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252
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Jiang S, Hong F, Hu H, Yan H, Liu Y. Understanding the Elementary Steps in DNA Tile-Based Self-Assembly. ACS NANO 2017; 11:9370-9381. [PMID: 28813590 DOI: 10.1021/acsnano.7b04845] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/07/2023]
Abstract
Although many models have been developed to guide the design and implementation of DNA tile-based self-assembly systems with increasing complexity, the fundamental assumptions of the models have not been thoroughly tested. To expand the quantitative understanding of DNA tile-based self-assembly and to test the fundamental assumptions of self-assembly models, we investigated DNA tile attachment to preformed "multi-tile" arrays in real time and obtained the thermodynamic and kinetic parameters of single tile attachment in various sticky end association scenarios. With more sticky ends, tile attachment becomes more thermostable with an approximately linear decrease in the free energy change (more negative). The total binding free energy of sticky ends is partially compromised by a sequence-independent energy penalty when tile attachment forms a constrained configuration: "loop". The minimal loop is a 2 × 2 tetramer (Loop4). The energy penalty of loops of 4, 6, and 8 tiles was analyzed with the independent loop model assuming no interloop tension, which is generalizable to arbitrary tile configurations. More sticky ends also contribute to a faster on-rate under isothermal conditions when nucleation is the rate-limiting step. Incorrect sticky end contributes to neither the thermostability nor the kinetics. The thermodynamic and kinetic parameters of DNA tile attachment elucidated here will contribute to the future improvement and optimization of tile assembly modeling, precise control of experimental conditions, and structural design for error-free self-assembly.
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Affiliation(s)
- Shuoxing Jiang
- Center for Molecular Design and Biomimetics at the Biodesign Institute, and School of Molecular Sciences, Arizona State University , Tempe, Arizona 85287, United States
| | - Fan Hong
- Center for Molecular Design and Biomimetics at the Biodesign Institute, and School of Molecular Sciences, Arizona State University , Tempe, Arizona 85287, United States
| | - Huiyu Hu
- Center for Molecular Design and Biomimetics at the Biodesign Institute, and School of Molecular Sciences, Arizona State University , Tempe, Arizona 85287, United States
| | - Hao Yan
- Center for Molecular Design and Biomimetics at the Biodesign Institute, and School of Molecular Sciences, Arizona State University , Tempe, Arizona 85287, United States
| | - Yan Liu
- Center for Molecular Design and Biomimetics at the Biodesign Institute, and School of Molecular Sciences, Arizona State University , Tempe, Arizona 85287, United States
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253
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Stewart JM, Subramanian HKK, Franco E. Self-assembly of multi-stranded RNA motifs into lattices and tubular structures. Nucleic Acids Res 2017; 45:5449-5457. [PMID: 28204562 PMCID: PMC5435959 DOI: 10.1093/nar/gkx063] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2016] [Accepted: 01/31/2017] [Indexed: 01/20/2023] Open
Abstract
Rational design of nucleic acid molecules yields self-assembling scaffolds with increasing complexity, size and functionality. It is an open question whether design methods tailored to build DNA nanostructures can be adapted to build RNA nanostructures with comparable features. Here we demonstrate the formation of RNA lattices and tubular assemblies from double crossover (DX) tiles, a canonical motif in DNA nanotechnology. Tubular structures can exceed 1 μm in length, suggesting that this DX motif can produce very robust lattices. Some of these tubes spontaneously form with left-handed chirality. We obtain assemblies by using two methods: a protocol where gel-extracted RNA strands are slowly annealed, and a one-pot transcription and anneal procedure. We identify the tile nick position as a structural requirement for lattice formation. Our results demonstrate that stable RNA structures can be obtained with design tools imported from DNA nanotechnology. These large assemblies could be potentially integrated with a variety of functional RNA motifs for drug or nanoparticle delivery, or for colocalization of cellular components.
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Affiliation(s)
- Jaimie Marie Stewart
- Department of Bioengineering, University of California, 900 University Avenue, Riverside, CA 92521, USA
| | - Hari K K Subramanian
- Department of Mechanical Engineering, University of California, 900 University Avenue, Riverside, CA 92521, USA
| | - Elisa Franco
- Department of Mechanical Engineering, University of California, 900 University Avenue, Riverside, CA 92521, USA
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254
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Wu D, Wang L, Li W, Xu X, Jiang W. DNA nanostructure-based drug delivery nanosystems in cancer therapy. Int J Pharm 2017; 533:169-178. [PMID: 28923770 DOI: 10.1016/j.ijpharm.2017.09.032] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2017] [Revised: 09/12/2017] [Accepted: 09/14/2017] [Indexed: 01/04/2023]
Abstract
DNA as a novel biomaterial can be used to fabricate different kinds of DNA nanostructures based on its principle of GC/AT complementary base pairing. Studies have shown that DNA nanostructure is a nice drug carrier to overcome big obstacles existing in cancer therapy such as systemic toxicity and unsatisfied drug efficacy. Thus, different types of DNA nanostructure-based drug delivery nanosystems have been designed in cancer therapy. To improve treating efficacy, they are also developed into more functional drug delivery nanosystems. In recent years, some important progresses have been made. The objective of this review is to make a retrospect and summary about these different kinds of DNA nanostructure-based drug delivery nanosystems and their latest progresses: (1) active targeting; (2) mutidrug co-delivery; (3) construction of stimuli-responsive/intelligent nanosystems.
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Affiliation(s)
- Dandan Wu
- Key Laboratory of Natural Products Chemical Biology, Ministry of Education, School of Pharmacy, Shandong University, Jinan, 250012, PR China
| | - Lei Wang
- Key Laboratory of Natural Products Chemical Biology, Ministry of Education, School of Pharmacy, Shandong University, Jinan, 250012, PR China
| | - Wei Li
- Key Laboratory of Natural Products Chemical Biology, Ministry of Education, School of Pharmacy, Shandong University, Jinan, 250012, PR China
| | - Xiaowen Xu
- School of Chemistry and Chemical Engineering, Shandong University, Jinan, 250100, PR China
| | - Wei Jiang
- Key Laboratory of Natural Products Chemical Biology, Ministry of Education, School of Pharmacy, Shandong University, Jinan, 250012, PR China; School of Chemistry and Chemical Engineering, Shandong University, Jinan, 250100, PR China.
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255
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Protein-driven RNA nanostructured devices that function in vitro and control mammalian cell fate. Nat Commun 2017; 8:540. [PMID: 28912471 PMCID: PMC5599586 DOI: 10.1038/s41467-017-00459-x] [Citation(s) in RCA: 35] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2017] [Accepted: 06/29/2017] [Indexed: 11/22/2022] Open
Abstract
Nucleic acid nanotechnology has great potential for future therapeutic applications. However, the construction of nanostructured devices that control cell fate by detecting and amplifying protein signals has remained a challenge. Here we design and build protein-driven RNA-nanostructured devices that actuate in vitro by RNA-binding-protein-inducible conformational change and regulate mammalian cell fate by RNA–protein interaction-mediated protein assembly. The conformation and function of the RNA nanostructures are dynamically controlled by RNA-binding protein signals. The protein-responsive RNA nanodevices are constructed inside cells using RNA-only delivery, which may provide a safe tool for building functional RNA–protein nanostructures. Moreover, the designed RNA scaffolds that control the assembly and oligomerization of apoptosis-regulatory proteins on a nanometre scale selectively kill target cells via specific RNA–protein interactions. These findings suggest that synthetic RNA nanodevices could function as molecular robots that detect signals and localize target proteins, induce RNA conformational changes, and programme mammalian cellular behaviour. Nucleic acid nanotechnology has great potential for future therapeutic applications. Here the authors build protein-driven RNA nanostructures that can function within mammalian cells and regulate the cell fate.
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256
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Peng R, Wang H, Lyu Y, Xu L, Liu H, Kuai H, Liu Q, Tan W. Facile Assembly/Disassembly of DNA Nanostructures Anchored on Cell-Mimicking Giant Vesicles. J Am Chem Soc 2017; 139:12410-12413. [PMID: 28841373 PMCID: PMC5877790 DOI: 10.1021/jacs.7b07485] [Citation(s) in RCA: 59] [Impact Index Per Article: 8.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
DNA nanostructures assembled on living cell membranes have become powerful research tools. Synthetic lipid membranes have been used as a membrane model to study the dynamic behavior of DNA nanostructures on fluid soft lipid bilayers, but without the inherent complexity of natural membranes. Herein, we report the assembly and disassembly of DNA nanoprisms on cell-mimicking micrometer-scale giant membrane vesicles derived from living mammalian cells. Three-dimensional DNA nanoprisms with a DNA arm and a cholesterol anchor were efficiently localized on the membrane surface. The assembly and disassembly of DNA nanoprisms were dynamically manipulated by DNA strand hybridization and toehold-mediated strand displacement. Furthermore, the heterogeneity of reversible assembly/disassembly of DNA nanoprisms was monitored by Förster resonance energy transfer. This study suggests the feasibility of DNA-mediated functional biomolecular assembly on cell membranes for biomimetics studies and delivery systems.
