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Tabuchi T, Yokobayashi Y. Cell-free riboswitches. RSC Chem Biol 2021; 2:1430-1440. [PMID: 34704047 PMCID: PMC8496063 DOI: 10.1039/d1cb00138h] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2021] [Accepted: 07/26/2021] [Indexed: 12/16/2022] Open
Abstract
The emerging community of cell-free synthetic biology aspires to build complex biochemical and genetic systems with functions that mimic or even exceed those in living cells. To achieve such functions, cell-free systems must be able to sense and respond to the complex chemical signals within and outside the system. Cell-free riboswitches can detect chemical signals via RNA-ligand interaction and respond by regulating protein synthesis in cell-free protein synthesis systems. In this article, we review synthetic cell-free riboswitches that function in both prokaryotic and eukaryotic cell-free systems reported to date to provide a current perspective on the state of cell-free riboswitch technologies and their limitations.
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Affiliation(s)
- Takeshi Tabuchi
- Nucleic Acid Chemistry and Engineering Unit, Okinawa Institute of Science and Technology Graduate University Onna Okinawa 904-0495 Japan
| | - Yohei Yokobayashi
- Nucleic Acid Chemistry and Engineering Unit, Okinawa Institute of Science and Technology Graduate University Onna Okinawa 904-0495 Japan
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2
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Patel S, Panchasara H, Braddick D, Gohil N, Singh V. Synthetic small RNAs: Current status, challenges, and opportunities. J Cell Biochem 2018; 119:9619-9639. [DOI: 10.1002/jcb.27252] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2018] [Accepted: 06/20/2018] [Indexed: 12/25/2022]
Affiliation(s)
- Shreya Patel
- Department of Microbiology, Synthetic Biology Laboratory School of Biological Sciences and Biotechnology, Institute of Advanced Research, Koba Institutional Area Gandhinagar India
| | - Happy Panchasara
- Department of Microbiology, Synthetic Biology Laboratory School of Biological Sciences and Biotechnology, Institute of Advanced Research, Koba Institutional Area Gandhinagar India
| | | | - Nisarg Gohil
- Department of Microbiology, Synthetic Biology Laboratory School of Biological Sciences and Biotechnology, Institute of Advanced Research, Koba Institutional Area Gandhinagar India
| | - Vijai Singh
- Department of Microbiology, Synthetic Biology Laboratory School of Biological Sciences and Biotechnology, Institute of Advanced Research, Koba Institutional Area Gandhinagar India
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Ogawa A, Tabuchi J, Doi Y, Takamatsu M. Biofunction-assisted DNA detection through RNase H-enhanced 3' processing of a premature tRNA probe in a wheat germ extract. Bioorg Med Chem Lett 2016; 26:3658-61. [PMID: 27289318 DOI: 10.1016/j.bmcl.2016.05.091] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2016] [Revised: 05/27/2016] [Accepted: 05/31/2016] [Indexed: 12/22/2022]
Abstract
We have developed a novel type of biofunction-assisted, signal-turn-on sensor for simply and homogenously detecting DNA. This sensor system is composed of two types of in vitro-transcribed label-free RNAs (a 3' premature amber suppressor tRNA probe and an amber-mutated mRNA encoding a reporter protein), RNase H, and a wheat germ extract (WGE). A target DNA induces the 3' end maturation of the tRNA probe, which is enhanced by RNase H and leads to the expression of a full-length reporter protein through amber suppression in WGE, while there is almost no expression without the target due to the inactivity of the premature probe. Therefore, the target can be readily detected with the activity of the translated reporter. The catalytic reuse of the target with the help of RNase H in addition to various bioprocesses in WGE enables this sensor system to exhibit relatively high selectivity and sensitivity.
