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Li J, Mohammed-Elsabagh M, Paczkowski F, Li Y. Circular Nucleic Acids: Discovery, Functions and Applications. Chembiochem 2020; 21:1547-1566. [PMID: 32176816 DOI: 10.1002/cbic.202000003] [Citation(s) in RCA: 31] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/02/2020] [Revised: 02/13/2020] [Indexed: 12/14/2022]
Abstract
Circular nucleic acids (CNAs) are nucleic acid molecules with a closed-loop structure. This feature comes with a number of advantages including complete resistance to exonuclease degradation, much better thermodynamic stability, and the capability of being replicated by a DNA polymerase in a rolling circle manner. Circular functional nucleic acids, CNAs containing at least a ribozyme/DNAzyme or a DNA/RNA aptamer, not only inherit the advantages of CNAs but also offer some unique application opportunities, such as the design of topology-controlled or enabled molecular devices. This article will begin by summarizing the discovery, biogenesis, and applications of naturally occurring CNAs, followed by discussing the methods for constructing artificial CNAs. The exploitation of circular functional nucleic acids for applications in nanodevice engineering, biosensing, and drug delivery will be reviewed next. Finally, the efforts to couple functional nucleic acids with rolling circle amplification for ultra-sensitive biosensing and for synthesizing multivalent molecular scaffolds for unique applications in biosensing and drug delivery will be recapitulated.
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Affiliation(s)
- Jiuxing Li
- M.G. DeGroote Institute for Infectious Disease Research Department of Biochemistry and Biomedical Sciences, McMaster University, 1280 Main Street West, Hamilton, L8S 4K1, Canada
| | - Mostafa Mohammed-Elsabagh
- M.G. DeGroote Institute for Infectious Disease Research Department of Biochemistry and Biomedical Sciences, McMaster University, 1280 Main Street West, Hamilton, L8S 4K1, Canada
| | - Freeman Paczkowski
- M.G. DeGroote Institute for Infectious Disease Research Department of Biochemistry and Biomedical Sciences, McMaster University, 1280 Main Street West, Hamilton, L8S 4K1, Canada
| | - Yingfu Li
- M.G. DeGroote Institute for Infectious Disease Research Department of Biochemistry and Biomedical Sciences, McMaster University, 1280 Main Street West, Hamilton, L8S 4K1, Canada
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Kageyama R, Kawamata I, Tanabe K, Suzuki Y, Nomura SIM, Murata S. Construction of T-Motif-Based DNA Nanostructures through Enzymatic Reactions. Chembiochem 2018; 19:873-876. [PMID: 29399977 DOI: 10.1002/cbic.201700682] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2017] [Indexed: 11/06/2022]
Abstract
The most common way to fabricate DNA nanostructures is to mix individually synthesized DNA oligomers in one pot. However, if DNA nanostructures could be produced through enzymatic reactions, they could be applied in various environments, including in vivo. Herein, an enzymatic method developed to construct a DNA nanostructure from a simple motif called a T-motif is reported. A long, repeated structure was replicated from a circular template by rolling circle amplification and then cleaved into T-motif segments by restriction enzymes. These motifs have been successfully assembled into a ladder-like nanostructure without purification or controlled annealing. This approach is widely applicable to constructing a variety of DNA nanostructures through enzymatic reactions.