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Affiliation(s)
- Ruizi Peng
- Molecular Science and Biomedicine Laboratory, State Key Laboratory of Chemo/Bio-Sensing and Chemometrics, College of Chemistry and Chemical Engineering, College of Life Sciences, and Aptamer Engineering Center of Hunan Province, Hunan University, Changsha, Hunan 410082, China
| | - Huijing Wang
- Molecular Science and Biomedicine Laboratory, State Key Laboratory of Chemo/Bio-Sensing and Chemometrics, College of Chemistry and Chemical Engineering, College of Life Sciences, and Aptamer Engineering Center of Hunan Province, Hunan University, Changsha, Hunan 410082, China
| | - Yifan Lyu
- Molecular Science and Biomedicine Laboratory, State Key Laboratory of Chemo/Bio-Sensing and Chemometrics, College of Chemistry and Chemical Engineering, College of Life Sciences, and Aptamer Engineering Center of Hunan Province, Hunan University, Changsha, Hunan 410082, China
- Department of Chemistry and Department of Physiology and Functional Genomics, Center for Research at the Bio/Nano Interface, Health Cancer Center, UF Genetics Institute, McKnight Brain Institute, University of Florida, Gainesville, Florida 32611-7200, United States
| | - Liujun Xu
- Molecular Science and Biomedicine Laboratory, State Key Laboratory of Chemo/Bio-Sensing and Chemometrics, College of Chemistry and Chemical Engineering, College of Life Sciences, and Aptamer Engineering Center of Hunan Province, Hunan University, Changsha, Hunan 410082, China
| | - Hui Liu
- Molecular Science and Biomedicine Laboratory, State Key Laboratory of Chemo/Bio-Sensing and Chemometrics, College of Chemistry and Chemical Engineering, College of Life Sciences, and Aptamer Engineering Center of Hunan Province, Hunan University, Changsha, Hunan 410082, China
| | - Hailan Kuai
- Molecular Science and Biomedicine Laboratory, State Key Laboratory of Chemo/Bio-Sensing and Chemometrics, College of Chemistry and Chemical Engineering, College of Life Sciences, and Aptamer Engineering Center of Hunan Province, Hunan University, Changsha, Hunan 410082, China
| | - Qiaoling Liu
- Molecular Science and Biomedicine Laboratory, State Key Laboratory of Chemo/Bio-Sensing and Chemometrics, College of Chemistry and Chemical Engineering, College of Life Sciences, and Aptamer Engineering Center of Hunan Province, Hunan University, Changsha, Hunan 410082, China
| | - Weihong Tan
- Molecular Science and Biomedicine Laboratory, State Key Laboratory of Chemo/Bio-Sensing and Chemometrics, College of Chemistry and Chemical Engineering, College of Life Sciences, and Aptamer Engineering Center of Hunan Province, Hunan University, Changsha, Hunan 410082, China
- Department of Chemistry and Department of Physiology and Functional Genomics, Center for Research at the Bio/Nano Interface, Health Cancer Center, UF Genetics Institute, McKnight Brain Institute, University of Florida, Gainesville, Florida 32611-7200, United States
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257
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Stross A, Iadevaia G, Núñez-Villanueva D, Hunter CA. Sequence-Selective Formation of Synthetic H-Bonded Duplexes. J Am Chem Soc 2017; 139:12655-12663. [PMID: 28857551 PMCID: PMC5627343 DOI: 10.1021/jacs.7b06619] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2017] [Indexed: 11/30/2022]
Abstract
Oligomers equipped with a sequence of phenol and pyridine N-oxide groups form duplexes via H-bonding interactions between these recognition units. Reductive amination chemistry was used to synthesize all possible 3-mer sequences: AAA, AAD, ADA, DAA, ADD, DAD, DDA, and DDD. Pairwise interactions between the oligomers were investigated using NMR titration and dilution experiments in toluene. The measured association constants vary by 3 orders of magnitude (102 to 105 M-1). Antiparallel sequence-complementary oligomers generally form more stable complexes than mismatched duplexes. Mismatched duplexes that have an excess of H-bond donors are stabilized by the interaction of two phenol donors with one pyridine N-oxide acceptor. Oligomers that have a H-bond donor and acceptor on the ends of the chain can fold to form intramolecular H-bonds in the free state. The 1,3-folding equilibrium competes with duplex formation and lowers the stability of duplexes involving these sequences. As a result, some of the mismatch duplexes are more stable than some of the sequence-complementary duplexes. However, the most stable mismatch duplexes contain DDD and compete with the most stable sequence-complementary duplex, AAA·DDD, so in mixtures that contain all eight sequences, sequence-complementary duplexes dominate. Even higher fidelity sequence selectivity can be achieved if alternating donor-acceptor sequences are avoided.
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Affiliation(s)
- Alexander
E. Stross
- Department of Chemistry, University of Cambridge, Lensfield Road, Cambridge CB2 1EW, U.K.
| | - Giulia Iadevaia
- Department of Chemistry, University of Cambridge, Lensfield Road, Cambridge CB2 1EW, U.K.
| | - Diego Núñez-Villanueva
- Department of Chemistry, University of Cambridge, Lensfield Road, Cambridge CB2 1EW, U.K.
| | - Christopher A. Hunter
- Department of Chemistry, University of Cambridge, Lensfield Road, Cambridge CB2 1EW, U.K.
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258
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Zhang W, Tung CH. Sequence-Independent DNA Nanogel as a Potential Drug Carrier. Macromol Rapid Commun 2017; 38. [PMID: 28895266 DOI: 10.1002/marc.201700366] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2017] [Revised: 08/01/2017] [Indexed: 01/21/2023]
Abstract
DNA nanostructures largely rely on pairing DNA bases; thus, sequence designing is required. Here, this study demonstrates a sequence-independent strategy to fabricate DNA nanogel (NG) inspired by cisplatin, a chemotherapeutic drug that acts as a DNA crosslinker. A simple heating and cooling of the genomic DNA extracts and cisplatin produces DNA NG with a size controlled by the heating time. Furthermore, the drug-loaded NG is formulated by spontaneously mixing DNA segments, cisplatin, and doxorubicin. The in vitro cell studies demonstrate that the doxorubicin-loaded NG alters the drug distribution in cells while its cytotoxic potential is well-maintained. This chemotherapeutic-inspired method provides a facile one-pot and cost-effective strategy to fabricate size-controllable DNA NG that potentially acts as drug carrier.
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Affiliation(s)
- Weiqi Zhang
- Molecular Imaging Innovations Institute, Department of Radioloy, Weill Cornell Medicine, 413 East 69th Street Box 290, New York, NY, 10021, USA
| | - Ching-Hsuan Tung
- Molecular Imaging Innovations Institute, Department of Radioloy, Weill Cornell Medicine, 413 East 69th Street Box 290, New York, NY, 10021, USA
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259
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Hou C, Guan S, Wang R, Zhang W, Meng F, Zhao L, Xu J, Liu J. Supramolecular Protein Assemblies Based on DNA Templates. J Phys Chem Lett 2017; 8:3970-3979. [PMID: 28792224 DOI: 10.1021/acs.jpclett.7b01564] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/07/2023]
Abstract
DNA plays an important role in the process of protein assembly. DNA viruses such as the M13 virus are typical examples in which single DNA genomes behave as templates to induce the assembly of multiple major coat protein (PVIII) monomers. Thus, the design of protein assemblies based on DNA templates attracts much interest in the construction of supramolecular structures and materials. With the development of DNA nanotechnology, precise 1D and 3D protein nanostructures have been designed and constructed by using DNA templates through DNA-protein interactions, protein-ligand interactions, and protein-adapter interactions. These DNA-templated protein assemblies show great potential in catalysis, medicine, light-responsive systems, drug delivery, and signal transduction. Herein, we review the progress on DNA-based protein nanostructures that possess sophisticated nanometer-sized structures with programmable shapes and stimuli-responsive parameters, and we present their great potential in the design of biomaterials and biodevices in the future.
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Affiliation(s)
| | | | - Ruidi Wang
- Department of Chemistry, University of British Columbia , Vancouver, British Columbia V6T 1Z1, Canada
| | - Wei Zhang
- Zhuhai United Laboratories Co., Ltd. , Nation High & New Technology Industry Development Zone, Zhuhai 519040, China
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260
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Auvinen H, Zhang H, Nonappa, Kopilow A, Niemelä EH, Nummelin S, Correia A, Santos HA, Linko V, Kostiainen MA. Protein Coating of DNA Nanostructures for Enhanced Stability and Immunocompatibility. Adv Healthc Mater 2017; 6. [PMID: 28738444 DOI: 10.1002/adhm.201700692] [Citation(s) in RCA: 138] [Impact Index Per Article: 19.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2017] [Revised: 06/15/2017] [Indexed: 12/24/2022]
Abstract
Fully addressable DNA nanostructures, especially DNA origami, possess huge potential to serve as inherently biocompatible and versatile molecular platforms. However, their use as delivery vehicles in therapeutics is compromised by their low stability and poor transfection rates. This study shows that DNA origami can be coated by precisely defined one-to-one protein-dendron conjugates to tackle the aforementioned issues. The dendron part of the conjugate serves as a cationic binding domain that attaches to the negatively charged DNA origami surface via electrostatic interactions. The protein is attached to dendron through cysteine-maleimide bond, making the modular approach highly versatile. This work demonstrates the coating using two different proteins: bovine serum albumin (BSA) and class II hydrophobin (HFBI). The results reveal that BSA-coating significantly improves the origami stability against endonucleases (DNase I) and enhances the transfection into human embryonic kidney (HEK293) cells. Importantly, it is observed that BSA-coating attenuates the activation of immune response in mouse primary splenocytes. Serum albumin is the most abundant protein in the blood with a long circulation half-life and has already found clinically approved applications in drug delivery. It is therefore envisioned that the proposed system can open up further opportunities to tune the properties of DNA nanostructures in biological environment, and enable their use in various delivery applications.
