Size for Cancer Targeting. ADVANCED MATERIALS (DEERFIELD BEACH, FLA.) 2016; 28:7501-7. [PMID: 27322097 PMCID: PMC5059845 DOI: 10.1002/adma.201601976] [Citation(s) in RCA: 60] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/13/2016] [Revised: 05/11/2016] [Indexed: 05/20/2023]
Abstract
RNA tetrahedral nanoparticles with two different sizes are successfully assembled by a one-pot bottom-up approach with high efficiency and thermal stability. The reported design principles can be extended to construct higher-order polyhedral RNA architectures for various applications such as targeted cancer imaging and therapy.
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Affiliation(s)
- Hui Li
- College of Pharmacy/Division of Pharmaceutics and Pharmaceutical Chemistry, College of Medicine/Department of Physiology and Cell Biology/Dorothy M. Davis Heart and Lung Research Institute, The Ohio State University, Columbus, OH, 43210, USA
| | - Kaiming Zhang
- Verna and Marrs McLean Department of Biochemistry and Molecular Biology, National Center for Macromolecular Imaging, Baylor College of Medicine, Houston, TX, 77030, USA
| | - Fengmei Pi
- College of Pharmacy/Division of Pharmaceutics and Pharmaceutical Chemistry, College of Medicine/Department of Physiology and Cell Biology/Dorothy M. Davis Heart and Lung Research Institute, The Ohio State University, Columbus, OH, 43210, USA
| | - Sijin Guo
- College of Pharmacy/Division of Pharmaceutics and Pharmaceutical Chemistry, College of Medicine/Department of Physiology and Cell Biology/Dorothy M. Davis Heart and Lung Research Institute, The Ohio State University, Columbus, OH, 43210, USA
| | - Luda Shlyakhtenko
- Department of Pharmaceutical Sciences, University of Nebraska Medical Center, Omaha, NE, 68198, USA
| | - Wah Chiu
- Verna and Marrs McLean Department of Biochemistry and Molecular Biology, National Center for Macromolecular Imaging, Baylor College of Medicine, Houston, TX, 77030, USA
| | - Dan Shu
- College of Pharmacy/Division of Pharmaceutics and Pharmaceutical Chemistry, College of Medicine/Department of Physiology and Cell Biology/Dorothy M. Davis Heart and Lung Research Institute, The Ohio State University, Columbus, OH, 43210, USA
| | - Peixuan Guo
- College of Pharmacy/Division of Pharmaceutics and Pharmaceutical Chemistry, College of Medicine/Department of Physiology and Cell Biology/Dorothy M. Davis Heart and Lung Research Institute, The Ohio State University, Columbus, OH, 43210, USA.
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308
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Bis-three-way junction nanostructure and DNA machineries for ultrasensitive and specific detection of BCR/ABL fusion gene by chemiluminescence imaging. Sci Rep 2016; 6:32370. [PMID: 27577607 PMCID: PMC5006031 DOI: 10.1038/srep32370] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2016] [Accepted: 08/04/2016] [Indexed: 01/07/2023] Open
Abstract
A novel G-quadruplex DNAzyme-driven chemiluminescence (CL) imaging method has been developed for ultrasensitive and specific detection of BCR/ABL fusion gene based on bis-three-way junction (bis-3WJ) nanostructure and cascade DNA machineries. Bis-3WJ probes are designed logically to recognize BCR/ABL fusion gene, which forms the stable bis-3WJ nanostructure for the activation of polymerase/nicking enzyme machineries in cascade, resulting in synthesis of DNAzyme subunits. These DNAzyme subunits can form integrated DNAzyme by self-assembly to catalyze CL substrate, thus providing an amplified signal for the sensing events or outputs for AND logic operation. The imaging method achieved ultrasensitive detection of BCR/ABL fusion gene with a low detection limit down to 23 fM. And this method exhibited wide linear ranges over seven orders of magnitude and excellent discrimination ability toward target. In addition, an acceptable recovery was obtained in complex matrix. It is notable that this biosensing strategy possesses merits of homogenous, isothermal and label-free assay system. Therefore, these merits endow the developed imaging method with a potential tool for CML diagnosis.
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309
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Yonamine Y, Cervantes-Salguero K, Nakanishi W, Kawamata I, Minami K, Komatsu H, Murata S, Hill JP, Ariga K. In situ 2D-extraction of DNA wheels by 3D through-solution transport. Phys Chem Chem Phys 2016; 17:32122-5. [PMID: 26583486 DOI: 10.1039/c5cp05765e] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Controlled transfer of DNA nanowheels from a hydrophilic to a hydrophobic surface was achieved by complexation of the nanowheels with a cationic lipid (2C12N(+)). 2D surface-assisted extraction, '2D-extraction', enabled structure-persistent transfer of DNA wheels, which could not be achieved by simple drop-casting.
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Affiliation(s)
- Yusuke Yonamine
- World Premier International (WPI) Research Centre for Materials Nanoarchitectonics (MANA), National Institute for Materials Science (NIMS) 1-1 Namiki, Tsukuba, Ibaraki, 305-0044, Japan. and CREST, JST, Sanbancho, Chiyoda-ku, Tokyo 102-0075, Japan
| | - Keitel Cervantes-Salguero
- Department of Bioengineering and Robotics, Tohoku University, 6-6-1 Aobayama, Sendai, 980-8579, Japan.
| | - Waka Nakanishi
- World Premier International (WPI) Research Centre for Materials Nanoarchitectonics (MANA), National Institute for Materials Science (NIMS) 1-1 Namiki, Tsukuba, Ibaraki, 305-0044, Japan.
| | - Ibuki Kawamata
- Department of Bioengineering and Robotics, Tohoku University, 6-6-1 Aobayama, Sendai, 980-8579, Japan.
| | - Kosuke Minami
- World Premier International (WPI) Research Centre for Materials Nanoarchitectonics (MANA), National Institute for Materials Science (NIMS) 1-1 Namiki, Tsukuba, Ibaraki, 305-0044, Japan.
| | - Hirokazu Komatsu
- World Premier International (WPI) Research Centre for Materials Nanoarchitectonics (MANA), National Institute for Materials Science (NIMS) 1-1 Namiki, Tsukuba, Ibaraki, 305-0044, Japan.
| | - Satoshi Murata
- Department of Bioengineering and Robotics, Tohoku University, 6-6-1 Aobayama, Sendai, 980-8579, Japan.
| | - Jonathan P Hill
- World Premier International (WPI) Research Centre for Materials Nanoarchitectonics (MANA), National Institute for Materials Science (NIMS) 1-1 Namiki, Tsukuba, Ibaraki, 305-0044, Japan. and CREST, JST, Sanbancho, Chiyoda-ku, Tokyo 102-0075, Japan
| | - Katsuhiko Ariga
- World Premier International (WPI) Research Centre for Materials Nanoarchitectonics (MANA), National Institute for Materials Science (NIMS) 1-1 Namiki, Tsukuba, Ibaraki, 305-0044, Japan. and CREST, JST, Sanbancho, Chiyoda-ku, Tokyo 102-0075, Japan
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310
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Aslan H, Krissanaprasit A, Besenbacher F, Gothelf KV, Dong M. Protein patterning by a DNA origami framework. NANOSCALE 2016; 8:15233-15240. [PMID: 27487933 DOI: 10.1039/c6nr03199d] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/06/2023]
Abstract
A spatial arrangement of proteins provides structural and functional advantages in vast technological applications as well as fundamental research. Most protein patterning procedures employ complicated, time consuming and very costly nanofabrication techniques. As an alternative route, we developed a fully biomolecular self-assembly method using DNA Origami Frames (DOF) as a template for both small and large scale protein patterning. We employed a triangular DOF (tDOF) to arrange the Bovine Serum Albumin (BSA) protein. Our in situ protein patterning strategy provides a novel, fully organic platform using a fast and low-cost surface approach with possible utilization in fundamental science and technological applications.
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Affiliation(s)
- Hüsnü Aslan
- Center for DNA Nanotechnology (CDNA) and Interdisciplinary Nanoscience (iNANO) Center, Aarhus University, Gustav Wieds Vej 14, 8000 Aarhus C, Denmark.
| | - Abhichart Krissanaprasit
- Center for DNA Nanotechnology (CDNA) and Interdisciplinary Nanoscience (iNANO) Center, Aarhus University, Gustav Wieds Vej 14, 8000 Aarhus C, Denmark.
| | - Flemming Besenbacher
- Center for DNA Nanotechnology (CDNA) and Interdisciplinary Nanoscience (iNANO) Center, Aarhus University, Gustav Wieds Vej 14, 8000 Aarhus C, Denmark.
| | - Kurt V Gothelf
- Center for DNA Nanotechnology (CDNA) and Interdisciplinary Nanoscience (iNANO) Center, Aarhus University, Gustav Wieds Vej 14, 8000 Aarhus C, Denmark.
| | - Mingdong Dong
- Center for DNA Nanotechnology (CDNA) and Interdisciplinary Nanoscience (iNANO) Center, Aarhus University, Gustav Wieds Vej 14, 8000 Aarhus C, Denmark.