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Affiliation(s)
- Atsushi Ogawa
- Proteo-Science Center, Ehime University, 3 Bunkyo-cho, Matsuyama, Ehime 790-8577, Japan.
| | - Junichiro Tabuchi
- Proteo-Science Center, Ehime University, 3 Bunkyo-cho, Matsuyama, Ehime 790-8577, Japan
| | - Yasunori Doi
- Proteo-Science Center, Ehime University, 3 Bunkyo-cho, Matsuyama, Ehime 790-8577, Japan
| | - Masashi Takamatsu
- Proteo-Science Center, Ehime University, 3 Bunkyo-cho, Matsuyama, Ehime 790-8577, Japan
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Zhang X, Liu H, Li R, Zhang N, Xiong Y, Niu S. Chemiluminescence detection of DNA/microRNA based on cation-exchange of CuS nanoparticles and rolling circle amplification. Chem Commun (Camb) 2015; 51:6952-5. [DOI: 10.1039/c5cc01317h] [Citation(s) in RCA: 38] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
Cation-exchange-based chemiluminescence amplification was developed. After amplification by rolling circle amplification, the proposed strategy was used to detect miRNA sensitively.
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Affiliation(s)
- Xiaoru Zhang
- Key Laboratory of Sensor Analysis of Tumor Marker
- Ministry of Education
- College of Chemistry and Molecular Engineering
- Qingdao University of Science and Technology
- Qingdao 266042
| | - Hongxia Liu
- Key Laboratory of Sensor Analysis of Tumor Marker
- Ministry of Education
- College of Chemistry and Molecular Engineering
- Qingdao University of Science and Technology
- Qingdao 266042
| | - Ruijuan Li
- Key Laboratory of Sensor Analysis of Tumor Marker
- Ministry of Education
- College of Chemistry and Molecular Engineering
- Qingdao University of Science and Technology
- Qingdao 266042
| | - Ningbo Zhang
- Key Laboratory of Detection Technology of Shandong Province for Tumor Marker
- College of Chemistry and Chemical Engineering
- Linyi University
- Linyi 276005
- P. R. China
| | - Ying Xiong
- Key Laboratory of Sensor Analysis of Tumor Marker
- Ministry of Education
- College of Chemistry and Molecular Engineering
- Qingdao University of Science and Technology
- Qingdao 266042
| | - Shuyan Niu
- Key Laboratory of Sensor Analysis of Tumor Marker
- Ministry of Education
- College of Chemistry and Molecular Engineering
- Qingdao University of Science and Technology
- Qingdao 266042
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6
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Feng S, Shang Y, Wu F, Ding F, Li B, Xu J, Xu L, Zhou X. DNA nanomachines as evolved molecular beacons for in vitro and in vivo detection. Talanta 2013; 120:141-7. [PMID: 24468353 DOI: 10.1016/j.talanta.2013.11.038] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2013] [Revised: 11/12/2013] [Accepted: 11/13/2013] [Indexed: 11/30/2022]
Abstract
Modern biosensors require high sensitivity, great signal enhancement and extensive applicability for detection and diagnostic purposes. Traditional molecular beacons (MBs) do not meet these requirements because of the lack of signal amplification. The current amplification pathways using enzymes, DNAzymes and nanoparticles are usually quite sophisticated and are limited to specific applications. Herein, we developed simple biosensors based on the structure of kissing-hairpin. Through hybridization amplification of these nanomachines, the evolved MBs could greatly enhance the detected signals (approximately 10-fold higher than the signals generated by traditional molecular beacons), reduce the sensing limits for targets and, remarkably, distinguish single-base mismatches specifically for nucleic acid detection. In addition, these new MBs can be directly applied in living cells. By introducing aptamer sequences, these novel sensors can also detect proteins and small molecules. These properties were exemplified by the detection of both the β-actin gene and thrombin. The simplicity, sensitivity and flexibility of these devices make them appropriate for more expansive applications.