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Affiliation(s)
- Henni Auvinen
- Department of Bioproducts and Biosystems Aalto University FI‐00076 Aalto Finland
| | - Hongbo Zhang
- Drug Research Program, Division of Pharmaceutical Chemistry and Technology Faculty of Pharmacy University of Helsinki FI‐00014 Helsinki Finland
- Department of Pharmaceutical Sciences Åbo Akademi University FI‐20520 Turku Finland
| | - Nonappa
- Molecular Materials, Department of Applied Physics Aalto University FI‐00076 Aalto Finland
| | - Alisa Kopilow
- Department of Bioproducts and Biosystems Aalto University FI‐00076 Aalto Finland
| | - Elina H. Niemelä
- Research Programs Unit, Faculty of Medicine University of Helsinki P.O. Box 63 FI‐00014 Helsinki Finland
| | - Sami Nummelin
- Department of Bioproducts and Biosystems Aalto University FI‐00076 Aalto Finland
| | - Alexandra Correia
- Drug Research Program, Division of Pharmaceutical Chemistry and Technology Faculty of Pharmacy University of Helsinki FI‐00014 Helsinki Finland
| | - Hélder A. Santos
- Drug Research Program, Division of Pharmaceutical Chemistry and Technology Faculty of Pharmacy University of Helsinki FI‐00014 Helsinki Finland
- Helsinki Institute of Life Science University of Helsinki Helsinki FI‐00014 Finland
| | - Veikko Linko
- Department of Bioproducts and Biosystems Aalto University FI‐00076 Aalto Finland
| | - Mauri A. Kostiainen
- Department of Bioproducts and Biosystems Aalto University FI‐00076 Aalto Finland
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261
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In vitro and in vivo behavior of DNA tetrahedrons as tumor-targeting nanocarriers for doxorubicin delivery. Colloids Surf B Biointerfaces 2017. [DOI: 10.1016/j.colsurfb.2017.06.014] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023]
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262
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Massey M, Medintz IL, Ancona MG, Algar WR. Time-Gated FRET and DNA-Based Photonic Molecular Logic Gates: AND, OR, NAND, and NOR. ACS Sens 2017; 2:1205-1214. [PMID: 28787151 DOI: 10.1021/acssensors.7b00355] [Citation(s) in RCA: 34] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Molecular logic devices (MLDs) constructed from DNA are promising for applications in bioanalysis, computing, and other applications requiring Boolean logic. These MLDs accept oligonucleotide inputs and generate fluorescence output through changes in structure. Although fluorescent dyes are most common in MLD designs, nontraditional luminescent materials with unique optical properties can potentially enhance MLD capabilities. In this context, luminescent lanthanide complexes (LLCs) have been largely overlooked. Here, we demonstrate a set of high-contrast DNA photonic logic gates based on toehold-mediated strand displacement and time-gated FRET. The gates include NAND, NOR, OR, and AND designs that accept two unlabeled target oligonucleotide sequences as inputs. Bright "true" output states utilize time-gated, FRET-sensitized emission from an Alexa Fluor 546 (A546) dye acceptor paired with a luminescent terbium cryptate (Tb) donor. Dark "false" output states are generated through either displacement of the A546, or through competitive and sequential quenching of the Tb or A546 by a dark quencher. Time-gated FRET and the long luminescence lifetime and spectrally narrow emission lines of the Tb donor enable 4-10-fold contrast between Boolean outputs, ≤10% signal variation for a common output, multicolor implementation of two logic gates in parallel, and effective performance in buffer and serum. These metrics exceed those reported for many other logic gate designs with only fluorescent dyes and with other non-LLC materials. Preliminary three-input AND and NAND gates are also demonstrated. The powerful combination of an LLC FRET donor with DNA-based logic gates is anticipated to have many future applications in bioanalysis.
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Affiliation(s)
- Melissa Massey
- Department
of Chemistry, University of British Columbia, 2036 Main Mall, Vancouver, British Columbia V6T 1Z1, Canada
| | | | | | - W. Russ Algar
- Department
of Chemistry, University of British Columbia, 2036 Main Mall, Vancouver, British Columbia V6T 1Z1, Canada
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263
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He MQ, Wang K, Wang WJ, Yu YL, Wang JH. Smart DNA Machine for Carcinoembryonic Antigen Detection by Exonuclease III-Assisted Target Recycling and DNA Walker Cascade Amplification. Anal Chem 2017; 89:9292-9298. [PMID: 28806060 DOI: 10.1021/acs.analchem.7b02073] [Citation(s) in RCA: 130] [Impact Index Per Article: 18.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Abstract
A synthetic DNA machine performs quasi-mechanical movements in response to external intervention, suggesting the promise of constructing sensitive and specific biosensors. Herein, a smart DNA walker biosensor for label-free detection of carcinoembryonic antigen (CEA) is developed for the first time by a novel cascade amplification strategy of exonuclease (Exo) III-assisted target recycling amplification (ERA) and DNA walker. ERA as the first stage of amplification generates the walker DNA, while the autonomous traveling of the walker DNA on the substrate-modified silica microspheres as the second stage of amplification produces an ultrasensitive fluorescent signal with the help of N-methylmesoporphyrin IX (NMM). The DNA machine as a biosensor could be applied for transducing and quantifying signals from isothermal molecular amplifications, avoiding the complicated reporter elements and thermal cycling. The present biosensor achieves a detection limit of 1.2 pg·mL-1 within a linear range of 10 pg·mL-1 to 100 ng·mL-1 for CEA, along with a favorable specificity. The practical applicability of the biosensor is demonstrated by the detection of CEA in human serum with satisfactory results; thus, it shows great potential in clinical diagnosis.
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Affiliation(s)
- Meng-Qi He
- Research Center for Analytical Sciences, Department of Chemistry, College of Sciences, Northeastern University , Box 332, Shenyang 110819, China
| | - Kun Wang
- Research Center for Analytical Sciences, Department of Chemistry, College of Sciences, Northeastern University , Box 332, Shenyang 110819, China
| | - Wen-Jing Wang
- Research Center for Analytical Sciences, Department of Chemistry, College of Sciences, Northeastern University , Box 332, Shenyang 110819, China
| | - Yong-Liang Yu
- Research Center for Analytical Sciences, Department of Chemistry, College of Sciences, Northeastern University , Box 332, Shenyang 110819, China
| | - Jian-Hua Wang
- Research Center for Analytical Sciences, Department of Chemistry, College of Sciences, Northeastern University , Box 332, Shenyang 110819, China
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264
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Schwenger A, Birchall N, Richert C. Solution-Phase Synthesis of Branched Oligonucleotides with up to 32 Nucleotides and the Reversible Formation of Materials. European J Org Chem 2017. [DOI: 10.1002/ejoc.201700686] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2023]
Affiliation(s)
- Alexander Schwenger
- Institut für Organische Chemie; Universität Stuttgart; 70569 Stuttgart Germany
| | - Nicholas Birchall
- Institut für Organische Chemie; Universität Stuttgart; 70569 Stuttgart Germany
| | - Clemens Richert
- Institut für Organische Chemie; Universität Stuttgart; 70569 Stuttgart Germany
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265
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Li M, Zuo H, Yu J, Zhao X, Mao C. One DNA strand homo-polymerizes into defined nanostructures. NANOSCALE 2017; 9:10601-10605. [PMID: 28726950 DOI: 10.1039/c7nr03640j] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/07/2023]
Abstract
We report a strategy for programmed DNA self-assembly that is favorable in terms of both thermodynamics and kinetics. In a previous study, it has been demonstrated that DNA self-assembly is primarily driven by thermodynamics and the assembly kinetics is not considered. To reach such stable states at equilibria, prolonged annealing duration is needed. In addition, there are cases where the desired structures could not compete with alternative structures. For example, a single-stranded DNA with a palindromic sequence quickly folds into a one-stranded hairpin instead of forming a two-stranded DNA duplex. Given that most of the DNA tiles are multi-stranded complexes, the kinetic trap represents a challenge to DNA self-assembly. To overcome this problem, we have developed a one-stranded motif that can intramolecularly and quickly fold from a single DNA strand and can be programmed to assemble into a range of nanostructures, including a one-dimensional (1D) ladder, a 1D chain, a two-dimensional (2D) array, and a three-dimensional (3D) triangular prism. All structures have been characterized by polyacrylamide gel electrophoresis (PAGE) and atomic force microscopy (AFM) imaging.
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Affiliation(s)
- Mo Li
- Department of Chemistry, Purdue University, West Lafayette, IN 47907, USA.
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266
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Zhou L, Morel M, Rudiuk S, Baigl D. Intramolecularly Protein-Crosslinked DNA Gels: New Biohybrid Nanomaterials with Controllable Size and Catalytic Activity. SMALL (WEINHEIM AN DER BERGSTRASSE, GERMANY) 2017; 13:1700706. [PMID: 28561941 DOI: 10.1002/smll.201700706] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/02/2017] [Revised: 04/11/2017] [Indexed: 06/07/2023]
Abstract
DNA micro- and nanogels-small-sized hydrogels made of a crosslinked DNA backbone-constitute new promising materials, but their functions have mainly been limited to those brought by DNA. Here a new way is described to prepare sub-micrometer-sized DNA gels of controllable crosslinking density that are able to embed novel functions, such as an enzymatic activity. It consists of using proteins, instead of traditional base-pairing assembly or covalent approaches, to form crosslinks inside individual DNA molecules, resulting in structures referred to as intramolecularly protein-crosslinked DNA gels (IPDGs). It is first shown that the addition of streptavidin to biotinylated T4DNA results in the successful formation of thermally stable IPDGs with a controllable crosslinking density, forming structures ranging from elongated to raspberry-shaped and pearl-necklace-like morphologies. Using reversible DNA condensation strategies, this paper shows that the gels can be reversibly actuated at a low crosslinking density, or further stabilized when they are highly crosslinked. Finally, by using streptavidin-protein conjugates, IPDGs with various enzymes are successfully functionalized. It is demonstrated that the enzymes keep their catalytic activity upon their incorporation into the gels, opening perspectives ranging from biotechnologies (e.g., enzyme manipulation) to nanomedicine (e.g., vectorization).
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Affiliation(s)
- Li Zhou
- PASTEUR, Department of Chemistry, École normale supérieure, UPMC Univ. Paris 06, CNRS, PSL Research University, 75005, Paris, France
- Sorbonne Universités, UPMC Univ. Paris 06, Ecole normale supérieure, CNRS, PASTEUR, 75005, Paris, France
| | - Mathieu Morel
- PASTEUR, Department of Chemistry, École normale supérieure, UPMC Univ. Paris 06, CNRS, PSL Research University, 75005, Paris, France
- Sorbonne Universités, UPMC Univ. Paris 06, Ecole normale supérieure, CNRS, PASTEUR, 75005, Paris, France
| | - Sergii Rudiuk
- PASTEUR, Department of Chemistry, École normale supérieure, UPMC Univ. Paris 06, CNRS, PSL Research University, 75005, Paris, France
- Sorbonne Universités, UPMC Univ. Paris 06, Ecole normale supérieure, CNRS, PASTEUR, 75005, Paris, France
| | - Damien Baigl
- PASTEUR, Department of Chemistry, École normale supérieure, UPMC Univ. Paris 06, CNRS, PSL Research University, 75005, Paris, France
- Sorbonne Universités, UPMC Univ. Paris 06, Ecole normale supérieure, CNRS, PASTEUR, 75005, Paris, France
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267
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Synthetic biology engineering of biofilms as nanomaterials factories. Biochem Soc Trans 2017; 45:585-597. [DOI: 10.1042/bst20160348] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2017] [Revised: 02/26/2017] [Accepted: 02/28/2017] [Indexed: 11/17/2022]
Abstract
Bottom-up fabrication of nanoscale materials has been a significant focus in materials science for expanding our technological frontiers. This assembly concept, however, is old news to biology — all living organisms fabricate themselves using bottom-up principles through a vast self-organizing system of incredibly complex biomolecules, a marvelous dynamic that we are still attempting to unravel. Can we use what we have gleaned from biology thus far to illuminate alternative strategies for designer nanomaterial manufacturing? In the present review article, new synthetic biology efforts toward using bacterial biofilms as platforms for the synthesis and secretion of programmable nanomaterials are described. Particular focus is given to self-assembling functional amyloids found in bacterial biofilms as re-engineerable modular nanomolecular components. Potential applications and existing challenges for this technology are also explored. This novel approach for repurposing biofilm systems will enable future technologies for using engineered living systems to grow artificial nanomaterials.