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311
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Jiang D, England CG, Cai W. DNA nanomaterials for preclinical imaging and drug delivery. J Control Release 2016; 239:27-38. [PMID: 27527555 DOI: 10.1016/j.jconrel.2016.08.013] [Citation(s) in RCA: 48] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2016] [Revised: 08/09/2016] [Accepted: 08/10/2016] [Indexed: 12/31/2022]
Abstract
Besides being the carrier of genetic information, DNA is also an excellent biological organizer to establish well-designed nanostructures in the fields of material engineering, nanotechnology, and biomedicine. DNA-based materials represent a diverse nanoscale system primarily due to their predictable base pairing and highly regulated conformations, which greatly facilitate the construction of DNA nanostructures with distinct shapes and sizes. Integrating the emerging advancements in bioconjugation techniques, DNA nanostructures can be readily functionalized with high precision for many purposes ranging from biosensors to imaging to drug delivery. Recent progress in the field of DNA nanotechnology has exhibited collective efforts to employ DNA nanostructures as smart imaging agents or delivery platforms within living organisms. Despite significant improvements in the development of DNA nanostructures, there is limited knowledge regarding the in vivo biological fate of these intriguing nanomaterials. In this review, we summarize the current strategies for designing and purifying highly-versatile DNA nanostructures for biological applications, including molecular imaging and drug delivery. Since DNA nanostructures may elicit an immune response in vivo, we also present a short discussion of their potential toxicities in biomedical applications. Lastly, we discuss future perspectives and potential challenges that may limit the effective preclinical and clinical employment of DNA nanostructures. Due to their unique properties, we predict that DNA nanomaterials will make excellent agents for effective diagnostic imaging and drug delivery, improving patient outcome in cancer and other related diseases in the near future.
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Affiliation(s)
- Dawei Jiang
- Department of Radiology, University of Wisconsin, Madison, WI 53705, USA
| | | | - Weibo Cai
- Department of Radiology, University of Wisconsin, Madison, WI 53705, USA; Department of Medical Physics, University of Wisconsin, Madison, WI 53705, USA; University of Wisconsin Carbone Cancer Center, Madison, WI 53705, USA.
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312
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San BH, Li Y, Tarbet EB, Yu SM. Nanoparticle Assembly and Gelatin Binding Mediated by Triple Helical Collagen Mimetic Peptide. ACS APPLIED MATERIALS & INTERFACES 2016; 8:19907-19915. [PMID: 27403657 PMCID: PMC5453869 DOI: 10.1021/acsami.6b05707] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/29/2023]
Abstract
Peptide-conjugated nanoparticles (NPs) have promising potential for applications in biosensing, diagnosis, and therapeutics because of their appropriate size, unique self-assembly, and specific substrate-binding properties. However, controlled assembly and selective target binding are difficult to achieve with simple peptides on NP surfaces because high surface energy makes NPs prone to self-aggregate and adhere nonspecifically. Here, we report the self-assembly and gelatin binding properties of collagen mimetic peptide (CMP) conjugated gold NPs (CMP-NPs). We show that the orientation of CMPs displayed on the NP surface can control NP assembly either by promoting or hindering triple helical folding between CMPs of neighboring NPs. We also show that CMP-NPs can specifically bind to denatured collagen by forming triple-helical hybrids between denatured collagen strands and CMPs, demonstrating their potential use for detection and selective removal of gelatin from protein mixtures. CMP conjugated NPs offer a simple and effective method for NP assembly and for targeting denatured collagens with high specificity. Therefore, they may lead to new types of functional nanomaterials for detection and study of denatured collagen associated with diseases characterized by high levels of collagen degradation.
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Affiliation(s)
- Boi Hoa San
- Department of Bioengineering, University of Utah, Salt Lake City, Utah 84112, United States
| | - Yang Li
- Department of Bioengineering, University of Utah, Salt Lake City, Utah 84112, United States
| | - E. Bart Tarbet
- Institute for Antiviral Research, Utah State University, Logan, Utah 84322, United States
| | - S. Michael Yu
- Department of Bioengineering, University of Utah, Salt Lake City, Utah 84112, United States
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313
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Morisue M, Hoshino Y, Shimizu M, Uemura S, Sakurai S. A Tightly Stretched Ultralong Supramolecular Multiporphyrin Array Propagated by Double-Strand Formation. Chemistry 2016; 22:13019-22. [DOI: 10.1002/chem.201602968] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2016] [Indexed: 12/17/2022]
Affiliation(s)
- Mitsuhiko Morisue
- Faculty of Molecular Chemistry and Engineering; Kyoto Institute of Technology, Matsugasaki, Sakyo-ku; Kyoto 606-8585 Japan
| | - Yuki Hoshino
- Faculty of Molecular Chemistry and Engineering; Kyoto Institute of Technology, Matsugasaki, Sakyo-ku; Kyoto 606-8585 Japan
| | - Masaki Shimizu
- Faculty of Molecular Chemistry and Engineering; Kyoto Institute of Technology, Matsugasaki, Sakyo-ku; Kyoto 606-8585 Japan
| | - Shinobu Uemura
- Department of Engineering; Kagawa University, Hayashi-cho; Takamatsu 761-0396 Japan
| | - Shinichi Sakurai
- Faculty of Biobased Materials Science; Kyoto Institute of Technology, Matsugasaki, Sakyo-ku; Kyoto 606-8585 Japan
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314
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Lau KL, Sleiman HF. Minimalist Approach to Complexity: Templating the Assembly of DNA Tile Structures with Sequentially Grown Input Strands. ACS NANO 2016; 10:6542-6551. [PMID: 27303951 DOI: 10.1021/acsnano.6b00134] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/06/2023]
Abstract
Given its highly predictable self-assembly properties, DNA has proven to be an excellent template toward the design of functional materials. Prominent examples include the remarkable complexity provided by DNA origami and single-stranded tile (SST) assemblies, which require hundreds of unique component strands. However, in many cases, the majority of the DNA assembly is purely structural, and only a small "working area" needs to be aperiodic. On the other hand, extended lattices formed by DNA tile motifs require only a few strands; but they suffer from lack of size control and limited periodic patterning. To overcome these limitations, we adopt a templation strategy, where an input strand of DNA dictates the size and patterning of resultant DNA tile structures. To prepare these templating input strands, a sequential growth technique developed in our lab is used, whereby extended DNA strands of defined sequence and length may be generated simply by controlling their order of addition. With these, we demonstrate the periodic patterning of size-controlled double-crossover (DX) and triple-crossover (TX) tile structures, as well as intentionally designed aperiodicity of a DX tile structure. As such, we are able to prepare size-controlled DNA structures featuring aperiodicity only where necessary with exceptional economy and efficiency.
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Affiliation(s)
- Kai Lin Lau
- Department of Chemistry, McGill University , 801 Sherbrooke Street West, Montreal, Quebec H3A 0B8, Canada
| | - Hanadi F Sleiman
- Department of Chemistry, McGill University , 801 Sherbrooke Street West, Montreal, Quebec H3A 0B8, Canada
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315
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Hernández-Ainsa S, Ricci M, Hilton L, Aviñó A, Eritja R, Keyser UF. Controlling the Reversible Assembly of Liposomes through a Multistimuli Responsive Anchored DNA. NANO LETTERS 2016; 16:4462-6. [PMID: 27367802 PMCID: PMC4956241 DOI: 10.1021/acs.nanolett.6b01618] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/20/2016] [Revised: 06/23/2016] [Indexed: 05/21/2023]
Abstract
We present a novel approach to reversibly control the assembly of liposomes through an anchored multistimuli responsive DNA oligonucleotide decorated with an azobenzene moiety (AZO-ON1). We show that liposomes assembly can be simultaneously controlled by three external stimuli: light, Mg(2+), and temperature. (i) Light alters the interaction of AZO-ON1 with liposomes, which influences DNA coating and consequently liposomes assembly. (ii) Mg(2+) induces the assembly, hence variation in its concentration enables for reversibility. (iii) Double-stranded AZO-ON1 is more efficient than single-stranded AZO-ON1 in triggering the assembly of liposomes and temperature has been used for controllable assembly through DNA thermal denaturation. Our multiresponsive AZO-ON1 represents a unique example in which multiple stimuli can be simultaneously applied to regulate the reversible assembly of liposomes.
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Affiliation(s)
- Silvia Hernández-Ainsa
- Cavendish Laboratory, Department of Physics, University of Cambridge, JJ Thomson Avenue, Cambridge, CB3 0HE, United Kingdom
| | - Maria Ricci
- Cavendish Laboratory, Department of Physics, University of Cambridge, JJ Thomson Avenue, Cambridge, CB3 0HE, United Kingdom
| | - Lloyd Hilton
- Cavendish Laboratory, Department of Physics, University of Cambridge, JJ Thomson Avenue, Cambridge, CB3 0HE, United Kingdom
| | - Anna Aviñó
- IQAC−CSIC, CIBER-BBN Networking Centre on Bioengineering,
Biomaterials and Nanomedicine, c/Jordi Girona 18-26, 08034 Barcelona, Spain
| | - Ramon Eritja
- IQAC−CSIC, CIBER-BBN Networking Centre on Bioengineering,
Biomaterials and Nanomedicine, c/Jordi Girona 18-26, 08034 Barcelona, Spain
| | - Ulrich F. Keyser
- Cavendish Laboratory, Department of Physics, University of Cambridge, JJ Thomson Avenue, Cambridge, CB3 0HE, United Kingdom
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316
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Programming a topologically constrained DNA nanostructure into a sensor. Nat Commun 2016; 7:12074. [PMID: 27337657 PMCID: PMC4931013 DOI: 10.1038/ncomms12074] [Citation(s) in RCA: 54] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2016] [Accepted: 05/27/2016] [Indexed: 01/21/2023] Open
Abstract
Many rationally engineered DNA nanostructures use mechanically interlocked topologies to connect individual DNA components, and their physical connectivity is achieved through the formation of a strong linking duplex. The existence of such a structural element also poses a significant topological constraint on functions of component rings. Herein, we hypothesize and confirm that DNA catenanes with a strong linking duplex prevent component rings from acting as the template for rolling circle amplification (RCA). However, by using an RNA-containing DNA [2] catenane with a strong linking duplex, we show that a stimuli-responsive RNA-cleaving DNAzyme can linearize one component ring, and thus enable RCA, producing an ultra-sensitive biosensing system. As an example, a DNA catenane biosensor is engineered to detect the model bacterial pathogen Escherichia coli through binding of a secreted protein, with a detection limit of 10 cells ml−1, thus establishing a new platform for further applications of mechanically interlocked DNA nanostructures. DNA nanostructures with interlocked topologies will tend to display different behaviour to the linear counterparts. Here, the authors show a DNA catenane that is inactive for rolling circle amplification but is activated upon cleavage of one ring, and exploit this for the development of a biosensing system.