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Affiliation(s)
- Shuo Feng
- College of Chemistry and Molecular Sciences, Key Laboratory of Biomedical Polymers of Ministry of Education, State Key Laboratory of Virology, Wuhan University, Wuhan, Hubei, 430072, PR China
| | - Ye Shang
- College of Life Sciences, Wuhan University, Wuhan, Hubei, 430072, PR China
| | - Fan Wu
- College of Chemistry and Molecular Sciences, Key Laboratory of Biomedical Polymers of Ministry of Education, State Key Laboratory of Virology, Wuhan University, Wuhan, Hubei, 430072, PR China
| | - Fei Ding
- College of Chemistry and Molecular Sciences, Key Laboratory of Biomedical Polymers of Ministry of Education, State Key Laboratory of Virology, Wuhan University, Wuhan, Hubei, 430072, PR China
| | - Bin Li
- College of Chemistry and Molecular Sciences, Key Laboratory of Biomedical Polymers of Ministry of Education, State Key Laboratory of Virology, Wuhan University, Wuhan, Hubei, 430072, PR China
| | - Jiahui Xu
- College of Chemistry and Molecular Sciences, Key Laboratory of Biomedical Polymers of Ministry of Education, State Key Laboratory of Virology, Wuhan University, Wuhan, Hubei, 430072, PR China
| | - Liang Xu
- College of Chemistry and Molecular Sciences, Key Laboratory of Biomedical Polymers of Ministry of Education, State Key Laboratory of Virology, Wuhan University, Wuhan, Hubei, 430072, PR China
| | - Xiang Zhou
- College of Chemistry and Molecular Sciences, Key Laboratory of Biomedical Polymers of Ministry of Education, State Key Laboratory of Virology, Wuhan University, Wuhan, Hubei, 430072, PR China; State Key Laboratory of Natural and Biomimetic Drugs, Peking University, Beijing, PR China.
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7
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Ogawa A. Rational construction of eukaryotic OFF-riboswitches that downregulate internal ribosome entry site-mediated translation in response to their ligands. Bioorg Med Chem Lett 2012; 22:1639-42. [DOI: 10.1016/j.bmcl.2011.12.118] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2011] [Revised: 12/26/2011] [Accepted: 12/26/2011] [Indexed: 11/16/2022]
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Abstract
This protocol describes a new and rapid isothermal reaction process designed to amplify and detect a specific DNA sequence in purified DNA extracted from cultured cells. The protocol uses a DNA nanomachine that comprises two molecular switches that function in concert to isothermally amplify and detect a DNA target. First, a molecular beacon detection switch is 'activated' only if a DNA target sequence is present. A DNA primer and DNA polymerase are used to lock the beacon in an activated conformation. Second, an amplification and signal-transduction switch is initiated following successful activation. A nicking endonuclease and the DNA polymerase are used to replicate the DNA target. Both switches operate simultaneously at 40 °C in a single reaction to rapidly generate multiple copies of the DNA target in a cyclic polymerization reaction. This protocol enables femtomole amounts of a DNA target to be reproducibly amplified and detected in <40 min. We demonstrate the successful use of this protocol in assays containing synthetic DNA components and purified DNA extracted from biological samples.
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Affiliation(s)
- Ashley R Connolly
- Centre for Biomarker Research and Development, Australian Institute for Bioengineering and Nanotechnology, University of Queensland, St. Lucia, Brisbane, Queensland, Australia.
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Ogawa A. Multiple-Catalytic Sensing of Nucleic Acid Sequences by Utilising a DNA-RNA-DNA Chimeric Antisense Probe and RNase H with a Eukaryotic Cell-Free Translation System. Chembiochem 2011; 12:881-5. [DOI: 10.1002/cbic.201000744] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2010] [Indexed: 02/05/2023]
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10
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Sando S. Design of Functional Nucleic Acid Systems for Biomolecular Analysis. BULLETIN OF THE CHEMICAL SOCIETY OF JAPAN 2011. [DOI: 10.1246/bcsj.20100278] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
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11
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The ODN probes conjugating the Cu(II) complex enhance the luminol chemiluminescence by assembling on the DNA template. Bioorg Med Chem 2010; 18:8614-7. [PMID: 21115284 DOI: 10.1016/j.bmc.2010.10.007] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2010] [Revised: 10/02/2010] [Accepted: 10/05/2010] [Indexed: 11/21/2022]
Abstract
Potent peroxidase-like activity of the β-ketoenamine (1)-dicopper (II) complex (2) for the chemiluminescence (CL) of luminol either in the presence or absence of H(2)O(2) has been previously demonstrated by our group. In this study, the β-ketoenamine (1) as the ligand unit for copper(II) was incorporated into the oligonucleotide (ODN) probes. It has been shown that the catalytic activity of the ODN probes conjugating the ligand-Cu(II) complex is activated by hybridization with the target DNA with the complementary sequence. Thus, this study has successfully demonstrated the basic concept for the sensitive detection of nucleic acids by CL based on the template-inductive activation of the catalytic unit for CL.