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268
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Zhu B, Wang L, Li J, Fan C. Precisely Tailored DNA Nanostructures and their Theranostic Applications. CHEM REC 2017; 17:1213-1230. [DOI: 10.1002/tcr.201700019] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2017] [Indexed: 01/06/2023]
Affiliation(s)
- Bing Zhu
- Division of Physical Biology & Bioimaging Center, Shanghai Synchrotron Radiation Facility, Shanghai Institute of Applied PhysicsChinese Academy of Sciences Shanghai 201800 China
- University of Chinese Academy of Sciences Beijing 10049 China
| | - Lihua Wang
- Division of Physical Biology & Bioimaging Center, Shanghai Synchrotron Radiation Facility, Shanghai Institute of Applied PhysicsChinese Academy of Sciences Shanghai 201800 China
| | - Jiang Li
- Division of Physical Biology & Bioimaging Center, Shanghai Synchrotron Radiation Facility, Shanghai Institute of Applied PhysicsChinese Academy of Sciences Shanghai 201800 China
| | - Chunhai Fan
- Division of Physical Biology & Bioimaging Center, Shanghai Synchrotron Radiation Facility, Shanghai Institute of Applied PhysicsChinese Academy of Sciences Shanghai 201800 China
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269
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Hong F, Zhang F, Liu Y, Yan H. DNA Origami: Scaffolds for Creating Higher Order Structures. Chem Rev 2017; 117:12584-12640. [DOI: 10.1021/acs.chemrev.6b00825] [Citation(s) in RCA: 645] [Impact Index Per Article: 92.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Affiliation(s)
- Fan Hong
- The Biodesign Institute and
School of Molecular Sciences, Arizona State University, Tempe, Arizona 85287, United States
| | - Fei Zhang
- The Biodesign Institute and
School of Molecular Sciences, Arizona State University, Tempe, Arizona 85287, United States
| | - Yan Liu
- The Biodesign Institute and
School of Molecular Sciences, Arizona State University, Tempe, Arizona 85287, United States
| | - Hao Yan
- The Biodesign Institute and
School of Molecular Sciences, Arizona State University, Tempe, Arizona 85287, United States
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270
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Li N, Wang M, Gao X, Yu Z, Pan W, Wang H, Tang B. A DNA Tetrahedron Nanoprobe with Controlled Distance of Dyes for Multiple Detection in Living Cells and in Vivo. Anal Chem 2017; 89:6670-6677. [DOI: 10.1021/acs.analchem.7b00889] [Citation(s) in RCA: 58] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Affiliation(s)
- Na Li
- College of Chemistry, Chemical
Engineering and Materials Science, Collaborative Innovation Center
of Functionalized Probes for Chemical Imaging in Universities of Shandong,
Key Laboratory of Molecular and Nano Probes, Ministry of Education,
Institute of Molecular and Nano Science, Shandong Normal University, Jinan 250014, P. R. China
| | - Meimei Wang
- College of Chemistry, Chemical
Engineering and Materials Science, Collaborative Innovation Center
of Functionalized Probes for Chemical Imaging in Universities of Shandong,
Key Laboratory of Molecular and Nano Probes, Ministry of Education,
Institute of Molecular and Nano Science, Shandong Normal University, Jinan 250014, P. R. China
| | - Xiaonan Gao
- College of Chemistry, Chemical
Engineering and Materials Science, Collaborative Innovation Center
of Functionalized Probes for Chemical Imaging in Universities of Shandong,
Key Laboratory of Molecular and Nano Probes, Ministry of Education,
Institute of Molecular and Nano Science, Shandong Normal University, Jinan 250014, P. R. China
| | - Zhengze Yu
- College of Chemistry, Chemical
Engineering and Materials Science, Collaborative Innovation Center
of Functionalized Probes for Chemical Imaging in Universities of Shandong,
Key Laboratory of Molecular and Nano Probes, Ministry of Education,
Institute of Molecular and Nano Science, Shandong Normal University, Jinan 250014, P. R. China
| | - Wei Pan
- College of Chemistry, Chemical
Engineering and Materials Science, Collaborative Innovation Center
of Functionalized Probes for Chemical Imaging in Universities of Shandong,
Key Laboratory of Molecular and Nano Probes, Ministry of Education,
Institute of Molecular and Nano Science, Shandong Normal University, Jinan 250014, P. R. China
| | - Hongyu Wang
- College of Chemistry, Chemical
Engineering and Materials Science, Collaborative Innovation Center
of Functionalized Probes for Chemical Imaging in Universities of Shandong,
Key Laboratory of Molecular and Nano Probes, Ministry of Education,
Institute of Molecular and Nano Science, Shandong Normal University, Jinan 250014, P. R. China
| | - Bo Tang
- College of Chemistry, Chemical
Engineering and Materials Science, Collaborative Innovation Center
of Functionalized Probes for Chemical Imaging in Universities of Shandong,
Key Laboratory of Molecular and Nano Probes, Ministry of Education,
Institute of Molecular and Nano Science, Shandong Normal University, Jinan 250014, P. R. China
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271
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Meng HM, Liu H, Kuai H, Peng R, Mo L, Zhang XB. Aptamer-integrated DNA nanostructures for biosensing, bioimaging and cancer therapy. Chem Soc Rev 2017; 45:2583-602. [PMID: 26954935 DOI: 10.1039/c5cs00645g] [Citation(s) in RCA: 414] [Impact Index Per Article: 59.1] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
The combination of nanostructures with biomolecules leading to the generation of functional nanosystems holds great promise for biotechnological and biomedical applications. As a naturally occurring biomacromolecule, DNA exhibits excellent biocompatibility and programmability. Also, scalable synthesis can be readily realized through automated instruments. Such unique properties, together with Watson-Crick base-pairing interactions, make DNA a particularly promising candidate to be used as a building block material for a wide variety of nanostructures. In the past few decades, various DNA nanostructures have been developed, including one-, two- and three-dimensional nanomaterials. Aptamers are single-stranded DNA or RNA molecules selected by Systematic Evolution of Ligands by Exponential Enrichment (SELEX), with specific recognition abilities to their targets. Therefore, integrating aptamers into DNA nanostructures results in powerful tools for biosensing and bioimaging applications. Furthermore, owing to their high loading capability, aptamer-modified DNA nanostructures have also been altered to play the role of drug nanocarriers for in vivo applications and targeted cancer therapy. In this review, we summarize recent progress in the design of aptamers and related DNA molecule-integrated DNA nanostructures as well as their applications in biosensing, bioimaging and cancer therapy. To begin with, we first introduce the SELEX technology. Subsequently, the methodologies for the preparation of aptamer-integrated DNA nanostructures are presented. Then, we highlight their applications in biosensing and bioimaging for various targets, as well as targeted cancer therapy applications. Finally, we discuss several challenges and further opportunities in this emerging field.
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Affiliation(s)
- Hong-Min Meng
- Molecular Science and Biomedicine Laboratory, State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Chemistry and Chemical Engineering, Collaborative Innovation Center for Molecular Engineering for Theranostics, Hunan University, Changsha, 410082, China. and Collaborative Innovation Center of Henan Province for Green Manufacturing of Fine Chemicals, Key Laboratory of Green Chemical Media and Reactions, Ministry of Education, School of Chemistry and Chemical Engineering, Henan Normal University, Xinxiang, Henan 453007, P. R. China
| | - Hui Liu
- Molecular Science and Biomedicine Laboratory, State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Chemistry and Chemical Engineering, Collaborative Innovation Center for Molecular Engineering for Theranostics, Hunan University, Changsha, 410082, China.
| | - Hailan Kuai
- Molecular Science and Biomedicine Laboratory, State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Chemistry and Chemical Engineering, Collaborative Innovation Center for Molecular Engineering for Theranostics, Hunan University, Changsha, 410082, China.
| | - Ruizi Peng
- Molecular Science and Biomedicine Laboratory, State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Chemistry and Chemical Engineering, Collaborative Innovation Center for Molecular Engineering for Theranostics, Hunan University, Changsha, 410082, China.
| | - Liuting Mo
- Molecular Science and Biomedicine Laboratory, State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Chemistry and Chemical Engineering, Collaborative Innovation Center for Molecular Engineering for Theranostics, Hunan University, Changsha, 410082, China.
| | - Xiao-Bing Zhang
- Molecular Science and Biomedicine Laboratory, State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Chemistry and Chemical Engineering, Collaborative Innovation Center for Molecular Engineering for Theranostics, Hunan University, Changsha, 410082, China.
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272
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Fozooni T, Ravan H, Sasan H. Signal Amplification Technologies for the Detection of Nucleic Acids: from Cell-Free Analysis to Live-Cell Imaging. Appl Biochem Biotechnol 2017; 183:1224-1253. [DOI: 10.1007/s12010-017-2494-4] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2017] [Accepted: 04/24/2017] [Indexed: 12/15/2022]
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273
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Ueki R, Atsuta S, Ueki A, Sando S. Nongenetic Reprogramming of the Ligand Specificity of Growth Factor Receptors by Bispecific DNA Aptamers. J Am Chem Soc 2017; 139:6554-6557. [PMID: 28459560 DOI: 10.1021/jacs.7b02411] [Citation(s) in RCA: 70] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/26/2023]
Abstract
The reprogramming of receptor-ligand interactions affords an opportunity to direct cells to respond to user-defined external cues. Although this has often been achieved via the genetic engineering of receptors, an alternative, nongenetic approach is highly demanded. In this article, we propose the design of oligonucleotide-based synthetic switches that feature the ability to reprogram the ligand specificity of the growth factor receptor. We demonstrated that our synthetic switches induced growth factor signaling via the formation of the dynamic complex with specific external cues that would otherwise not induce the signaling. This chemical approach may be applied to designing a new class of chemical tools that can control the activities of native cells and represent smart and safer regenerative drugs.