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Affiliation(s)
- Ryo Kageyama
- Graduate School of Engineering, Tohoku University, 6-6-01 Aramaki-Aza Aoba, Aoba-ku, Sendai, Miyagi, 980-8579, Japan
| | - Ibuki Kawamata
- Graduate School of Engineering, Tohoku University, 6-6-01 Aramaki-Aza Aoba, Aoba-ku, Sendai, Miyagi, 980-8579, Japan
| | - Kaori Tanabe
- Graduate School of Engineering, Tohoku University, 6-6-01 Aramaki-Aza Aoba, Aoba-ku, Sendai, Miyagi, 980-8579, Japan
| | - Yuki Suzuki
- Graduate School of Engineering, Tohoku University, 6-6-01 Aramaki-Aza Aoba, Aoba-ku, Sendai, Miyagi, 980-8579, Japan.,Frontier Research Institute for Interdisciplinary Sciences, Tohoku University, 6-3 Aramaki-aza Aoba, Aoba-ku, Sendai, Miyagi, 980-8578, Japan
| | - Shin-Ichiro M Nomura
- Graduate School of Engineering, Tohoku University, 6-6-01 Aramaki-Aza Aoba, Aoba-ku, Sendai, Miyagi, 980-8579, Japan
| | - Satoshi Murata
- Graduate School of Engineering, Tohoku University, 6-6-01 Aramaki-Aza Aoba, Aoba-ku, Sendai, Miyagi, 980-8579, Japan
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3
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Liu M, Zhang W, Zhang Q, Brennan JD, Li Y. Biosensing by Tandem Reactions of Structure Switching, Nucleolytic Digestion, and DNA Amplification of a DNA Assembly. Angew Chem Int Ed Engl 2015. [DOI: 10.1002/ange.201503182] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
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4
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Liu M, Zhang W, Zhang Q, Brennan JD, Li Y. Biosensing by Tandem Reactions of Structure Switching, Nucleolytic Digestion, and DNA Amplification of a DNA Assembly. Angew Chem Int Ed Engl 2015; 54:9637-41. [PMID: 26119600 DOI: 10.1002/anie.201503182] [Citation(s) in RCA: 60] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2015] [Revised: 05/28/2015] [Indexed: 12/20/2022]
Abstract
ϕ29 DNA polymerase (ϕ29DP) is able to carry out repetitive rounds of DNA synthesis using a circular DNA template by rolling circle amplification (RCA). It also has the ability to execute 3'-5' digestion of single-stranded but not double-stranded DNA. A biosensor engineering strategy is presented that takes advantage of these two properties of ϕ29DP coupled with structure-switching DNA aptamers. The design employs a DNA assembly made of a circular DNA template, a DNA aptamer, and a pre-primer. The DNA assembly is unable to undergo RCA in the absence of cognate target owing to the formation of duplex structures. The presence of the target, however, triggers a structure-switching event that causes nucleolytic conversion of the pre-primer by ϕ29DP into a mature primer to facilitate RCA. This method relays target detection by the aptamer to the production of massive DNA amplicons, giving rise to dramatically enhanced detection sensitivity.
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Affiliation(s)
- Meng Liu
- Department of Biochemistry and Biomedical Sciences, McMaster University, 1280 Main Street West, Hamilton, ON, L8S 4K1 (Canada)
| | - Wenqing Zhang
- Department of Biochemistry and Biomedical Sciences, McMaster University, 1280 Main Street West, Hamilton, ON, L8S 4K1 (Canada)
| | - Qiang Zhang
- Department of Chemistry and Chemical Biology, McMaster University, 1280 Main Street West, Hamilton, ON, L8S 4K1 (Canada)
| | - John D Brennan
- Department of Chemistry and Chemical Biology, McMaster University, 1280 Main Street West, Hamilton, ON, L8S 4K1 (Canada).
| | - Yingfu Li
- Department of Biochemistry and Biomedical Sciences, McMaster University, 1280 Main Street West, Hamilton, ON, L8S 4K1 (Canada). .,Department of Chemistry and Chemical Biology, McMaster University, 1280 Main Street West, Hamilton, ON, L8S 4K1 (Canada).