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317
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Taylor AI, Beuron F, Peak-Chew SY, Morris EP, Herdewijn P, Holliger P. Nanostructures from Synthetic Genetic Polymers. Chembiochem 2016; 17:1107-10. [PMID: 26992063 PMCID: PMC4973672 DOI: 10.1002/cbic.201600136] [Citation(s) in RCA: 46] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2016] [Indexed: 12/22/2022]
Abstract
Nanoscale objects of increasing complexity can be constructed from DNA or RNA. However, the scope of potential applications could be enhanced by expanding beyond the moderate chemical diversity of natural nucleic acids. Here, we explore the construction of nano-objects made entirely from alternative building blocks: synthetic genetic polymers not found in nature, also called xeno nucleic acids (XNAs). Specifically, we describe assembly of 70 kDa tetrahedra elaborated in four different XNA chemistries (2'-fluro-2'-deoxy-ribofuranose nucleic acid (2'F-RNA), 2'-fluoroarabino nucleic acids (FANA), hexitol nucleic acids (HNA), and cyclohexene nucleic acids (CeNA)), as well as mixed designs, and a ∼600 kDa all-FANA octahedron, visualised by electron microscopy. Our results extend the chemical scope for programmable nanostructure assembly, with implications for the design of nano-objects and materials with an expanded range of structural and physicochemical properties, including enhanced biostability.
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Affiliation(s)
- Alexander I Taylor
- Medical Research Council Laboratory of Molecular Biology, Francis Crick Avenue, Cambridge, CB2 0QH, UK.
- Department of Biology/Centre for Applied Synthetic Biology, Concordia University, 7141 Rue Sherbrooke, Montreal, H4B 1R6, Canada.
| | - Fabienne Beuron
- Division of Structural Biology, The Institute of Cancer Research, Chester Beatty Laboratories), 237 Fulham Road, London, SW3 6JB, UK
| | - Sew-Yeu Peak-Chew
- Medical Research Council Laboratory of Molecular Biology, Francis Crick Avenue, Cambridge, CB2 0QH, UK
| | - Edward P Morris
- Division of Structural Biology, The Institute of Cancer Research, Chester Beatty Laboratories), 237 Fulham Road, London, SW3 6JB, UK
| | - Piet Herdewijn
- Rega Institute, KU Leuven, Minderbroedersstraat 10, 3000, Leuven, Belgium
- Institute of Systems and Synthetic Biology, Université Evry, 5 rue Henri Desbrueres, 91030, Evry Cedex, France
| | - Philipp Holliger
- Medical Research Council Laboratory of Molecular Biology, Francis Crick Avenue, Cambridge, CB2 0QH, UK.
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318
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Zhang F, Jiang S, Li W, Hunt A, Liu Y, Yan H. Self‐Assembly of Complex DNA Tessellations by Using Low‐Symmetry Multi‐arm DNA Tiles. Angew Chem Int Ed Engl 2016; 55:8860-3. [DOI: 10.1002/anie.201601944] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2016] [Revised: 04/28/2016] [Indexed: 01/25/2023]
Affiliation(s)
- Fei Zhang
- School of Molecular Sciences and The Biodesign Institute Arizona State University Tempe AZ 85287 USA
| | - Shuoxing Jiang
- School of Molecular Sciences and The Biodesign Institute Arizona State University Tempe AZ 85287 USA
| | - Wei Li
- School of Molecular Sciences and The Biodesign Institute Arizona State University Tempe AZ 85287 USA
| | - Ashley Hunt
- School of Molecular Sciences and The Biodesign Institute Arizona State University Tempe AZ 85287 USA
| | - Yan Liu
- School of Molecular Sciences and The Biodesign Institute Arizona State University Tempe AZ 85287 USA
| | - Hao Yan
- School of Molecular Sciences and The Biodesign Institute Arizona State University Tempe AZ 85287 USA
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319
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Takezawa Y, Kobayashi T, Shionoya M. The Effects of Magnesium Ions on the Enzymatic Synthesis of Ligand-Bearing Artificial DNA by Template-Independent Polymerase. Int J Mol Sci 2016; 17:E906. [PMID: 27338351 PMCID: PMC4926440 DOI: 10.3390/ijms17060906] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2016] [Revised: 06/03/2016] [Accepted: 06/04/2016] [Indexed: 02/04/2023] Open
Abstract
A metal-mediated base pair, composed of two ligand-bearing nucleotides and a bridging metal ion, is one of the most promising components for developing DNA-based functional molecules. We have recently reported an enzymatic method to synthesize hydroxypyridone (H)-type ligand-bearing artificial DNA strands. Terminal deoxynucleotidyl transferase (TdT), a template-independent DNA polymerase, was found to oligomerize H nucleotides to afford ligand-bearing DNAs, which were subsequently hybridized through copper-mediated base pairing (H-Cu(II)-H). In this study, we investigated the effects of a metal cofactor, Mg(II) ion, on the TdT-catalyzed polymerization of H nucleotides. At a high Mg(II) concentration (10 mM), the reaction was halted after several H nucleotides were appended. In contrast, at lower Mg(II) concentrations, H nucleotides were further appended to the H-tailed product to afford longer ligand-bearing DNA strands. An electrophoresis mobility shift assay revealed that the binding affinity of TdT to the H-tailed DNAs depends on the Mg(II) concentration. In the presence of excess Mg(II) ions, TdT did not bind to the H-tailed strands; thus, further elongation was impeded. This is possibly because the interaction with Mg(II) ions caused folding of the H-tailed strands into unfavorable secondary structures. This finding provides an insight into the enzymatic synthesis of longer ligand-bearing DNA strands.
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Affiliation(s)
- Yusuke Takezawa
- Department of Chemistry, Graduate School of Science, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-0033, Japan.
| | - Teruki Kobayashi
- Department of Chemistry, Graduate School of Science, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-0033, Japan.
| | - Mitsuhiko Shionoya
- Department of Chemistry, Graduate School of Science, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-0033, Japan.
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320
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Zhang F, Jiang S, Li W, Hunt A, Liu Y, Yan H. Self‐Assembly of Complex DNA Tessellations by Using Low‐Symmetry Multi‐arm DNA Tiles. Angew Chem Int Ed Engl 2016. [DOI: 10.1002/ange.201601944] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Affiliation(s)
- Fei Zhang
- School of Molecular Sciences and The Biodesign Institute Arizona State University Tempe AZ 85287 USA
| | - Shuoxing Jiang
- School of Molecular Sciences and The Biodesign Institute Arizona State University Tempe AZ 85287 USA
| | - Wei Li
- School of Molecular Sciences and The Biodesign Institute Arizona State University Tempe AZ 85287 USA
| | - Ashley Hunt
- School of Molecular Sciences and The Biodesign Institute Arizona State University Tempe AZ 85287 USA
| | - Yan Liu
- School of Molecular Sciences and The Biodesign Institute Arizona State University Tempe AZ 85287 USA
| | - Hao Yan
- School of Molecular Sciences and The Biodesign Institute Arizona State University Tempe AZ 85287 USA
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321
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Boyken SE, Chen Z, Groves B, Langan RA, Oberdorfer G, Ford A, Gilmore JM, Xu C, DiMaio F, Pereira JH, Sankaran B, Seelig G, Zwart PH, Baker D. De novo design of protein homo-oligomers with modular hydrogen-bond network-mediated specificity. Science 2016; 352:680-7. [PMID: 27151862 PMCID: PMC5497568 DOI: 10.1126/science.aad8865] [Citation(s) in RCA: 222] [Impact Index Per Article: 27.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2015] [Accepted: 03/23/2016] [Indexed: 12/26/2022]
Abstract
In nature, structural specificity in DNA and proteins is encoded differently: In DNA, specificity arises from modular hydrogen bonds in the core of the double helix, whereas in proteins, specificity arises largely from buried hydrophobic packing complemented by irregular peripheral polar interactions. Here, we describe a general approach for designing a wide range of protein homo-oligomers with specificity determined by modular arrays of central hydrogen-bond networks. We use the approach to design dimers, trimers, and tetramers consisting of two concentric rings of helices, including previously not seen triangular, square, and supercoiled topologies. X-ray crystallography confirms that the structures overall, and the hydrogen-bond networks in particular, are nearly identical to the design models, and the networks confer interaction specificity in vivo. The ability to design extensive hydrogen-bond networks with atomic accuracy enables the programming of protein interaction specificity for a broad range of synthetic biology applications; more generally, our results demonstrate that, even with the tremendous diversity observed in nature, there are fundamentally new modes of interaction to be discovered in proteins.