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Affiliation(s)
- Ryosuke Ueki
- Department of Chemistry and Biotechnology, Graduate School of Engineering, The University of Tokyo , 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-8656, Japan
| | - Saki Atsuta
- Department of Chemistry and Biotechnology, Graduate School of Engineering, The University of Tokyo , 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-8656, Japan
| | - Ayaka Ueki
- Department of Chemistry and Biotechnology, Graduate School of Engineering, The University of Tokyo , 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-8656, Japan
| | - Shinsuke Sando
- Department of Chemistry and Biotechnology, Graduate School of Engineering, The University of Tokyo , 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-8656, Japan
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274
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Affiliation(s)
- Masato Ikeda
- Department of Chemistry and Biomolecular Science, Faculty of Engineering, Gifu University, Gifu 501-1193
- United Graduate School of Drug Discovery and Medical Information Sciences, Gifu University, Gifu 501-1193
- Center for Highly Advanced Integration of Nano and Life Sciences, Gifu University (G-CHAIN), Gifu 501-1193
| | - Marina Kabumoto
- United Graduate School of Drug Discovery and Medical Information Sciences, Gifu University, Gifu 501-1193
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275
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Li Y, Mao C, Deng Z. Supramolecular Wireframe DNA Polyhedra: Assembly and Applications. CHINESE J CHEM 2017. [DOI: 10.1002/cjoc.201600789] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Affiliation(s)
- Yulin Li
- School of Chemistry and Chemical Engineering; Hefei University of Technology, 193 Tunxi Road; Hefei Anhui 230009 China
| | - Chengde Mao
- Department of Chemistry; Purdue University; West Lafayette Indiana 47907 USA
| | - Zhaoxiang Deng
- CAS Key Laboratory of Soft Matter Chemistry, School of Chemistry and Materials Science; University of Science and Technology of China; Hefei Anhui 230026 China
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276
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Qian Z, Ginger DS. Reversibly Reconfigurable Colloidal Plasmonic Nanomaterials. J Am Chem Soc 2017; 139:5266-5276. [DOI: 10.1021/jacs.7b00711] [Citation(s) in RCA: 62] [Impact Index Per Article: 8.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Affiliation(s)
- Zhaoxia Qian
- Department of Chemistry, University of Washington, Seattle, Washington 98105, United States
| | - David S. Ginger
- Department of Chemistry, University of Washington, Seattle, Washington 98105, United States
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277
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Huang D, Freeley M, Palma M. DNA-Mediated Patterning of Single Quantum Dot Nanoarrays: A Reusable Platform for Single-Molecule Control. Sci Rep 2017; 7:45591. [PMID: 28349982 PMCID: PMC5368656 DOI: 10.1038/srep45591] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2017] [Accepted: 02/28/2017] [Indexed: 12/29/2022] Open
Abstract
We present a facile strategy of general applicability for the assembly of individual nanoscale moieties in array configurations with single-molecule control. Combining the programming ability of DNA as a scaffolding material with a one-step lithographic process, we demonstrate the patterning of single quantum dots (QDs) at predefined locations on silicon and transparent glass surfaces: as proof of concept, clusters of either one, two, or three QDs were assembled in highly uniform arrays with a 60 nm interdot spacing within each cluster. Notably, the platform developed is reusable after a simple cleaning process and can be designed to exhibit different geometrical arrangements.
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Affiliation(s)
- Da Huang
- School of Biological and Chemical Sciences, Materials Research Institute, and Institute of Bioengineering, Queen Mary University of London, Mile End Road, London E1 4NS, UK
| | - Mark Freeley
- School of Biological and Chemical Sciences, Materials Research Institute, and Institute of Bioengineering, Queen Mary University of London, Mile End Road, London E1 4NS, UK
| | - Matteo Palma
- School of Biological and Chemical Sciences, Materials Research Institute, and Institute of Bioengineering, Queen Mary University of London, Mile End Road, London E1 4NS, UK
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278
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Song T, Wang X, Liang H. Engineering chemical reaction modules via programming the assembly of DNA hairpins. J Mater Chem B 2017; 5:2297-2301. [PMID: 32263620 DOI: 10.1039/c6tb03098j] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
The architect of enzyme-free chemical reaction modules, working as building blocks in implementing complex computing tasks, was achieved by modulating the assembly of DNA hairpins, including non-catalytic and catalytic systems. The performance of heterogeneous outputted sequences, which were programmed on different hairpins for triggering the downstream reaction, was asymmetric in the non-catalytic system, whereas symmetric in the catalytic system. Furthermore, complicated DNA-only chemical modules possessing controllable species of inputs or outputs were constructed based on our strategy. The kinetic studies revealed that the performance of the chemical modules was toehold length correlated; on the basis of which, a DNA concentration monitor was constructed.
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Affiliation(s)
- Tingjie Song
- CAS Key Laboratory of Soft Matter Chemistry, iChEM (Collaborative Innovation Center of Chemistry for Energy Materials), Department of Polymer Science and Engineering, University of Science and Technology of China, Hefei, Anhui 230026, P. R. China.
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279
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Brown CW, Buckhout-White S, Díaz SA, Melinger JS, Ancona MG, Goldman ER, Medintz IL. Evaluating Dye-Labeled DNA Dendrimers for Potential Applications in Molecular Biosensing. ACS Sens 2017; 2:401-410. [PMID: 28723206 DOI: 10.1021/acssensors.6b00778] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Abstract
DNA nanostructures provide a reliable and predictable scaffold for precisely positioning fluorescent dyes to form energy transfer cascades. Furthermore, these structures and their attendant dye networks can be dynamically manipulated by biochemical inputs, with the changes reflected in the spectral response. However, the complexity of DNA structures that have undergone such types of manipulation for direct biosensing applications is quite limited. Here, we investigate four different modification strategies to effect such dynamic manipulations using a DNA dendrimer scaffold as a testbed, and with applications to biosensing in mind. The dendrimer has a 2:1 branching ratio that organizes the dyes into a FRET-based antenna in which excitonic energy generated on multiple initial Cy3 dyes displayed at the periphery is then transferred inward through Cy3.5 and/or Cy5 relay dyes to a Cy5.5 final acceptor at the focus. Advantages of this design included good transfer efficiency, large spectral separation between the initial donor and final acceptor emissions for signal transduction, and an inherent tolerance to defects. Of the approaches to structural rearrangement, the first two mechanisms we consider employed either toehold-mediated strand displacement or strand replacement and their impact was mainly via direct transfer efficiency, while the other two were more global in their effect using either a belting mechanism or an 8-arm star nanostructure to compress the nanostructure and thereby modulate its spectral response through an enhancement in parallelism. The performance of these mechanisms, their ability to reset, and how they might be utilized in biosensing applications are discussed.
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Affiliation(s)
- Carl W. Brown
- College
of Science, George Mason University, Fairfax, Virginia 22030, United States
| | | | - Sebastián A. Díaz
- American Society for Engineering Education, Washington, DC 20036, United States
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280
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Shoji T, Kim S, Chiba K. Synthesis of Azanucleosides by Anodic Oxidation in a Lithium Perchlorate-Nitroalkane Medium and Diversification at the 4′-Nitrogen Position. Angew Chem Int Ed Engl 2017; 56:4011-4014. [DOI: 10.1002/anie.201700547] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2017] [Indexed: 12/17/2022]
Affiliation(s)
- Takao Shoji
- Department of Applied Biological Science; Tokyo University of Agriculture and Technology; 3-5-8 Saiwai-cho, Fuchu Tokyo 183-8509 Japan
| | - Shokaku Kim
- Department of Applied Biological Science; Tokyo University of Agriculture and Technology; 3-5-8 Saiwai-cho, Fuchu Tokyo 183-8509 Japan
| | - Kazuhiro Chiba
- Department of Applied Biological Science; Tokyo University of Agriculture and Technology; 3-5-8 Saiwai-cho, Fuchu Tokyo 183-8509 Japan
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281
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Shoji T, Kim S, Chiba K. Synthesis of Azanucleosides by Anodic Oxidation in a Lithium Perchlorate-Nitroalkane Medium and Diversification at the 4′-Nitrogen Position. Angew Chem Int Ed Engl 2017. [DOI: 10.1002/ange.201700547] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Affiliation(s)
- Takao Shoji
- Department of Applied Biological Science; Tokyo University of Agriculture and Technology; 3-5-8 Saiwai-cho, Fuchu Tokyo 183-8509 Japan
| | - Shokaku Kim
- Department of Applied Biological Science; Tokyo University of Agriculture and Technology; 3-5-8 Saiwai-cho, Fuchu Tokyo 183-8509 Japan
| | - Kazuhiro Chiba
- Department of Applied Biological Science; Tokyo University of Agriculture and Technology; 3-5-8 Saiwai-cho, Fuchu Tokyo 183-8509 Japan
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282
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A microRNA-initiated DNAzyme motor operating in living cells. Nat Commun 2017; 8:14378. [PMID: 28262725 PMCID: PMC5343503 DOI: 10.1038/ncomms14378] [Citation(s) in RCA: 378] [Impact Index Per Article: 54.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2016] [Accepted: 12/16/2016] [Indexed: 12/21/2022] Open
Abstract
Synthetic DNA motors have great potential to mimic natural protein motors in cells but the operation of synthetic DNA motors in living cells remains challenging and has not been demonstrated. Here we report a DNAzyme motor that operates in living cells in response to a specific intracellular target. The whole motor system is constructed on a 20 nm gold nanoparticle (AuNP) decorated with hundreds of substrate strands serving as DNA tracks and dozens of DNAzyme molecules each silenced by a locking strand. Intracellular interaction of a target molecule with the motor system initiates the autonomous walking of the motor on the AuNP. An example DNAzyme motor responsive to a specific microRNA enables amplified detection of the specific microRNA in individual cancer cells. Activated by specific intracellular targets, these self-powered DNAzyme motors will have diverse applications in the control and modulation of biological functions. Synthetic DNA nanomachines have been designed to perform a variety of tasks in vitro. Here, the authors build a nanomotor system that integrates a DNAzyme and DNA track on a gold nanoparticle, to facilitate cellular uptake, and apply it as a real-time miRNA imaging tool in living cells.