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12
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Masu H, Narita A, Tokunaga T, Ohashi M, Aoyama Y, Sando S. An Activatable siRNA Probe: Trigger-RNA-Dependent Activation of RNAi Function. Angew Chem Int Ed Engl 2009; 48:9481-3. [DOI: 10.1002/anie.200903925] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022]
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13
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Masu H, Narita A, Tokunaga T, Ohashi M, Aoyama Y, Sando S. An Activatable siRNA Probe: Trigger-RNA-Dependent Activation of RNAi Function. Angew Chem Int Ed Engl 2009. [DOI: 10.1002/ange.200903925] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
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14
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Aoyama Y. Structure and Function of Molecular Assembly. A Personal Reminiscence. BULLETIN OF THE CHEMICAL SOCIETY OF JAPAN 2009. [DOI: 10.1246/bcsj.82.419] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
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15
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Muranaka N, Sharma V, Nomura Y, Yokobayashi Y. Efficient Design Strategy for Whole-Cell and Cell-Free Biosensors based on Engineered Riboswitches. ANAL LETT 2009. [DOI: 10.1080/00032710802568556] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
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16
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Sando S, Narita A, Hayami M, Aoyama Y. Transcription monitoring using fused RNA with a dye-binding light-up aptamer as a tag: a blue fluorescent RNA. Chem Commun (Camb) 2008:3858-60. [PMID: 18726014 DOI: 10.1039/b808449a] [Citation(s) in RCA: 73] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
The "light-up" RNA aptamer-Hoechst pair can be used as a fluorescent tag to monitor transcription processes.
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Affiliation(s)
- Shinsuke Sando
- Department of Synthetic Chemistry and Biological Chemistry, Graduate School of Engineering, Kyoto University, Katsura, Nishikyo-ku, Kyoto, Japan.
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17
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Ding C, Zhong H, Zhang S. Ultrasensitive flow injection chemiluminescence detection of DNA hybridization using nanoCuS tags. Biosens Bioelectron 2008; 23:1314-8. [DOI: 10.1016/j.bios.2007.12.005] [Citation(s) in RCA: 46] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/27/2007] [Revised: 11/24/2007] [Accepted: 12/10/2007] [Indexed: 11/29/2022]
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18
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Sando S, Narita A, Aoyama Y. Light-up Hoechst-DNA aptamer pair: generation of an aptamer-selective fluorophore from a conventional DNA-staining dye. Chembiochem 2008; 8:1795-803. [PMID: 17806095 DOI: 10.1002/cbic.200700325] [Citation(s) in RCA: 60] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Abstract
We have designed a strategy to generate a light-up fluorophore-aptamer pair based on a down-modification of a conventional DNA-staining dye to suppress its affinity to the original dsDNA targets, followed by reselection of aptamers that would bind to the modified dye. Following this line, we prepared a micropolarity-sensitive Hoechst derivative possessing two tBu groups with low affinity to the usual AT-rich dsDNA targets. DNA aptamers selected in vitro from a random pool worked as triggers to enhance the fluorescence of an otherwise nonfluorescent Hoechst derivative, and the shortened 25-mer sequence showed remarkable enhancement (light-up). The 25-mer sequence was split into binary aptamer probes, thus enabling us to detect a target nucleic acid sequence with a single-nucleotide resolution by use of unmodified DNA as a probe.
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Affiliation(s)
- Shinsuke Sando
- Department of Synthetic Chemistry and Biological Chemistry, Graduate School of Engineering, Kyoto University, Katsura, Nishikyo-ku, Kyoto 615-8510, Japan.