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5
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Carrasquilla C, Little JRL, Li Y, Brennan JD. Patterned paper sensors printed with long-chain DNA aptamers. Chemistry 2015; 21:7369-73. [PMID: 25820300 DOI: 10.1002/chem.201500949] [Citation(s) in RCA: 51] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2015] [Indexed: 01/02/2023]
Abstract
There is growing interest in developing printable paper sensors to enable rapid testing of analytes for environmental, food safety, and clinical applications. A major challenge is to find suitable bioinks that are amenable to high-speed printing and remain functional after printing. We report on a simple and effective approach wherein an aqueous ink composed of megadalton-sized tandem repeating structure-switching DNA aptamers (concatemeric aptamers) is used to rapidly create patterned paper sensors on filter paper by inkjet printing. These concatemeric aptamer reporters remain immobilized at the point of printing through strong adsorption but retain sufficient segmental mobility to undergo structure switching and fluorescence signaling to provide both qualitative and quantitative detection of small molecules and protein targets. The convenience of inkjet printing allows for the patterning of internally referenced sensors with multiplexed detection, and provides a generic platform for on-demand printing of sensors even in remote locations.
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Affiliation(s)
- Carmen Carrasquilla
- Biointerfaces Institute and Department of Chemistry and Chemical Biology, McMaster University, 1280 Main St. W., Hamilton, ON, L8S 4L8 (Canada)
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Yan J, Hu C, Wang P, Zhao B, Ouyang X, Zhou J, Liu R, He D, Fan C, Song S. Growth and Origami Folding of DNA on Nanoparticles for High-Efficiency Molecular Transport in Cellular Imaging and Drug Delivery. Angew Chem Int Ed Engl 2015; 54:2431-5. [DOI: 10.1002/anie.201408247] [Citation(s) in RCA: 91] [Impact Index Per Article: 10.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2014] [Revised: 10/22/2014] [Indexed: 01/02/2023]
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7
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Yan J, Hu C, Wang P, Zhao B, Ouyang X, Zhou J, Liu R, He D, Fan C, Song S. Growth and Origami Folding of DNA on Nanoparticles for High-Efficiency Molecular Transport in Cellular Imaging and Drug Delivery. Angew Chem Int Ed Engl 2015. [DOI: 10.1002/ange.201408247] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
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Jiang HX, Zhao MY, Niu CD, Kong DM. Real-time monitoring of rolling circle amplification using aggregation-induced emission: applications in biological detection. Chem Commun (Camb) 2015; 51:16518-21. [DOI: 10.1039/c5cc07340e] [Citation(s) in RCA: 34] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Real-time monitoring of rolling circle amplification (RCA) was achieved by the super-aggregation of a tetraphenylethene dye QAPTE along single-stranded DNA products and consequent enhanced aggregation-induced emission, it can work for all RCA reactions.
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Affiliation(s)
- Hong-Xin Jiang
- State Key Laboratory of Medicinal Chemical Biology
- Nankai University
- Tianjin
- People's Republic of China
- Collaborative Innovation Center of Chemical Science and Engineering (Tianjin)
| | - Meng-Yao Zhao
- State Key Laboratory of Medicinal Chemical Biology
- Nankai University
- Tianjin
- People's Republic of China
- Collaborative Innovation Center of Chemical Science and Engineering (Tianjin)
| | - Chen-Di Niu
- State Key Laboratory of Medicinal Chemical Biology
- Nankai University
- Tianjin
- People's Republic of China
- Collaborative Innovation Center of Chemical Science and Engineering (Tianjin)
| | - De-Ming Kong
- State Key Laboratory of Medicinal Chemical Biology
- Nankai University
- Tianjin
- People's Republic of China
- Collaborative Innovation Center of Chemical Science and Engineering (Tianjin)
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Zhang Z, Eckert MA, Ali MM, Liu L, Kang DK, Chang E, Pone EJ, Sender LS, Fruman DA, Zhao W. DNA-Scaffolded Multivalent Ligands to Modulate Cell Function. Chembiochem 2014; 15:1268-73. [DOI: 10.1002/cbic.201402100] [Citation(s) in RCA: 40] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2014] [Indexed: 12/21/2022]
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Lau KL, Hamblin GD, Sleiman HF. Gold nanoparticle 3D-DNA building blocks: high purity preparation and use for modular access to nanoparticle assemblies. SMALL (WEINHEIM AN DER BERGSTRASSE, GERMANY) 2014; 10:660-666. [PMID: 24115591 DOI: 10.1002/smll.201301562] [Citation(s) in RCA: 37] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/21/2013] [Revised: 07/12/2013] [Indexed: 06/02/2023]
Abstract
Using highly functional 'building-blocks' of AuNPs mono-conjugated to three-dimensional DNA 'rung' structures, both discrete and extended linear assemblies are controllably prepared via addition of various templating backbone strands. This unique approach presents a facile alternative to other methods of AuNP organization through DNA, and has potential utility in the fields of nanophotonics and nanoelectronics.