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283
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Dohno C, Makishi S, Nakatani K, Contera S. Amphiphilic DNA tiles for controlled insertion and 2D assembly on fluid lipid membranes: the effect on mechanical properties. NANOSCALE 2017; 9:3051-3058. [PMID: 28186523 DOI: 10.1039/c6nr07084a] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/06/2023]
Abstract
Future lipid membrane-associated DNA nanostructures are expected to find applications ranging from synthetic biology to nanomedicine. Here we have designed and synthesized DNA tiles and modified them with amphiphilic covalent moieties. dod-DEG groups, which consist of a hydrophilic diethylene glycol (DEG) and a hydrophobic dodecyl group, are introduced at the phosphate backbone to create amphiphilic DNA strands which are subsequently introduced into one face of the DNA tiles. In this way the tile becomes able to stably bind to lipid membranes by insertion of the hydrophobic groups inside the bilayer core. The functionalized tiles do not aggregate in solution. Our results show that these amphiphilic DNA tiles can bind and assemble into 2D lattices on both gel and fluid lipid bilayers. The binding of the DNA structures to membranes is dependent on the lipid phase of the membrane, the concentration of Mg2+ cations, the length of the amphiphilic modifications to the DNA as well as on the density of the modifications within the tile. Atomic force microscopy-based force spectroscopy is used to investigate the effect of the inserted DNA tiles on the mechanical properties of the lipid membranes. The results indicate that the insertion of DNA tiles produces an approx. 20% increase of the bilayer breakthrough force.
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Affiliation(s)
- Chikara Dohno
- Department of Regulatory Bioorganic Chemistry, The Institute of Scientific and Industrial Research (ISIR), Osaka University, Osaka, Ibaraki 567-0047, Japan. and PRESTO, Japan Science and Technology Agency, 4-1-8 Honcho Kawaguchi, Saitama 332-0012, Japan
| | - Shingo Makishi
- Department of Regulatory Bioorganic Chemistry, The Institute of Scientific and Industrial Research (ISIR), Osaka University, Osaka, Ibaraki 567-0047, Japan.
| | - Kazuhiko Nakatani
- Department of Regulatory Bioorganic Chemistry, The Institute of Scientific and Industrial Research (ISIR), Osaka University, Osaka, Ibaraki 567-0047, Japan.
| | - Sonia Contera
- Clarendon Laboratory, Physics Department, University of Oxford, Oxford, OX1 3PU, UK.
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284
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Abstract
Emerging protein design strategies are enabling the creation of diverse, self-assembling supramolecular structures with precision on the atomic scale. The design possibilities include various types of architectures: finite cages or shells, essentially unbounded two-dimensional and three-dimensional arrays (i.e., crystals), and linear or tubular filaments. In nature, structures of those types are generally symmetric, and, accordingly, symmetry provides a powerful guide for developing new design approaches. Recent design studies have produced numerous protein assemblies in close agreement with geometric specifications. For certain design approaches, a complete list of allowable symmetry combinations that can be used for construction has been articulated, opening a path to a rich diversity of geometrically defined protein materials. Future challenges include improving and elaborating on current strategies and endowing designed protein nanomaterials with properties useful in nanomedicine and material science applications.
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Affiliation(s)
- Todd O Yeates
- Department of Chemistry and Biochemistry, University of California, Los Angeles, California 90095.,UCLA-DOE Institute for Genomics and Proteomics, Los Angeles, California 90095;
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285
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Mathur D, Medintz IL. Analyzing DNA Nanotechnology: A Call to Arms For The Analytical Chemistry Community. Anal Chem 2017; 89:2646-2663. [DOI: 10.1021/acs.analchem.6b04033] [Citation(s) in RCA: 51] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
Affiliation(s)
- Divita Mathur
- College of Science, George Mason University, Fairfax, Virginia 22030, United States
- Center
for Bio/Molecular Science and Engineering, U.S. Naval Research Laboratory, Code 6900, Washington, D.C. 20375, United States
| | - Igor L. Medintz
- Center
for Bio/Molecular Science and Engineering, U.S. Naval Research Laboratory, Code 6900, Washington, D.C. 20375, United States
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286
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Haußmann A, Gemeinhardt A, Schröder M, Kämpfe T, Eng LM. Bottom-Up Assembly of Molecular Nanostructures by Means of Ferroelectric Lithography. LANGMUIR : THE ACS JOURNAL OF SURFACES AND COLLOIDS 2017; 33:475-484. [PMID: 27989215 DOI: 10.1021/acs.langmuir.6b03405] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/06/2023]
Abstract
Here, we report on the photochemical deposition of Rhodamine 6G (Rh6G) and Alexa647 molecules from aqueous and methanolic solution along 180° ferroelectric (FE) domain walls (DWs) of z-cut lithium niobate (LNO) single crystals. Molecules and FE domains were investigated by means of dynamic-mode AFM, piezoresponse force microscopy (PFM), and confocal scanning fluorescence microscopy. A high deposition affinity for 180° DWs on the LNO surface is observed, leading to the formation of molecular nanowires. Additionally, a more complex deposition pattern for Rh6G adsorbed to the domain areas of freshly poled samples was equally observed, being associated with the DW dynamics. These results are explained by considering contributions from screening-charge-dependent photochemistry as confined to the DWs, UV-induced DW motion, and transient electrostatic fields arising from the metastable defect distribution shortly after poling. Hence, tuning these effects offers the possibility for accurately controlling the complex bottom-up assembly of functional molecular nanostructures through domain-structured ferroelectric templates.
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Affiliation(s)
- Alexander Haußmann
- Institut für Angewandte Physik and Center for Advancing Electronics Dresden (cfaed), Technische Universität Dresden , D-01062 Dresden, Germany
| | - André Gemeinhardt
- Institut für Angewandte Physik and Center for Advancing Electronics Dresden (cfaed), Technische Universität Dresden , D-01062 Dresden, Germany
| | - Mathias Schröder
- Institut für Angewandte Physik and Center for Advancing Electronics Dresden (cfaed), Technische Universität Dresden , D-01062 Dresden, Germany
| | - Thomas Kämpfe
- Institut für Angewandte Physik and Center for Advancing Electronics Dresden (cfaed), Technische Universität Dresden , D-01062 Dresden, Germany
| | - Lukas M Eng
- Institut für Angewandte Physik and Center for Advancing Electronics Dresden (cfaed), Technische Universität Dresden , D-01062 Dresden, Germany
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287
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Intrinsic Dynamics Analysis of a DNA Octahedron by Elastic Network Model. Molecules 2017; 22:molecules22010145. [PMID: 28275219 PMCID: PMC6155889 DOI: 10.3390/molecules22010145] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2016] [Revised: 01/09/2017] [Accepted: 01/10/2017] [Indexed: 01/10/2023] Open
Abstract
DNA is a fundamental component of living systems where it plays a crucial role at both functional and structural level. The programmable properties of DNA make it an interesting building block for the construction of nanostructures. However, molecular mechanisms for the arrangement of these well-defined DNA assemblies are not fully understood. In this paper, the intrinsic dynamics of a DNA octahedron has been investigated by using two types of Elastic Network Models (ENMs). The application of ENMs to DNA nanocages include the analysis of the intrinsic flexibilities of DNA double-helices and hinge sites through the calculation of the square fluctuations, as well as the intrinsic collective dynamics in terms of cross-collective map calculation coupled with global motions analysis. The dynamics profiles derived from ENMs have then been evaluated and compared with previous classical molecular dynamics simulation trajectories. The results presented here revealed that ENMs can provide useful insights into the intrinsic dynamics of large DNA nanocages and represent a useful tool in the field of structural DNA nanotechnology.