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Affiliation(s)
- Scott E Boyken
- Department of Biochemistry, University of Washington, Seattle, WA 98195, USA. Institute for Protein Design, University of Washington, Seattle, WA 98195, USA. Howard Hughes Medical Institute, University of Washington, Seattle, WA 98195, USA
| | - Zibo Chen
- Department of Biochemistry, University of Washington, Seattle, WA 98195, USA. Institute for Protein Design, University of Washington, Seattle, WA 98195, USA. Graduate Program in Biological Physics, Structure, and Design, University of Washington, Seattle, WA 98195, USA
| | - Benjamin Groves
- Department of Electrical Engineering, University of Washington, Seattle, WA 98195, USA
| | - Robert A Langan
- Department of Biochemistry, University of Washington, Seattle, WA 98195, USA. Institute for Protein Design, University of Washington, Seattle, WA 98195, USA
| | - Gustav Oberdorfer
- Department of Biochemistry, University of Washington, Seattle, WA 98195, USA. Institute for Protein Design, University of Washington, Seattle, WA 98195, USA. Department of Computer Science and Engineering, University of Washington, Seattle, WA 98195, USA
| | - Alex Ford
- Department of Biochemistry, University of Washington, Seattle, WA 98195, USA. Institute for Protein Design, University of Washington, Seattle, WA 98195, USA
| | - Jason M Gilmore
- Department of Biochemistry, University of Washington, Seattle, WA 98195, USA. Institute for Protein Design, University of Washington, Seattle, WA 98195, USA
| | - Chunfu Xu
- Department of Biochemistry, University of Washington, Seattle, WA 98195, USA. Institute for Protein Design, University of Washington, Seattle, WA 98195, USA
| | - Frank DiMaio
- Department of Biochemistry, University of Washington, Seattle, WA 98195, USA. Institute for Protein Design, University of Washington, Seattle, WA 98195, USA
| | - Jose Henrique Pereira
- Institute of Molecular Biosciences, University of Graz, Humboldtstrasse 50/3, 8010-Graz, Austria. Joint BioEnergy Institute, Emeryville, CA 94608, USA
| | - Banumathi Sankaran
- Physical Biosciences Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
| | - Georg Seelig
- Department of Electrical Engineering, University of Washington, Seattle, WA 98195, USA. Berkeley Center for Structural Biology, Molecular Biophysics and Integrated Bioimaging, Lawrence Berkeley Laboratory, 1 Cyclotron Road, Berkeley, CA 94720, USA
| | - Peter H Zwart
- Physical Biosciences Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA. The Center for Advanced Mathematics for Energy Research Applications, Lawrence Berkeley National Laboratories, 1 Cyclotron Road, Berkeley, CA 94720, USA
| | - David Baker
- Department of Biochemistry, University of Washington, Seattle, WA 98195, USA. Institute for Protein Design, University of Washington, Seattle, WA 98195, USA. Howard Hughes Medical Institute, University of Washington, Seattle, WA 98195, USA.
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322
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Programmable DNA Nanosystem for Molecular Interrogation. Sci Rep 2016; 6:27413. [PMID: 27270162 PMCID: PMC4895238 DOI: 10.1038/srep27413] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2015] [Accepted: 05/18/2016] [Indexed: 12/17/2022] Open
Abstract
We describe a self-assembling DNA-based nanosystem for interrogating molecular interactions. The nanosystem contains a rigid supporting dumbbell-shaped frame, a cylindrical central core, and a mobile ring that is coaxial with the core. Motion of the ring is influenced by several control elements whose force-generating capability is based on the transition of single-stranded DNA to double-stranded DNA. These forces can be directed to act in opposition to adhesive forces between the ring and the frame thereby providing a mechanism for molecular detection and interrogation at the ring-frame interface. As proof of principle we use this system to evaluate base stacking adhesion and demonstrate detection of a soluble nucleic acid viral genome mimic.
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323
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Chen N, Shi X, Wang Y. Molecularly Regulated Reversible DNA Polymerization. Angew Chem Int Ed Engl 2016; 55:6657-61. [PMID: 27100911 PMCID: PMC4884157 DOI: 10.1002/anie.201601008] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2016] [Revised: 04/03/2016] [Indexed: 12/13/2022]
Abstract
Natural polymers are synthesized and decomposed under physiological conditions. However, it is challenging to develop synthetic polymers whose formation and reversibility can be both controlled under physiological conditions. Here we show that both linear and branched DNA polymers can be synthesized via molecular hybridization in aqueous solutions, on the particle surface, and in the extracellular matrix (ECM) without the involvement of any harsh conditions. More importantly, these polymers can be effectively reversed to dissociate under the control of molecular triggers. Since nucleic acids can be conjugated with various molecules or materials, we anticipate that molecularly regulated reversible DNA polymerization holds potential for broad biological and biomedical applications.
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Affiliation(s)
- Niancao Chen
- Department of Biomedical Engineering, Pennsylvania State University, 202 Hallowell Building, University Park, PA, 16802, USA
| | - Xuechen Shi
- Department of Biomedical Engineering, Pennsylvania State University, 202 Hallowell Building, University Park, PA, 16802, USA
| | - Yong Wang
- Department of Biomedical Engineering, Pennsylvania State University, 232 Hallowell Building, University Park, PA, 16802, USA.
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324
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Gür FN, Schwarz FW, Ye J, Diez S, Schmidt TL. Toward Self-Assembled Plasmonic Devices: High-Yield Arrangement of Gold Nanoparticles on DNA Origami Templates. ACS NANO 2016; 10:5374-82. [PMID: 27159647 DOI: 10.1021/acsnano.6b01537] [Citation(s) in RCA: 90] [Impact Index Per Article: 11.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/17/2023]
Abstract
Plasmonic structures allow the manipulation of light with materials that are smaller than the optical wavelength. Such structures can consist of plasmonically active metal nanoparticles and can be fabricated through scalable bottom-up self-assembly on DNA origami templates. To produce functional devices, the precise and high-yield arrangement of each of the nanoparticles on a structure is of vital importance as the absence of a single particle can destroy the functionality of the entire device. Nevertheless, the parameters influencing the yield of the multistep assembly process are still poorly understood. To overcome this deficiency, we employed a test system consisting of a tubular six-helix bundle DNA origami with binding sites for eight oligonucleotide-functionalized gold nanoparticles. We systematically studied the assembly yield as a function of a wide range of parameters such as ionic strength, stoichiometric ratio, oligonucleotide linker chemistry, and assembly kinetics by an automated high-throughput analysis of electron micrographs of the formed heterocomplexes. Our optimized protocols enable particle placement yields up to 98.7% and promise the reliable production of sophisticated DNA-based multiparticle plasmonic devices for applications in photonics, optoelectronics, and nanomedicine.
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Affiliation(s)
- Fatih N Gür
- Center for Advancing Electronics Dresden (cfaed), Technische Universität Dresden , 01062 Dresden, Germany
| | - Friedrich W Schwarz
- Center for Advancing Electronics Dresden (cfaed), Technische Universität Dresden , 01062 Dresden, Germany
- B CUBE - Center for Molecular Bioengineering, Technische Universität Dresden , 01307 Dresden, Germany
| | - Jingjing Ye
- Center for Advancing Electronics Dresden (cfaed), Technische Universität Dresden , 01062 Dresden, Germany
| | - Stefan Diez
- Center for Advancing Electronics Dresden (cfaed), Technische Universität Dresden , 01062 Dresden, Germany
- B CUBE - Center for Molecular Bioengineering, Technische Universität Dresden , 01307 Dresden, Germany
- Max Planck Institute of Molecular Cell Biology and Genetics , 01307 Dresden, Germany
| | - Thorsten L Schmidt
- Center for Advancing Electronics Dresden (cfaed), Technische Universität Dresden , 01062 Dresden, Germany
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325
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Gliddon HD, Howes PD, Kaforou M, Levin M, Stevens MM. A nucleic acid strand displacement system for the multiplexed detection of tuberculosis-specific mRNA using quantum dots. NANOSCALE 2016; 8:10087-95. [PMID: 27088427 DOI: 10.1039/c6nr00484a] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/04/2023]
Abstract
The development of rapid, robust and high performance point-of-care diagnostics relies on the advancement and combination of various areas of research. We have developed an assay for the detection of multiple mRNA molecules that combines DNA nanotechnology with fluorescent nanomaterials. The core switching mechanism is toehold-mediated strand displacement. We have used fluorescent quantum dots (QDs) as signal transducers in this assay, as they bring many benefits including bright fluorescence and multiplexing abilities. The resulting assay is capable of multiplexed detection of long RNA targets against a high concentration of background non-target RNA, with high sensitivity and specificity and limits of detection in the nanomolar range using only a standard laboratory plate reader. We demonstrate the utility of our QD-based system for the detection of two genes selected from a microarray-derived tuberculosis-specific gene expression signature. Levels of up- and downregulated gene transcripts comprising this signature can be combined to give a disease risk score, making the signature more amenable for use as a diagnostic marker. Our QD-based approach to detect these transcripts could pave the way for novel diagnostic assays for tuberculosis.
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Affiliation(s)
- H D Gliddon
- Department of Materials, Department of Bioengineering, and Institute of Biomedical Engineering, Imperial College London, UK.