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Affiliation(s)
- Kai Lin Lau
- Department of Chemistry, McGill University, Montreal, QC, H3A 2K6, Canada
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Hong CA, Jang B, Jeong EH, Jeong H, Lee H. Self-assembled DNA nanostructures prepared by rolling circle amplification for the delivery of siRNA conjugates. Chem Commun (Camb) 2014; 50:13049-51. [DOI: 10.1039/c4cc03834g] [Citation(s) in RCA: 34] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023]
Abstract
Large-scale preparation of DNA nanostructures for siRNA delivery has been achieved by an isothermal enzymatic amplification process.
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Affiliation(s)
- Cheol Am Hong
- College of Pharmacy
- Graduate School of Pharmaceutical Sciences
- Ewha Womans University
- Seoul 120-750, Republic of Korea
| | - Bora Jang
- College of Pharmacy
- Graduate School of Pharmaceutical Sciences
- Ewha Womans University
- Seoul 120-750, Republic of Korea
| | - Eun Hye Jeong
- College of Pharmacy
- Graduate School of Pharmaceutical Sciences
- Ewha Womans University
- Seoul 120-750, Republic of Korea
| | - Hansaem Jeong
- College of Pharmacy
- Graduate School of Pharmaceutical Sciences
- Ewha Womans University
- Seoul 120-750, Republic of Korea
| | - Hyukjin Lee
- College of Pharmacy
- Graduate School of Pharmaceutical Sciences
- Ewha Womans University
- Seoul 120-750, Republic of Korea
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Lin MY, Ho FH, Yang CY, Yeh JA, Yang YS. Functionalization, re-functionalization and rejuvenation of ssDNA nanotemplates. Chem Commun (Camb) 2012; 48:4902-4. [PMID: 22499154 DOI: 10.1039/c2cc30748k] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Single-stranded DNA (ssDNA) with repetitive sequence was demonstrated to be a versatile nanotemplate for introducing biological activity in a self-assembled manner. Re-functionalization and rejuvenation of the ssDNA nanotemplate were achieved under mild biological conditions without using high temperature and strong alkaline treatment to denature DNA.
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Affiliation(s)
- Ming-Yu Lin
- Institute of Molecular Medicine and Bioengineering, National Chiao Tung University, Hsinchu, Taiwan
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13
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14
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Wang ZG, Elbaz J, Willner I. A Dynamically Programmed DNA Transporter. Angew Chem Int Ed Engl 2012; 51:4322-6. [DOI: 10.1002/anie.201107855] [Citation(s) in RCA: 54] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2011] [Indexed: 12/24/2022]
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16
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Baccaro A, Steck AL, Marx A. Barcoded nucleotides. Angew Chem Int Ed Engl 2011; 51:254-7. [PMID: 22083884 DOI: 10.1002/anie.201105717] [Citation(s) in RCA: 64] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2011] [Revised: 09/15/2011] [Indexed: 12/20/2022]
Affiliation(s)
- Anna Baccaro
- Department of Chemistry and Konstanz Research School Chemical Biology, University of Konstanz, Universitätsstrasse 10, 78457 Konstanz, Germany
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Reiss E, Hölzel R, Bier FF. Synthesis and stretching of rolling circle amplification products in a flow-through system. SMALL (WEINHEIM AN DER BERGSTRASSE, GERMANY) 2009; 5:2316-22. [PMID: 19492351 DOI: 10.1002/smll.200900319] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/17/2023]
Abstract
Enzymatic isothermal rolling circle amplification (RCA) produces long concatemeric single-stranded DNA (ssDNA) molecules if a small circular ssDNA molecule is applied as the template. A method is presented here in which the RCA reaction is carried out in a flow-through system, starting from isolated surface-tethered DNA primers. This approach combines gentle fluidic handling of the single-stranded RCA products, such as staining or stretching via a receding meniscus, with the option of simultaneous (fluorescence) microscopic observation. It is shown that the stretched and surface-attached RCA products are accessible for hybridization of complementary oligonucleotides, which demonstrates their addressability by complementary base pairing. The long RCA products should be well suited to bridge the gap between biomolecular nanoscale building-blocks and structures at the micro- and macroscale, especially at the single-molecule level presented here.