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288
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Wang J, Chao J, Liu H, Su S, Wang L, Huang W, Willner I, Fan C. Clamped Hybridization Chain Reactions for the Self-Assembly of Patterned DNA Hydrogels. Angew Chem Int Ed Engl 2017; 56:2171-2175. [DOI: 10.1002/anie.201610125] [Citation(s) in RCA: 123] [Impact Index Per Article: 17.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2016] [Indexed: 02/01/2023]
Affiliation(s)
- Jianbang Wang
- Division of Physical Biology & Bioimaging Center; Shanghai Synchrotron Radiation Facility; CAS Key Laboratory of Interfacial Physics and Technology; Shanghai Institute of Applied Physics; Chinese Academy of Sciences; Shanghai 201800 China
| | - Jie Chao
- Key Laboratory for Organic Electronics & Information Displays (KLOEID); Institute of Advanced Materials (IAM) and School of Materials Science and Engineering; Nanjing University of Posts & Telecommunications Institution; 9 Wenyuan Road Nanjing 210046 China
| | - Huajie Liu
- Division of Physical Biology & Bioimaging Center; Shanghai Synchrotron Radiation Facility; CAS Key Laboratory of Interfacial Physics and Technology; Shanghai Institute of Applied Physics; Chinese Academy of Sciences; Shanghai 201800 China
| | - Shao Su
- Key Laboratory for Organic Electronics & Information Displays (KLOEID); Institute of Advanced Materials (IAM) and School of Materials Science and Engineering; Nanjing University of Posts & Telecommunications Institution; 9 Wenyuan Road Nanjing 210046 China
| | - Lianhui Wang
- Key Laboratory for Organic Electronics & Information Displays (KLOEID); Institute of Advanced Materials (IAM) and School of Materials Science and Engineering; Nanjing University of Posts & Telecommunications Institution; 9 Wenyuan Road Nanjing 210046 China
| | - Wei Huang
- Key Laboratory for Organic Electronics & Information Displays (KLOEID); Institute of Advanced Materials (IAM) and School of Materials Science and Engineering; Nanjing University of Posts & Telecommunications Institution; 9 Wenyuan Road Nanjing 210046 China
| | - Itamar Willner
- Institute of Chemistry; The Hebrew University of Jerusalem; Jerusalem 91904 Israel
| | - Chunhai Fan
- Division of Physical Biology & Bioimaging Center; Shanghai Synchrotron Radiation Facility; CAS Key Laboratory of Interfacial Physics and Technology; Shanghai Institute of Applied Physics; Chinese Academy of Sciences; Shanghai 201800 China
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289
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Wang J, Chao J, Liu H, Su S, Wang L, Huang W, Willner I, Fan C. Clamped Hybridization Chain Reactions for the Self-Assembly of Patterned DNA Hydrogels. Angew Chem Int Ed Engl 2017. [DOI: 10.1002/ange.201610125] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
Affiliation(s)
- Jianbang Wang
- Division of Physical Biology & Bioimaging Center; Shanghai Synchrotron Radiation Facility; CAS Key Laboratory of Interfacial Physics and Technology; Shanghai Institute of Applied Physics; Chinese Academy of Sciences; Shanghai 201800 China
| | - Jie Chao
- Key Laboratory for Organic Electronics & Information Displays (KLOEID); Institute of Advanced Materials (IAM) and School of Materials Science and Engineering; Nanjing University of Posts & Telecommunications Institution; 9 Wenyuan Road Nanjing 210046 China
| | - Huajie Liu
- Division of Physical Biology & Bioimaging Center; Shanghai Synchrotron Radiation Facility; CAS Key Laboratory of Interfacial Physics and Technology; Shanghai Institute of Applied Physics; Chinese Academy of Sciences; Shanghai 201800 China
| | - Shao Su
- Key Laboratory for Organic Electronics & Information Displays (KLOEID); Institute of Advanced Materials (IAM) and School of Materials Science and Engineering; Nanjing University of Posts & Telecommunications Institution; 9 Wenyuan Road Nanjing 210046 China
| | - Lianhui Wang
- Key Laboratory for Organic Electronics & Information Displays (KLOEID); Institute of Advanced Materials (IAM) and School of Materials Science and Engineering; Nanjing University of Posts & Telecommunications Institution; 9 Wenyuan Road Nanjing 210046 China
| | - Wei Huang
- Key Laboratory for Organic Electronics & Information Displays (KLOEID); Institute of Advanced Materials (IAM) and School of Materials Science and Engineering; Nanjing University of Posts & Telecommunications Institution; 9 Wenyuan Road Nanjing 210046 China
| | - Itamar Willner
- Institute of Chemistry; The Hebrew University of Jerusalem; Jerusalem 91904 Israel
| | - Chunhai Fan
- Division of Physical Biology & Bioimaging Center; Shanghai Synchrotron Radiation Facility; CAS Key Laboratory of Interfacial Physics and Technology; Shanghai Institute of Applied Physics; Chinese Academy of Sciences; Shanghai 201800 China
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290
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Zhang P, Lin Z, Zhuo Y, Yuan R, Chai Y. Dual microRNAs-Fueled DNA Nanogears: A Case of Regenerated Strategy for Multiple Electrochemiluminescence Detection of microRNAs with Single Luminophore. Anal Chem 2017; 89:1338-1345. [DOI: 10.1021/acs.analchem.6b04402] [Citation(s) in RCA: 56] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Affiliation(s)
- Pu Zhang
- Key Laboratory
of Luminescent
and Real-Time Analytical Chemistry (Southwest University), Ministry
of Education, College of Chemistry and Chemical Engineering, Southwest University, Chongqing 400715, PR China
| | - Zongfan Lin
- Key Laboratory
of Luminescent
and Real-Time Analytical Chemistry (Southwest University), Ministry
of Education, College of Chemistry and Chemical Engineering, Southwest University, Chongqing 400715, PR China
| | - Ying Zhuo
- Key Laboratory
of Luminescent
and Real-Time Analytical Chemistry (Southwest University), Ministry
of Education, College of Chemistry and Chemical Engineering, Southwest University, Chongqing 400715, PR China
| | - Ruo Yuan
- Key Laboratory
of Luminescent
and Real-Time Analytical Chemistry (Southwest University), Ministry
of Education, College of Chemistry and Chemical Engineering, Southwest University, Chongqing 400715, PR China
| | - Yaqin Chai
- Key Laboratory
of Luminescent
and Real-Time Analytical Chemistry (Southwest University), Ministry
of Education, College of Chemistry and Chemical Engineering, Southwest University, Chongqing 400715, PR China
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291
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Zhu X, Chen X, Ban F, Cao Y, Zhao J, Chen G, Li G. The design of a mechanical wave-like DNA nanomachine for the fabrication of a programmable and multifunctional molecular device. Chem Commun (Camb) 2017; 53:10504-10507. [DOI: 10.1039/c7cc05174c] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
A DNA nanomachine is designed for switching just like a mechanical wave upon binding with an input.
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Affiliation(s)
- Xiaoli Zhu
- Center for Molecular Recognition and Biosensing
- School of Life Sciences
- Shanghai University
- Shanghai 200444
- China
| | - Xiaoxia Chen
- Center for Molecular Recognition and Biosensing
- School of Life Sciences
- Shanghai University
- Shanghai 200444
- China
| | - Fangfang Ban
- Center for Molecular Recognition and Biosensing
- School of Life Sciences
- Shanghai University
- Shanghai 200444
- China
| | - Ya Cao
- Center for Molecular Recognition and Biosensing
- School of Life Sciences
- Shanghai University
- Shanghai 200444
- China
| | - Jing Zhao
- Center for Molecular Recognition and Biosensing
- School of Life Sciences
- Shanghai University
- Shanghai 200444
- China
| | - Guifang Chen
- Center for Molecular Recognition and Biosensing
- School of Life Sciences
- Shanghai University
- Shanghai 200444
- China
| | - Genxi Li
- Center for Molecular Recognition and Biosensing
- School of Life Sciences
- Shanghai University
- Shanghai 200444
- China
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292
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Núñez-Villanueva D, Hunter CA. Homochiral oligomers with highly flexible backbones form stable H-bonded duplexes. Chem Sci 2017; 8:206-213. [PMID: 28451167 PMCID: PMC5308278 DOI: 10.1039/c6sc02995g] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2016] [Accepted: 08/02/2016] [Indexed: 12/24/2022] Open
Abstract
Two homochiral building blocks featuring a protected thiol, an alkene and a H-bond recognition unit (phenol or phosphine oxide) have been prepared. Iterative photochemical thiol-ene coupling reactions were used to synthesize oligomers containing 1-4 phosphine oxide and 1-4 phenol recognition sites. Length-complementary H-bond donor and H-bond acceptor oligomers were found to form stable duplexes in toluene. NMR titrations and thermal denaturation experiments show that the association constant and the enthalpy of duplex formation increase significantly for every additional H-bonding unit added to the chain. There is an order of magnitude increase in stability for each additional H-bonding interaction at room temperature indicating that all of the H-bonding sites are fully bound to their complements in the duplexes. The backbone of the thiol-ene duplexes is a highly flexible alkane chain, but this conformational flexibility does not have a negative impact on binding affinity. The average effective molarity for the intramolecular H-bonding interactions that zip up the duplexes is 18 mM. This value is somewhat higher than the EM of 14 mM found for a related family of duplexes, which have the same recognition units but a more rigid backbone prepared using reductive amination chemistry. The flexible thiol-ene AAAA·DDDD duplex is an order of magnitude more stable than the rigid reductive amination AAAA·DDDD duplex. The backbone of the thiol-ene system retains much of its conformational flexibility in the duplex, and these results show that highly flexible molecules can make very stable complexes, provided there is no significant restriction of degrees of freedom on complexation.
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Affiliation(s)
- Diego Núñez-Villanueva
- Department of Chemistry , University of Cambridge , Lensfield Road , Cambridge CB2 1EW , UK .
| | - Christopher A Hunter
- Department of Chemistry , University of Cambridge , Lensfield Road , Cambridge CB2 1EW , UK .
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293
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Bi S, Yue S, Zhang S. Hybridization chain reaction: a versatile molecular tool for biosensing, bioimaging, and biomedicine. Chem Soc Rev 2017; 46:4281-4298. [DOI: 10.1039/c7cs00055c] [Citation(s) in RCA: 393] [Impact Index Per Article: 56.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
This review provides a comprehensive overview of the fundamental principles, analysis techniques, and application fields of hybridization chain reaction and its development status.
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Affiliation(s)
- Sai Bi
- Collaborative Innovation Center for Marine Biomass Fiber
- Materials and Textiles of Shandong Province
- College of Chemistry and Chemical Engineering
- Shandong Sino-Japanese Center for Collaborative Research of Carbon Nanomaterials
- Laboratory of Fiber Materials and Modern Textiles
| | - Shuzhen Yue
- Collaborative Innovation Center for Marine Biomass Fiber
- Materials and Textiles of Shandong Province
- College of Chemistry and Chemical Engineering
- Shandong Sino-Japanese Center for Collaborative Research of Carbon Nanomaterials
- Laboratory of Fiber Materials and Modern Textiles
| | - Shusheng Zhang
- Shandong Provincial Key Laboratory of Detection Technology for Tumor Makers
- College of Chemistry and Chemical Engineering
- Linyi University
- Linyi 276005
- P. R. China
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294
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Ishii-Mizuno Y, Umeki Y, Onuki Y, Watanabe H, Takahashi Y, Takakura Y, Nishikawa M. Improved sustained release of antigen from immunostimulatory DNA hydrogel by electrostatic interaction with chitosan. Int J Pharm 2017; 516:392-400. [DOI: 10.1016/j.ijpharm.2016.11.048] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2016] [Revised: 10/14/2016] [Accepted: 11/20/2016] [Indexed: 12/23/2022]
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295
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Olejko L, Bald I. FRET efficiency and antenna effect in multi-color DNA origami-based light harvesting systems. RSC Adv 2017. [DOI: 10.1039/c7ra02114c] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
Abstract
Artificial light harvesting complexes find applications in photosynthesis, photovoltaics and chemical sensors. Here, we present the characterization and optimization of a multi-color artificial light harvesting system on DNA origami structures.
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Affiliation(s)
- L. Olejko
- Department of Chemistry
- Physical Chemistry
- University of Potsdam
- 14476 Potsdam
- Germany
| | - I. Bald
- Department of Chemistry
- Physical Chemistry
- University of Potsdam
- 14476 Potsdam
- Germany
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296
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Chen J, Tang L, Chu X, Jiang J. Enzyme-free, signal-amplified nucleic acid circuits for biosensing and bioimaging analysis. Analyst 2017; 142:3048-3061. [DOI: 10.1039/c7an00967d] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Abstract
Enzyme-free, signal-amplified nucleic acid circuits utilize programmed assembly reactions between nucleic acid substrates to transduce a chemical input into an amplified detection signal.