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326
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Ke G, Liu M, Jiang S, Qi X, Yang YR, Wootten S, Zhang F, Zhu Z, Liu Y, Yang CJ, Yan H. Directional Regulation of Enzyme Pathways through the Control of Substrate Channeling on a DNA Origami Scaffold. Angew Chem Int Ed Engl 2016. [DOI: 10.1002/ange.201603183] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Affiliation(s)
- Guoliang Ke
- Center for Molecular Design and Biomimetics Biodesign Institute School of Molecular Sciences at Arizona State University Tempe Arizona 85287 USA
- The MOE Key Laboratory of Spectrochemical Analysis and Instrumentation State Key Laboratory of Physical Chemistry of Solid Surfaces Collaborative Innovation Center of Chemistry for Energy Materials Department of Chemical Biology College of Chemistry and Chemical Engineering Xiamen University Xiamen 361005 China
| | - Minghui Liu
- Center for Molecular Design and Biomimetics Biodesign Institute School of Molecular Sciences at Arizona State University Tempe Arizona 85287 USA
| | - Shuoxing Jiang
- Center for Molecular Design and Biomimetics Biodesign Institute School of Molecular Sciences at Arizona State University Tempe Arizona 85287 USA
| | - Xiaodong Qi
- Center for Molecular Design and Biomimetics Biodesign Institute School of Molecular Sciences at Arizona State University Tempe Arizona 85287 USA
| | - Yuhe Renee Yang
- Center for Molecular Design and Biomimetics Biodesign Institute School of Molecular Sciences at Arizona State University Tempe Arizona 85287 USA
| | - Shaun Wootten
- Center for Molecular Design and Biomimetics Biodesign Institute School of Molecular Sciences at Arizona State University Tempe Arizona 85287 USA
| | - Fei Zhang
- Center for Molecular Design and Biomimetics Biodesign Institute School of Molecular Sciences at Arizona State University Tempe Arizona 85287 USA
| | - Zhi Zhu
- The MOE Key Laboratory of Spectrochemical Analysis and Instrumentation State Key Laboratory of Physical Chemistry of Solid Surfaces Collaborative Innovation Center of Chemistry for Energy Materials Department of Chemical Biology College of Chemistry and Chemical Engineering Xiamen University Xiamen 361005 China
| | - Yan Liu
- Center for Molecular Design and Biomimetics Biodesign Institute School of Molecular Sciences at Arizona State University Tempe Arizona 85287 USA
| | - Chaoyong James Yang
- The MOE Key Laboratory of Spectrochemical Analysis and Instrumentation State Key Laboratory of Physical Chemistry of Solid Surfaces Collaborative Innovation Center of Chemistry for Energy Materials Department of Chemical Biology College of Chemistry and Chemical Engineering Xiamen University Xiamen 361005 China
| | - Hao Yan
- Center for Molecular Design and Biomimetics Biodesign Institute School of Molecular Sciences at Arizona State University Tempe Arizona 85287 USA
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327
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Ke G, Liu M, Jiang S, Qi X, Yang YR, Wootten S, Zhang F, Zhu Z, Liu Y, Yang CJ, Yan H. Directional Regulation of Enzyme Pathways through the Control of Substrate Channeling on a DNA Origami Scaffold. Angew Chem Int Ed Engl 2016; 55:7483-6. [PMID: 27159899 DOI: 10.1002/anie.201603183] [Citation(s) in RCA: 96] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2016] [Indexed: 11/11/2022]
Abstract
Artificial multi-enzyme systems with precise and dynamic control over the enzyme pathway activity are of great significance in bionanotechnology and synthetic biology. Herein, we exploit a spatially addressable DNA nanoplatform for the directional regulation of two enzyme pathways (G6pDH-MDH and G6pDH-LDH) through the control of NAD(+) substrate channeling by specifically shifting NAD(+) between the two enzyme pairs. We believe that this concept will be useful for the design of regulatory biological circuits for synthetic biology and biomedicine.
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Affiliation(s)
- Guoliang Ke
- Center for Molecular Design and Biomimetics, Biodesign Institute, School of Molecular Sciences at, Arizona State University, Tempe, Arizona, 85287, USA.,The MOE Key Laboratory of Spectrochemical Analysis and Instrumentation, State Key Laboratory of Physical Chemistry of Solid Surfaces, Collaborative Innovation Center of Chemistry for Energy Materials, Department of Chemical Biology, College of Chemistry and Chemical Engineering, Xiamen University, Xiamen, 361005, China
| | - Minghui Liu
- Center for Molecular Design and Biomimetics, Biodesign Institute, School of Molecular Sciences at, Arizona State University, Tempe, Arizona, 85287, USA
| | - Shuoxing Jiang
- Center for Molecular Design and Biomimetics, Biodesign Institute, School of Molecular Sciences at, Arizona State University, Tempe, Arizona, 85287, USA
| | - Xiaodong Qi
- Center for Molecular Design and Biomimetics, Biodesign Institute, School of Molecular Sciences at, Arizona State University, Tempe, Arizona, 85287, USA
| | - Yuhe Renee Yang
- Center for Molecular Design and Biomimetics, Biodesign Institute, School of Molecular Sciences at, Arizona State University, Tempe, Arizona, 85287, USA
| | - Shaun Wootten
- Center for Molecular Design and Biomimetics, Biodesign Institute, School of Molecular Sciences at, Arizona State University, Tempe, Arizona, 85287, USA
| | - Fei Zhang
- Center for Molecular Design and Biomimetics, Biodesign Institute, School of Molecular Sciences at, Arizona State University, Tempe, Arizona, 85287, USA
| | - Zhi Zhu
- The MOE Key Laboratory of Spectrochemical Analysis and Instrumentation, State Key Laboratory of Physical Chemistry of Solid Surfaces, Collaborative Innovation Center of Chemistry for Energy Materials, Department of Chemical Biology, College of Chemistry and Chemical Engineering, Xiamen University, Xiamen, 361005, China
| | - Yan Liu
- Center for Molecular Design and Biomimetics, Biodesign Institute, School of Molecular Sciences at, Arizona State University, Tempe, Arizona, 85287, USA.
| | - Chaoyong James Yang
- The MOE Key Laboratory of Spectrochemical Analysis and Instrumentation, State Key Laboratory of Physical Chemistry of Solid Surfaces, Collaborative Innovation Center of Chemistry for Energy Materials, Department of Chemical Biology, College of Chemistry and Chemical Engineering, Xiamen University, Xiamen, 361005, China.
| | - Hao Yan
- Center for Molecular Design and Biomimetics, Biodesign Institute, School of Molecular Sciences at, Arizona State University, Tempe, Arizona, 85287, USA.
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328
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Fenniri H, Tikhomirov GA, Brouwer DH, Bouatra S, El Bakkari M, Yan Z, Cho JY, Yamazaki T. High Field Solid-State NMR Spectroscopy Investigation of 15N-Labeled Rosette Nanotubes: Hydrogen Bond Network and Channel-Bound Water. J Am Chem Soc 2016; 138:6115-8. [DOI: 10.1021/jacs.6b02420] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Affiliation(s)
- Hicham Fenniri
- 313 Snell
Engineering Center, Northeastern University, 360 Huntington Avenue, Boston, Massachusetts 02115, United States
| | | | - Darren H. Brouwer
- Department of Chemistry, Redeemer University College, 777 Garner Road East, Ancaster, Ontario L9K 1J4, Canada
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329
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Palomo JM, Filice M. Biosynthesis of Metal Nanoparticles: Novel Efficient Heterogeneous Nanocatalysts. NANOMATERIALS (BASEL, SWITZERLAND) 2016; 6:E84. [PMID: 28335213 PMCID: PMC5302502 DOI: 10.3390/nano6050084] [Citation(s) in RCA: 46] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/17/2016] [Revised: 04/19/2016] [Accepted: 04/26/2016] [Indexed: 02/06/2023]
Abstract
This review compiles the most recent advances described in literature on the preparation of noble metal nanoparticles induced by biological entities. The use of different free or substituted carbohydrates, peptides, proteins, microorganisms or plants have been successfully applied as a new green concept in the development of innovative strategies to prepare these nanoparticles as different nanostructures with different forms and sizes. As a second part of this review, the application of their synthetic ability as new heterogonous catalysts has been described in C-C bond-forming reactions (as Suzuki, Heck, cycloaddition or multicomponent), oxidations and dynamic kinetic resolutions.
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Affiliation(s)
- Jose M Palomo
- Departament of Biocatalysis, Institute of Catalysis (CSIC), Marie Curie 2, Cantoblanco, Campus UAM, 28049 Madrid, Spain.
| | - Marco Filice
- Advanced Imaging Unit, Spanish National Research Center for Cardiovascular Disease (CNIC), 28049 Madrid, Spain.
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330
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Samanta A, Medintz IL. Nanoparticles and DNA - a powerful and growing functional combination in bionanotechnology. NANOSCALE 2016; 8:9037-95. [PMID: 27080924 DOI: 10.1039/c5nr08465b] [Citation(s) in RCA: 131] [Impact Index Per Article: 16.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/21/2023]
Abstract
Functionally integrating DNA and other nucleic acids with nanoparticles in all their different physicochemical forms has produced a rich variety of composite nanomaterials which, in many cases, display unique or augmented properties due to the synergistic activity of both components. These capabilities, in turn, are attracting greater attention from various research communities in search of new nanoscale tools for diverse applications that include (bio)sensing, labeling, targeted imaging, cellular delivery, diagnostics, therapeutics, theranostics, bioelectronics, and biocomputing to name just a few amongst many others. Here, we review this vibrant and growing research area from the perspective of the materials themselves and their unique capabilities. Inorganic nanocrystals such as quantum dots or those made from gold or other (noble) metals along with metal oxides and carbon allotropes are desired as participants in these hybrid materials since they can provide distinctive optical, physical, magnetic, and electrochemical properties. Beyond this, synthetic polymer-based and proteinaceous or viral nanoparticulate materials are also useful in the same role since they can provide a predefined and biocompatible cargo-carrying and targeting capability. The DNA component typically provides sequence-based addressability for probes along with, more recently, unique architectural properties that directly originate from the burgeoning structural DNA field. Additionally, DNA aptamers can also provide specific recognition capabilities against many diverse non-nucleic acid targets across a range of size scales from ions to full protein and cells. In addition to appending DNA to inorganic or polymeric nanoparticles, purely DNA-based nanoparticles have recently surfaced as an excellent assembly platform and have started finding application in areas like sensing, imaging and immunotherapy. We focus on selected and representative nanoparticle-DNA materials and highlight their myriad applications using examples from the literature. Overall, it is clear that this unique functional combination of nanomaterials has far more to offer than what we have seen to date and as new capabilities for each of these materials are developed, so, too, will new applications emerge.
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Affiliation(s)
- Anirban Samanta
- Center for Bio/Molecular Science and Engineering, Code 6900, U.S. Naval Research Laboratory, Washington, DC 20375, USA. and College of Science, George Mason University, Fairfax, Virginia 22030, USA
| | - Igor L Medintz
- Center for Bio/Molecular Science and Engineering, Code 6900, U.S. Naval Research Laboratory, Washington, DC 20375, USA.