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Affiliation(s)
- Edda Reiss
- Fraunhofer Institute for Biomedical Engineering, Branch Potsdam-Golm, Department of Nanobiotechnology & Nanomedicine ,Am Mühlenberg 13, 14476 Potsdam, Germany.
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Cheng Y, Zhang X, Li Z, Jiao X, Wang Y, Zhang Y. Highly sensitive determination of microRNA using target-primed and branched rolling-circle amplification. Angew Chem Int Ed Engl 2009; 48:3268-72. [PMID: 19219883 DOI: 10.1002/anie.200805665] [Citation(s) in RCA: 347] [Impact Index Per Article: 23.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/16/2023]
Abstract
One-nucleotide differences in microRNAs (miRNAs) can be discriminated in an assay based on a branched rolling-circle amplification (BRCA) reaction and fluorescence quantification. With the proposed method miRNA can be detected at concentrations as low as 10 fM, and the miRNA in a total RNA sample of a few nanograms can be determined.
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Affiliation(s)
- Yongqiang Cheng
- Key Laboratory of Medicine Chemistry and Molecular Diagnosis, Ministry of Education, College of Chemistry and Environment Science, Hebei University, Baoding 071002, Hebei Province, China
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Cheng Y, Zhang X, Li Z, Jiao X, Wang Y, Zhang Y. Highly Sensitive Determination of microRNA Using Target-Primed and Branched Rolling-Circle Amplification. Angew Chem Int Ed Engl 2009. [DOI: 10.1002/ange.200805665] [Citation(s) in RCA: 97] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/02/2023]
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Zhao W, Ali MM, Brook MA, Li Y. Rolling circle amplification: applications in nanotechnology and biodetection with functional nucleic acids. Angew Chem Int Ed Engl 2008; 47:6330-7. [PMID: 18680110 DOI: 10.1002/anie.200705982] [Citation(s) in RCA: 431] [Impact Index Per Article: 26.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/11/2023]
Abstract
Rolling circle amplification (RCA) is an isothermal, enzymatic process mediated by certain DNA polymerases in which long single-stranded (ss) DNA molecules are synthesized on a short circular ssDNA template by using a single DNA primer. A method traditionally used for ultrasensitive DNA detection in areas of genomics and diagnostics, RCA has been used more recently to generate large-scale DNA templates for the creation of periodic nanoassemblies. Various RCA strategies have also been developed for the production of repetitive sequences of DNA aptamers and DNAzymes as detection platforms for small molecules and proteins. In this way, RCA is rapidly becoming a highly versatile DNA amplification tool with wide-ranging applications in genomics, proteomics, diagnosis, biosensing, drug discovery, and nanotechnology.
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Affiliation(s)
- Weian Zhao
- Department of Chemistry, McMaster University, 1280 Main Street West, Hamilton, ON, L8P 4M1, Canada
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Zhao W, Ali M, Brook M, Li Y. Rolling-Circle-Amplifikation: Anwendungen in der Nanotechnologie und in der Biodetektion mit funktionellen Nucleinsäuren. Angew Chem Int Ed Engl 2008. [DOI: 10.1002/ange.200705982] [Citation(s) in RCA: 50] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
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