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Affiliation(s)
- Jiyun Chen
- Institute of Chemical Biology and Nanomedicine
- State Key Laboratory of Chemeo/Bio-Sensing and Chemometrics
- College of Chemistry and Chemical Engineering
- Hunan University
- Changsha
| | - Lijuan Tang
- Institute of Chemical Biology and Nanomedicine
- State Key Laboratory of Chemeo/Bio-Sensing and Chemometrics
- College of Chemistry and Chemical Engineering
- Hunan University
- Changsha
| | - Xia Chu
- Institute of Chemical Biology and Nanomedicine
- State Key Laboratory of Chemeo/Bio-Sensing and Chemometrics
- College of Chemistry and Chemical Engineering
- Hunan University
- Changsha
| | - Jianhui Jiang
- Institute of Chemical Biology and Nanomedicine
- State Key Laboratory of Chemeo/Bio-Sensing and Chemometrics
- College of Chemistry and Chemical Engineering
- Hunan University
- Changsha
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297
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Haque F, Xu C, Jasinski DL, Li H, Guo P. Using Planar Phi29 pRNA Three-Way Junction to Control Size and Shape of RNA Nanoparticles for Biodistribution Profiling in Mice. Methods Mol Biol 2017; 1632:359-380. [PMID: 28730451 DOI: 10.1007/978-1-4939-7138-1_23] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/07/2023]
Abstract
RNA is rapidly emerging as a versatile building block for nanoparticle assembly due to its simplicity in base pairing, while exhibiting diversity in function such as enzymatic activity similar to some proteins. Recent advances in RNA nanotechnology have generated significant interests in applying RNA nanoparticles for various applications in nanotechnology and nanomedicine. In particular, assessing the effect of size and shape on cell entry and intracellular trafficking as well as in vivo biodistribution of nanoparticles is challenging due to the lack of nanoparticles rich in structure while varying in size and shape. RNA nanotechnology exemplified by the packaging RNA (pRNA) of bacteriophage phi29 DNA packaging motor has provided a different prospect in nanoparticle designs. Of note, there is a robust three-way junction (3WJ) motif in pRNA which can serve as an adaptable scaffold to construct thermodynamically stable 2D planar and 3D globular RNA architectures with tunable shapes and sizes, and harboring various targeting, therapeutic, and imaging modules. This chapter focuses on the methods for constructing pRNA-3WJ based nanoparticles with controllable sizes and shapes, and assessment of their biodistribution profiles in cancer mouse models after systemic injection and ocular mouse models following subconjunctival injection.
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Affiliation(s)
- Farzin Haque
- Division of Pharmaceutics and Pharmaceutical Chemistry, College of Pharmacy, The Ohio State University, Columbus, OH, 43210, USA
- Department of Physiology and Cell Biology, College of Medicine, The Ohio State University, Columbus, OH, 43210, USA
- Dorothy M. Davis Heart and Lung Research Institute, The Ohio State University, Columbus, OH, 43210, USA
| | - Congcong Xu
- Division of Pharmaceutics and Pharmaceutical Chemistry, College of Pharmacy, The Ohio State University, Columbus, OH, 43210, USA
- Department of Physiology and Cell Biology, College of Medicine, The Ohio State University, Columbus, OH, 43210, USA
- Dorothy M. Davis Heart and Lung Research Institute, The Ohio State University, Columbus, OH, 43210, USA
| | - Daniel L Jasinski
- Division of Pharmaceutics and Pharmaceutical Chemistry, College of Pharmacy, The Ohio State University, Columbus, OH, 43210, USA
- Department of Physiology and Cell Biology, College of Medicine, The Ohio State University, Columbus, OH, 43210, USA
- Dorothy M. Davis Heart and Lung Research Institute, The Ohio State University, Columbus, OH, 43210, USA
| | - Hui Li
- Division of Pharmaceutics and Pharmaceutical Chemistry, College of Pharmacy, The Ohio State University, Columbus, OH, 43210, USA
- Department of Physiology and Cell Biology, College of Medicine, The Ohio State University, Columbus, OH, 43210, USA
- Dorothy M. Davis Heart and Lung Research Institute, The Ohio State University, Columbus, OH, 43210, USA
| | - Peixuan Guo
- Division of Pharmaceutics and Pharmaceutical Chemistry, College of Pharmacy, The Ohio State University, Columbus, OH, 43210, USA.
- Department of Physiology and Cell Biology, College of Medicine, The Ohio State University, Columbus, OH, 43210, USA.
- Dorothy M. Davis Heart and Lung Research Institute, The Ohio State University, Columbus, OH, 43210, USA.
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298
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Reddy GNM, Huqi A, Iuga D, Sakurai S, Marsh A, Davis JT, Masiero S, Brown SP. Co-existence of Distinct Supramolecular Assemblies in Solution and in the Solid State. Chemistry 2016; 23:2315-2322. [PMID: 27897351 PMCID: PMC5396329 DOI: 10.1002/chem.201604832] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2016] [Indexed: 11/24/2022]
Abstract
The formation of distinct supramolecular assemblies, including a metastable species, is revealed for a lipophilic guanosine (G) derivative in solution and in the solid state. Structurally different G‐quartet‐based assemblies are formed in chloroform depending on the nature of the cation, anion and the salt concentration, as characterized by circular dichroism and time course diffusion‐ordered NMR spectroscopy data. Intriguingly, even the presence of potassium ions that stabilize G‐quartets in chloroform was insufficient to exclusively retain such assemblies in the solid state, leading to the formation of mixed quartet and ribbon‐like assemblies as revealed by fast magic‐angle spinning (MAS) NMR spectroscopy. Distinct N−H⋅⋅⋅N and N−H⋅⋅⋅O intermolecular hydrogen bonding interactions drive quartet and ribbon‐like self‐assembly resulting in markedly different 2D 1H solid‐state NMR spectra, thus facilitating a direct identification of mixed assemblies. A dissolution NMR experiment confirmed that the quartet and ribbon interconversion is reversible–further demonstrating the changes that occur in the self‐assembly process of a lipophilic nucleoside upon a solid‐state to solution‐state transition and vice versa. A systematic study for complexation with different cations (K+, Sr2+) and anions (picrate, ethanoate and iodide) emphasizes that the existence of a stable solution or solid‐state structure may not reflect the stability of the same supramolecular entity in another phase.
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Affiliation(s)
- G N Manjunatha Reddy
- Department of Physics and Department of Chemistry, University of, Warwick, Coventry, CV4 7AL, UK
| | - Aida Huqi
- Dipartimento di Chimica "Giacomo Ciamician", Alma Mater Studiorum, Università di Bologna, 40126, Bologna, Italy
| | - Dinu Iuga
- Department of Physics and Department of Chemistry, University of, Warwick, Coventry, CV4 7AL, UK
| | - Satoshi Sakurai
- JEOL (UK), Silver Court, Watchmead, Welwyn Garden City, AL7 1LT, UK
| | - Andrew Marsh
- Department of Physics and Department of Chemistry, University of, Warwick, Coventry, CV4 7AL, UK
| | - Jeffery T Davis
- Department of Chemistry and Biochemistry, University of Maryland, College Park, MD, 20742, USA
| | - Stefano Masiero
- Dipartimento di Chimica "Giacomo Ciamician", Alma Mater Studiorum, Università di Bologna, 40126, Bologna, Italy
| | - Steven P Brown
- Department of Physics and Department of Chemistry, University of, Warwick, Coventry, CV4 7AL, UK
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299
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Satyavolu NSR, Tan LH, Lu Y. DNA-Mediated Morphological Control of Pd–Au Bimetallic Nanoparticles. J Am Chem Soc 2016; 138:16542-16548. [DOI: 10.1021/jacs.6b10983] [Citation(s) in RCA: 75] [Impact Index Per Article: 9.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Affiliation(s)
- Nitya Sai Reddy Satyavolu
- Department of Chemistry, University of Illinois at Urbana—Champaign, Urbana, Illinois 61801, United States
| | - Li Huey Tan
- Department of Chemistry, University of Illinois at Urbana—Champaign, Urbana, Illinois 61801, United States
| | - Yi Lu
- Department of Chemistry, University of Illinois at Urbana—Champaign, Urbana, Illinois 61801, United States
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300
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Cox AJ, Bengtson HN, Rohde KH, Kolpashchikov DM. DNA nanotechnology for nucleic acid analysis: multifunctional molecular DNA machine for RNA detection. Chem Commun (Camb) 2016; 52:14318-14321. [PMID: 27886299 PMCID: PMC5645153 DOI: 10.1039/c6cc06889h] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
The Nobel prize in chemistry in 2016 was awarded for 'the design and synthesis of molecular machines'. Here we designed and assembled a molecular machine for the detection of specific RNA molecules. An association of several DNA strands, named multifunctional DNA machine for RNA analysis (MDMR1), was designed to (i) unwind RNA with the help of RNA-binding arms, (ii) selectively recognize a targeted RNA fragment, (iii) attract a signal-producing substrate and (iv) amplify the fluorescent signal by catalysis. MDMR1 enabled detection of 16S rRNA at concentrations ∼24 times lower than that by a traditional deoxyribozyme probe.
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Affiliation(s)
- A J Cox
- Chemistry Department, University of Central Florida, Orlando, 32816, Florida, USA and Burnett School of Biomedical Sciences, University of Central Florida, Orlando, 32816, Florida, USA.
| | - H N Bengtson
- Chemistry Department, University of Central Florida, Orlando, 32816, Florida, USA and Burnett School of Biomedical Sciences, University of Central Florida, Orlando, 32816, Florida, USA.
| | - K H Rohde
- Burnett School of Biomedical Sciences, University of Central Florida, Orlando, 32816, Florida, USA.
| | - D M Kolpashchikov
- Chemistry Department, University of Central Florida, Orlando, 32816, Florida, USA and Burnett School of Biomedical Sciences, University of Central Florida, Orlando, 32816, Florida, USA.
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