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331
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De Stefano M, Vesterager Gothelf K. Dynamic Chemistry of Disulfide Terminated Oligonucleotides in Duplexes and Double-Crossover Tiles. Chembiochem 2016; 17:1122-6. [PMID: 26994867 DOI: 10.1002/cbic.201600076] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2016] [Indexed: 02/03/2023]
Abstract
Designed nanostructures formed by self-assembly of multiple DNA strands suffer from low stability at elevated temperature and under other denaturing conditions. Here, we propose a method for covalent coupling of DNA strands in such structures by the formation of disulfide bonds; this allows disassembly of the structure under reducing conditions. The dynamic chemistry of disulfides and thiols was applied to crosslink DNA strands with terminal disulfide modifications. The formation of disulfide-linked DNA duplexes consisting of three strands is demonstrated, as well as a more-complex DNA double-crossover tile. All the strands in the fully disulfide-linked structures are covalently and geometrically interlocked, and it is demonstrated that the structures are stable under heating and in the presence of denaturants. Such a reversible system can be exploited in applications where higher DNA stability is needed only temporarily, such as delivery of cargoes to cells by DNA nanostructures.
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Affiliation(s)
- Mattia De Stefano
- Danish National Research Foundation, Center for DNA Nanotechnology, Department of Chemistry and iNANO, Gustav Wieds Vej 14, 8000 Aarhus C, Denmark
| | - Kurt Vesterager Gothelf
- Danish National Research Foundation, Center for DNA Nanotechnology, Department of Chemistry and iNANO, Gustav Wieds Vej 14, 8000 Aarhus C, Denmark.
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332
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Affiliation(s)
- Niancao Chen
- Department of Biomedical Engineering Pennsylvania State University 202 Hallowell Building University Park PA 16802 USA
| | - Xuechen Shi
- Department of Biomedical Engineering Pennsylvania State University 202 Hallowell Building University Park PA 16802 USA
| | - Yong Wang
- Department of Biomedical Engineering Pennsylvania State University 232 Hallowell Building University Park PA 16802 USA
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333
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Yonamine Y, Cervantes-Salguero K, Minami K, Kawamata I, Nakanishi W, Hill JP, Murata S, Ariga K. Supramolecular 1-D polymerization of DNA origami through a dynamic process at the 2-dimensionally confined air-water interface. Phys Chem Chem Phys 2016; 18:12576-81. [PMID: 27091668 DOI: 10.1039/c6cp01586g] [Citation(s) in RCA: 66] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
In this study, a Langmuir-Blodgett (LB) system has been utilized for the regulation of polymerization of a DNA origami structure at the air-water interface as a two-dimensionally confined medium, which enables dynamic condensation of DNA origami units through variation of the film area at the macroscopic level (ca. 10-100 cm(2)). DNA origami sheets were conjugated with a cationic lipid (dioctadecyldimethylammonium bromide, 2C18N(+)) by electrostatic interaction and the corresponding LB-film was prepared. By applying dynamic pressure variation through compression-expansion processes, the lipid-modified DNA origami sheets underwent anisotropic polymerization forming a one-dimensionally assembled belt-shaped structure of a high aspect ratio although the thickness of the polymerized DNA origami was maintained at the unimolecular level. This approach opens up a new field of mechanical induction of the self-assembly of DNA origami structures.
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Affiliation(s)
- Yusuke Yonamine
- World Premier International (WPI) Research Centre for Materials Nanoarchitectonics (MANA), National Institute for Materials Science (NIMS) 1-1 Namiki, Tsukuba, Ibaraki 305-0044, Japan.
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334
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Alves C, Iacovelli F, Falconi M, Cardamone F, Morozzo Della Rocca B, de Oliveira CLP, Desideri A. A Simple and Fast Semiautomatic Procedure for the Atomistic Modeling of Complex DNA Polyhedra. J Chem Inf Model 2016; 56:941-9. [PMID: 27050675 DOI: 10.1021/acs.jcim.5b00586] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/11/2023]
Abstract
A semiautomatic procedure to build complex atomistic covalently linked DNA nanocages has been implemented in a user-friendly, free, and fast program. As a test set, seven different truncated DNA polyhedra, composed by B-DNA double helices connected through short single-stranded linkers, have been generated. The atomistic structures, including a tetrahedron, a cube, an octahedron, a dodecahedron, a triangular prism, a pentagonal prism, and a hexagonal prism, have been probed through classical molecular dynamics and analyzed to evaluate their structural and dynamical properties and to highlight possible building faults. The analysis of the simulated trajectories also allows us to investigate the role of the different geometries in defining nanocages stability and flexibility. The data indicate that the cages are stable and that their structural and dynamical parameters measured along the trajectories are slightly affected by the different geometries. These results demonstrate that the constraints imposed by the covalent links induce an almost identical conformational variability independently of the three-dimensional geometry and that the program presented here is a reliable and valid tool to engineer DNA nanostructures.
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Affiliation(s)
- Cassio Alves
- Instituto de Fisica, Grupo de Fluidos Complexos, Universidade de São Paulo , Caixa Postal 66318, 05314-970 Sao Paulo, Brazil.,Department of Engineering and Sciences, Federal University of Paraná , 85950-000 Palotina, Paraná, Brazil
| | - Federico Iacovelli
- Department of Biology, University of Rome "Tor Vergata" , Via della Ricerca Scientifica, 00133 Rome, Italy
| | - Mattia Falconi
- Department of Biology, University of Rome "Tor Vergata" , Via della Ricerca Scientifica, 00133 Rome, Italy
| | - Francesca Cardamone
- Department of Biology, University of Rome "Tor Vergata" , Via della Ricerca Scientifica, 00133 Rome, Italy
| | - Blasco Morozzo Della Rocca
- Department of Biology, University of Rome "Tor Vergata" , Via della Ricerca Scientifica, 00133 Rome, Italy
| | - Cristiano L P de Oliveira
- Instituto de Fisica, Grupo de Fluidos Complexos, Universidade de São Paulo , Caixa Postal 66318, 05314-970 Sao Paulo, Brazil
| | - Alessandro Desideri
- Department of Biology, University of Rome "Tor Vergata" , Via della Ricerca Scientifica, 00133 Rome, Italy
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335
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Kohman RE, Cha SS, Man HY, Han X. Light-Triggered Release of Bioactive Molecules from DNA Nanostructures. NANO LETTERS 2016; 16:2781-5. [PMID: 26935839 PMCID: PMC4959465 DOI: 10.1021/acs.nanolett.6b00530] [Citation(s) in RCA: 71] [Impact Index Per Article: 8.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/19/2023]
Abstract
Recent innovations in DNA nanofabrication allow the creation of intricately shaped nanostructures ideally suited for many biological applications. To advance the use of DNA nanotechnology for the controlled release of bioactive molecules, we report a general strategy that uses light to liberate encapsulated cargoes from DNA nanostructures with high spatiotemporal precision. Through the incorporation of a custom, photolabile cross-linker, we encapsulated cargoes ranging in size from small molecules to full-sized proteins within DNA nanocages and then released such cargoes upon brief exposure to light. This novel molecular uncaging technique offers a general approach for precisely releasing a large variety of bioactive molecules, allowing investigation into their mechanism of action, or finely tuned delivery with high temporal precision for broad biomedical and materials applications.
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Affiliation(s)
- Richie E Kohman
- Biomedical Engineering Department, Boston University , Boston, Massachusetts 02215, United States
| | - Susie S Cha
- Biomedical Engineering Department, Boston University , Boston, Massachusetts 02215, United States
| | - Heng-Ye Man
- Biology Department, Boston University , Boston, Massachusetts 02215, United States
| | - Xue Han
- Biomedical Engineering Department, Boston University , Boston, Massachusetts 02215, United States
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336
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Valero J, Lohmann F, Keppner D, Famulok M. Single-Stranded Tile Stoppers for Interlocked DNA Architectures. Chembiochem 2016; 17:1146-9. [DOI: 10.1002/cbic.201500685] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2015] [Indexed: 12/22/2022]
Affiliation(s)
- Julián Valero
- Life and Medical Science (LIMES) Institute; Chemical Biology & Medicinal Chemistry Unit; University of Bonn; Gerhard-Domagk Strasse 1 53121 Bonn Germany
| | - Finn Lohmann
- Life and Medical Science (LIMES) Institute; Chemical Biology & Medicinal Chemistry Unit; University of Bonn; Gerhard-Domagk Strasse 1 53121 Bonn Germany
| | - Daniel Keppner
- Life and Medical Science (LIMES) Institute; Chemical Biology & Medicinal Chemistry Unit; University of Bonn; Gerhard-Domagk Strasse 1 53121 Bonn Germany
| | - Michael Famulok
- Life and Medical Science (LIMES) Institute; Chemical Biology & Medicinal Chemistry Unit; University of Bonn; Gerhard-Domagk Strasse 1 53121 Bonn Germany
- Center of Advanced European Studies and Research (CAESAR); Ludwig-Erhard-Allee 2 53175 Bonn Germany
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337
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Abstract
Nanomanufacturing, the commercially scalable and economically sustainable mass production of nanoscale materials and devices, represents the tangible outcome of the nanotechnology revolution. In contrast to those used in nanofabrication for research purposes, nanomanufacturing processes must satisfy the additional constraints of cost, throughput, and time to market. Taking silicon integrated circuit manufacturing as a baseline, we consider the factors involved in matching processes with products, examining the characteristics and potential of top-down and bottom-up processes, and their combination. We also discuss how a careful assessment of the way in which function can be made to follow form can enable high-volume manufacturing of nanoscale structures with the desired useful, and exciting, properties.
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Affiliation(s)
- J. Alexander Liddle
- Center for Nanoscale Science and Technology, National Institute of Standards and Technology, 100 Bureau Drive, Gaithersburg, MD 20899
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338
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Kumar V, Palazzolo S, Bayda S, Corona G, Toffoli G, Rizzolio F. DNA Nanotechnology for Cancer Therapy. Am J Cancer Res 2016; 6:710-25. [PMID: 27022418 PMCID: PMC4805665 DOI: 10.7150/thno.14203] [Citation(s) in RCA: 94] [Impact Index Per Article: 11.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2015] [Accepted: 01/27/2016] [Indexed: 02/07/2023] Open
Abstract
DNA nanotechnology is an emerging and exciting field, and represents a forefront frontier for the biomedical field. The specificity of the interactions between complementary base pairs makes DNA an incredible building material for programmable and very versatile two- and three-dimensional nanostructures called DNA origami. Here, we analyze the DNA origami and DNA-based nanostructures as a drug delivery system. Besides their physical-chemical nature, we dissect the critical factors such as stability, loading capability, release and immunocompatibility, which mainly limit in vivo applications. Special attention was dedicated to highlighting the boundaries to be overcome to bring DNA nanostructures closer to the bedside of patients.
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339
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Takezawa Y, Yoneda S, Duprey JLHA, Nakama T, Shionoya M. Metal-responsive structural transformation between artificial DNA duplexes and three-way junctions. Chem Sci 2016; 7:3006-3010. [PMID: 29997789 PMCID: PMC6004775 DOI: 10.1039/c6sc00383d] [Citation(s) in RCA: 53] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2016] [Accepted: 02/15/2016] [Indexed: 12/15/2022] Open
Abstract
Metal-responsive structural transformation between DNA duplexes and three-way junction structures was demonstrated utilizing artificial oligonucleotides modified with a 2,2’-bipyridine ligand.
DNA three-way junctions (3WJs) are essential structural motifs for DNA nanoarchitectures and DNA-based materials. We report herein a metal-responsive structural transformation between DNA duplexes and 3WJs using artificial oligonucleotides modified with a 2,2′-bipyridine (bpy) ligand. A mixture of bpy-modified DNA strands and natural complementary strands were self-assembled exclusively into duplexes without any transition metal ions, while they formed 3WJs in the presence of NiII ions. This transformation was induced by the formation of an interstrand NiII(bpy)3 complex, which served as a template for the 3WJ assembly. Altering the amount and identity of the metal ion regulated the 3WJ induction efficiency. Removal of the metal using EDTA quantitatively regenerated the duplexes. The metal-dependent structural conversion shown here has many potential applications in the development of stimuli-responsive DNA materials.
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Affiliation(s)
- Yusuke Takezawa
- Department of Chemistry , Graduate School of Science , The University of Tokyo , 7-3-1 Hongo , Bunkyo-ku , Tokyo 113-0033 , Japan .
| | - Shuhei Yoneda
- Department of Chemistry , Graduate School of Science , The University of Tokyo , 7-3-1 Hongo , Bunkyo-ku , Tokyo 113-0033 , Japan .
| | - Jean-Louis H A Duprey
- Department of Chemistry , Graduate School of Science , The University of Tokyo , 7-3-1 Hongo , Bunkyo-ku , Tokyo 113-0033 , Japan .
| | - Takahiro Nakama
- Department of Chemistry , Graduate School of Science , The University of Tokyo , 7-3-1 Hongo , Bunkyo-ku , Tokyo 113-0033 , Japan .
| | - Mitsuhiko Shionoya
- Department of Chemistry , Graduate School of Science , The University of Tokyo , 7-3-1 Hongo , Bunkyo-ku , Tokyo 113-0033 , Japan .
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340
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Linko V, Eerikäinen M, Kostiainen MA. A modular DNA origami-based enzyme cascade nanoreactor. Chem Commun (Camb) 2016; 51:5351-4. [PMID: 25594847 DOI: 10.1039/c4cc08472a] [Citation(s) in RCA: 147] [Impact Index Per Article: 18.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
In this communication, we present a nanoscale reactor assembled from tuneable and spatially addressable tubular DNA origami units. We can controllably combine separate origami units equipped with glucose oxidase (GOx) and horseradish peroxidase (HRP), and demonstrate efficient GOx/HRP enzyme cascade reaction inside the tube. The reactor could be utilized as a nanoscale diagnostic tool, and modularity of the proposed system would further enable more complex reactions.
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Affiliation(s)
- Veikko Linko
- Biohybrid Materials, Department of Biotechnology and Chemical Technology, Aalto University, FI-00076 Aalto, Finland.
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341
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Zhang D, Paukstelis PJ. Enhancing DNA Crystal Durability through Chemical Crosslinking. Chembiochem 2016; 17:1163-70. [DOI: 10.1002/cbic.201500610] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2015] [Indexed: 11/09/2022]
Affiliation(s)
- Diana Zhang
- Department of Chemistry & Biochemistry; University of Maryland; 8314 Paint Branch Drive College Park 20742 MD USA
| | - Paul J. Paukstelis
- Department of Chemistry & Biochemistry; University of Maryland; 8314 Paint Branch Drive College Park 20742 MD USA
- Maryland NanoCenter; University of Maryland; College Park 20742 MD USA
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342
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Li Y, Cheng Y, Xu L, Du H, Zhang P, Wen Y, Zhang X. A Nanostructured SERS Switch Based on Molecular Beacon-Controlled Assembly of Gold Nanoparticles. NANOMATERIALS 2016; 6:nano6020024. [PMID: 28344281 PMCID: PMC5302489 DOI: 10.3390/nano6020024] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/15/2015] [Revised: 01/04/2016] [Accepted: 01/05/2016] [Indexed: 12/12/2022]
Abstract
In this paper, highly purified and stable gold nanoparticle (AuNP) dimers connected at the two ends of DNA linkage were prepared by a versatile method. A nanostructured, surface-enhanced Raman scattering (SERS) switching sensor system was fabricated based on the controlled organization of gold nanoparticles (AuNPs) by a DNA nanomachine through the controlled formation/deformation of SERS “hotspots”. This strategy not only opens opportunities in the precise engineering of gap distances in gold-gold nanostructures in a highly controllable and reproducible fashion, but also provides a unique ability to research the origin of SERS and sequence-specific DNA detection.
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Affiliation(s)
- Yansheng Li
- Department of Chemistry and Biological Engineering, University of Science and Technology, Beijing 100083, China.
| | - Yaya Cheng
- Department of Chemistry and Biological Engineering, University of Science and Technology, Beijing 100083, China.
| | - Liping Xu
- Department of Chemistry and Biological Engineering, University of Science and Technology, Beijing 100083, China.
| | - Hongwu Du
- Department of Chemistry and Biological Engineering, University of Science and Technology, Beijing 100083, China.
| | - Peixun Zhang
- Peking University People's Hospital, Beijing 100083, China.
| | - Yongqiang Wen
- Department of Chemistry and Biological Engineering, University of Science and Technology, Beijing 100083, China.
| | - Xueji Zhang
- Department of Chemistry and Biological Engineering, University of Science and Technology, Beijing 100083, China.
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343
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Wang L, Sun Y, Li Z, Wu A, Wei G. Bottom-Up Synthesis and Sensor Applications of Biomimetic Nanostructures. MATERIALS (BASEL, SWITZERLAND) 2016; 9:E53. [PMID: 28787853 PMCID: PMC5456561 DOI: 10.3390/ma9010053] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 11/25/2015] [Revised: 01/05/2016] [Accepted: 01/07/2016] [Indexed: 12/21/2022]
Abstract
The combination of nanotechnology, biology, and bioengineering greatly improved the developments of nanomaterials with unique functions and properties. Biomolecules as the nanoscale building blocks play very important roles for the final formation of functional nanostructures. Many kinds of novel nanostructures have been created by using the bioinspired self-assembly and subsequent binding with various nanoparticles. In this review, we summarized the studies on the fabrications and sensor applications of biomimetic nanostructures. The strategies for creating different bottom-up nanostructures by using biomolecules like DNA, protein, peptide, and virus, as well as microorganisms like bacteria and plant leaf are introduced. In addition, the potential applications of the synthesized biomimetic nanostructures for colorimetry, fluorescence, surface plasmon resonance, surface-enhanced Raman scattering, electrical resistance, electrochemistry, and quartz crystal microbalance sensors are presented. This review will promote the understanding of relationships between biomolecules/microorganisms and functional nanomaterials in one way, and in another way it will guide the design and synthesis of biomimetic nanomaterials with unique properties in the future.
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Affiliation(s)
- Li Wang
- College of Chemistry, Jilin Normal University, Haifeng Street 1301, Siping 136000, China.
| | - Yujing Sun
- State Key Laboratory of Electroanalytical Chemistry, Changchun Institute of Applied Chemistry, Chinese Academy of Sciences, Renmin Street 5625, Changchun 130022, China.
| | - Zhuang Li
- State Key Laboratory of Electroanalytical Chemistry, Changchun Institute of Applied Chemistry, Chinese Academy of Sciences, Renmin Street 5625, Changchun 130022, China.
| | - Aiguo Wu
- Key Laboratory of Magnetic Materials and Devices & Division of Functional Materials and Nanodevices, Ningbo Institute of Material Technology and Engineering, Chinese Academy Sciences, Ningbo 315201, China.
| | - Gang Wei
- Faculty of Production Engineering, University of Bremen, Am Fallturm 1, D-28359 Bremen, Germany.
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344
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Cai Y, Guo Z, Chen J, Li W, Zhong L, Gao Y, Jiang L, Chi L, Tian H, Zhu WH. Enabling Light Work in Helical Self-Assembly for Dynamic Amplification of Chirality with Photoreversibility. J Am Chem Soc 2016; 138:2219-24. [PMID: 26709946 DOI: 10.1021/jacs.5b11580] [Citation(s) in RCA: 104] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
Light-driven transcription and replication are always subordinate to a delicate chirality transfer. Enabling light work in construction of the helical self-assembly with reversible chiral transformation becomes attractive. Herein we demonstrate that a helical hydrogen-bonded self-assembly is reversibly photoswitched between photochromic open and closed forms upon irradiation with alternative UV and visible light, in which molecular chirality is amplified with the formation of helixes at supramolecular level. The characteristics in these superhelixes such as left-handed or right-handed twist and helical length, height, and pitch are revealed by SEM and AFM. The helical photoswitchable nanostructure provides an easily accessible route to an unprecedented photoreversible modulation in morphology, fluorescence, and helicity, with precise assembly/disassembly architectures similar to biological systems such as protein and DNA.
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Affiliation(s)
- Yunsong Cai
- Key Laboratory for Advanced Materials and Institute of Fine Chemicals, Shanghai Key Laboratory of Functional Materials Chemistry, East China University of Science and Technology , Shanghai 200237, P. R. China
| | - Zhiqian Guo
- Key Laboratory for Advanced Materials and Institute of Fine Chemicals, Shanghai Key Laboratory of Functional Materials Chemistry, East China University of Science and Technology , Shanghai 200237, P. R. China
| | - Jianmei Chen
- Institute of Functional Nano & Soft Materials (FUNSOM), Soochow University , Suzhou 215123, P. R. China
| | - Wenlong Li
- Key Laboratory for Advanced Materials and Institute of Fine Chemicals, Shanghai Key Laboratory of Functional Materials Chemistry, East China University of Science and Technology , Shanghai 200237, P. R. China
| | - Liubiao Zhong
- Institute of Functional Nano & Soft Materials (FUNSOM), Soochow University , Suzhou 215123, P. R. China
| | - Ya Gao
- College of Fundamental Studies, Shanghai University of Engineering Science , Shanghai 201620, P. R. China
| | - Lin Jiang
- Institute of Functional Nano & Soft Materials (FUNSOM), Soochow University , Suzhou 215123, P. R. China
| | - Lifeng Chi
- Institute of Functional Nano & Soft Materials (FUNSOM), Soochow University , Suzhou 215123, P. R. China.,Physikalisches Institut and Center for Nanotechnology (CeNTech), Universität Münster , Münster 48149, Germany
| | - He Tian
- Key Laboratory for Advanced Materials and Institute of Fine Chemicals, Shanghai Key Laboratory of Functional Materials Chemistry, East China University of Science and Technology , Shanghai 200237, P. R. China
| | - Wei-Hong Zhu
- Key Laboratory for Advanced Materials and Institute of Fine Chemicals, Shanghai Key Laboratory of Functional Materials Chemistry, East China University of Science and Technology , Shanghai 200237, P. R. China
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345
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Surin M. From nucleobase to DNA templates for precision supramolecular assemblies and synthetic polymers. Polym Chem 2016. [DOI: 10.1039/c6py00480f] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Abstract
In this minireview, we report on the recent advances of utilization of nucleobases and DNA as templates to achieve well-defined supramolecular polymers, synthetic polymers, and sequence-controlled polymers.
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Affiliation(s)
- Mathieu Surin
- Laboratory for Chemistry of Novel Materials
- Center for Innovation and Research in Materials and Polymers
- University of Mons – UMONS
- B-7000 Mons
- Belgium
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346
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Bi S, Ye J, Dong Y, Li H, Cao W. Target-triggered cascade recycling amplification for label-free detection of microRNA and molecular logic operations. Chem Commun (Camb) 2016; 52:402-5. [DOI: 10.1039/c5cc07046e] [Citation(s) in RCA: 33] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
A cascade recycling amplification (CRA) that implements cascade logic circuits with feedback amplification function is developed for label-free chemiluminescence detection of microRNA-122 with an ultrahigh sensitivity of 0.82 fM and excellent specificity, which is applied to construct a series of molecular-scale two-input logic gates by using microRNAs as inputs and CRA products as outputs.
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Affiliation(s)
- Sai Bi
- College of Chemical Science and Engineering
- Laboratory of Fiber Materials and Modern Textiles
- the Growing Base for State Key Laboratory
- Collaborative Innovation Center for Marine Biomass Fiber Materials and Textiles
- Shandong Sino-Japanese Center for Collaborative Research of Carbon Nanomaterials
| | - Jiayan Ye
- Key Laboratory of Sensor Analysis of Tumor Marker
- Ministry of Education
- College of Chemistry and Molecular Engineering
- Qingdao University of Science and Technology
- Qingdao 266042
| | - Ying Dong
- Key Laboratory of Sensor Analysis of Tumor Marker
- Ministry of Education
- College of Chemistry and Molecular Engineering
- Qingdao University of Science and Technology
- Qingdao 266042
| | - Haoting Li
- College of Chemical Science and Engineering
- Laboratory of Fiber Materials and Modern Textiles
- the Growing Base for State Key Laboratory
- Collaborative Innovation Center for Marine Biomass Fiber Materials and Textiles
- Shandong Sino-Japanese Center for Collaborative Research of Carbon Nanomaterials
| | - Wei Cao
- Key Laboratory of Sensor Analysis of Tumor Marker
- Ministry of Education
- College of Chemistry and Molecular Engineering
- Qingdao University of Science and Technology
- Qingdao 266042
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347
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Kim YN, Jung Y. Artificial supramolecular protein assemblies as functional high-order protein scaffolds. Org Biomol Chem 2016; 14:5352-6. [DOI: 10.1039/c6ob00116e] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/28/2023]
Abstract
Artificial supramolecular protein assemblies can serve as novel high-order scaffolds that can display various functional proteins with defined valencies and organization, offering unprecedented functional bio-architectures.
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Affiliation(s)
- Yu-na Kim
- Department of Chemistry
- Korea Advanced Institute of Science and Technology
- Daejeon 305-701
- Korea
| | - Yongwon Jung
- Department of Chemistry
- Korea Advanced Institute of Science and Technology
- Daejeon 305-701
- Korea
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348
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Henry SL, Withers JM, Singh I, Cooper JM, Clark AW, Burley GA, Cogdell RJ. DNA-directed spatial assembly of photosynthetic light-harvesting proteins. Org Biomol Chem 2016; 14:1359-62. [DOI: 10.1039/c5ob02351c] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
This manuscript describes the surface immobilization of a light-harvesting complex to prescribed locations directed by the sequence-selective recognition of duplex DNA.
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Affiliation(s)
- Sarah L. Henry
- Molecular Cell and Systems Biology
- College of Medical
- Veterinary and Life Sciences
- University of Glasgow
- Glasgow G12 8TA
| | - Jamie M. Withers
- Department of Pure and Applied Chemistry
- University of Strathclyde
- Glasgow G1 1XL
- UK
| | - Ishwar Singh
- Department of Pure and Applied Chemistry
- University of Strathclyde
- Glasgow G1 1XL
- UK
| | | | | | - Glenn A. Burley
- Department of Pure and Applied Chemistry
- University of Strathclyde
- Glasgow G1 1XL
- UK
| | - Richard J. Cogdell
- Molecular Cell and Systems Biology
- College of Medical
- Veterinary and Life Sciences
- University of Glasgow
- Glasgow G12 8TA
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349
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Panagiotidis C, Kath-Schorr S, von Kiedrowski G. Flexibility of C3h -Symmetrical Linkers in Tris-oligonucleotide-Based Tetrahedral Scaffolds. Chembiochem 2015; 17:254-9. [PMID: 26593127 DOI: 10.1002/cbic.201500436] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/27/2015] [Indexed: 01/04/2023]
Abstract
Flexibility of tris-oligonucleotides is determined by the length of their connecting hydrocarbon chains. Tris-oligonucleotides are branched DNA building blocks with three oligonucleotide arms attached to a C3h -symmetrical linker core at these chains. Four tris-oligonucleotides hybridise into a tetrahedral nanocage by sequence-determined self-assembly. The influence of methylene, ethylene and propylene chains was studied by synthesising sets of tris-oligonucleotides and analysing the relative stability of the hybridisation products against digestion by mung bean nuclease by using gel electrophoresis. Linkers with ethylene chains showed sufficient flexibility, whereas methylene-chain linkers were too rigid. Tris-oligonucleotides based on the latter still formed tetrahedral scaffolds in intermixing experiments with linkers of higher flexibility. Thus, a new generation of versatile isocyanurate-based linkers was established.
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Affiliation(s)
- Christos Panagiotidis
- Lehrstuhl für Organische Chemie I, Bioorganische Chemie, Ruhr-Universität Bochum, Universitätsstrasse 150, 44780, Bochum, Germany.
| | - Stephanie Kath-Schorr
- LIMES Institute, Chemical Biology and Medicinal Chemistry Unit, Universität Bonn, Gerhard-Domagk-Strasse 1, 53121, Bonn, Germany
| | - Günter von Kiedrowski
- Lehrstuhl für Organische Chemie I, Bioorganische Chemie, Ruhr-Universität Bochum, Universitätsstrasse 150, 44780, Bochum, Germany
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Affiliation(s)
- Stephen M. Oja
- Department of Chemistry, University of Washington, Seattle, Washington 98195-1700, United States
| | - Yunshan Fan
- Department of Chemistry, University of Washington, Seattle, Washington 98195-1700, United States
| | - Chadd M. Armstrong
- Department of Chemistry, University of Washington, Seattle, Washington 98195-1700, United States
| | - Peter Defnet
- Department of Chemistry, University of Washington, Seattle, Washington 98195-1700, United States
| | - Bo Zhang
- Department of Chemistry, University of Washington, Seattle, Washington 98195-1700, United States
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