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Narita A, Ogawa K, Sando S, Aoyama Y. Cis-regulatory hairpin-shaped mRNA encoding a reporter protein: catalytic sensing of nucleic acid sequence at single nucleotide resolution. Nat Protoc 2008; 2:1105-16. [PMID: 17546001 DOI: 10.1038/nprot.2007.140] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Abstract
DNA sensing at a single nucleotide resolution is achieved using a hairpin-shaped, unmodified (unlabeled) RNA probe or the precursor double-stranded DNA (dsDNA) in a prokaryotic cell-free translation medium. The molecular-beacon-like probe consists of a loop region that is complementary to the target sequence and a stem composed of a ribosome-binding site (RBS) and its docking domain; the RBS is followed by the gene for a reporter protein such as luciferase or beta-galactosidase. Target binding at the loop opens the hairpin to make RBS accessible by the ribosome to start translation of the reporter protein. This sensing system is signal amplifying by virtue of catalytic DNA-to-RNA transcription when using a dsDNA probe, catalytic RNA-to-protein translation, catalytic signal transduction by the enzymatic reaction of the translated reporter protein and, in the presence of RNase H, catalytic or even irreversible translation-activation of the target-probe heteroduplex. Preparation of a probe takes 1-3 d and gene sensing using the probe takes 1-3 h.
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Affiliation(s)
- Atsushi Narita
- Department of Synthetic Chemistry and Biological Chemistry, Graduate School of Engineering, Kyoto University, Katsura, Nishikyo-ku, Kyoto 615-8510, Japan
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Saito H, Inoue T. RNA and RNP as new molecular parts in synthetic biology. J Biotechnol 2007; 132:1-7. [PMID: 17875338 DOI: 10.1016/j.jbiotec.2007.07.952] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2007] [Accepted: 07/22/2007] [Indexed: 12/29/2022]
Abstract
Synthetic biology has a promising outlook in biotechnology and for understanding the self-organizing principle of biological molecules in life. However, synthetic biologists have been looking for new molecular "parts" that function as modular units required in designing and constructing new "devices" and "systems" for regulating cell function because the number of such parts is strictly limited at present. In this review, we focus on RNA/ribonucleoprotein (RNP) architectures that hold promise as new "parts" for synthetic biology. They are constructed with molecular design and an experimental evolution technique. So far, designed self-folding RNAs, RNA (RNP) enzymes, and nanoscale RNA architectures have been successfully constructed by utilizing Watson-Crick base-pairs together with specific RNA-RNA or RNA-protein binding motifs of known defined 3D structures. Riboregulators for regulating targeted gene expression have also been designed and produced in vitro as well as in vivo. Lately, RNA and ribonucleoprotein complexes have been strongly attracting the attention of molecular biologists because a variety of noncoding RNAs discovered in nature perform spatiotemporal gene expressions. Thus we hope that newly accumulating knowledge on naturally occurring RNAs and RNP complexes will provide a variety of new parts, devices and systems for synthetic biology.
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Affiliation(s)
- Hirohide Saito
- Department of Gene Mechanisms, Graduate School of Biostudies, Kyoto University, Kyoto 606-8502, Japan; ICORP, Japan Science and Technology Corporation (JST), Honcho, Kawaguchi-shi, Saitama 332-0012, Japan.
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21
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Ihara T, Mukae M. Homogeneous DNA-detection based on the non-enzymatic reactions promoted by target DNA. ANAL SCI 2007; 23:625-9. [PMID: 17575342 DOI: 10.2116/analsci.23.625] [Citation(s) in RCA: 15] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
Abstract
Much effort has focused on methods for detecting various genetic differences in individuals, including single nucleotide polymorphisms (SNPs). SNP can be characterized as a substitution, insertion, or deletion at a single base position on a DNA strand. There is expected to be on average one SNP for every 1000 bases of the human genome, and some variations located in genes are suspected to alter both the protein structure and the expression level. Therefore, highly sensitive techniques with a simple procedure would be desirable for a high-throughput screening of millions of SNPs widely dispersed throughout the human genome. In this short review, we consider recently reported unique techniques for genotyping in a homogeneous solution, and organize them in terms of the chemical and physical processes accelerated on DNA.
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Affiliation(s)
- Toshihiro Ihara
- Department of Applied Chemistry and Biochemistry, Graduate School of Science and Technology, Kumamoto University, Japan.
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22
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Graf N, Göritz M, Krämer R. A metal-ion-releasing probe for DNA detection by catalytic signal amplification. Angew Chem Int Ed Engl 2007; 45:4013-5. [PMID: 16683284 DOI: 10.1002/anie.200504319] [Citation(s) in RCA: 55] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
Affiliation(s)
- Nora Graf
- Anorganisch-Chemisches Institut, Universität Heidelberg, Im Neuenheimer Feld 270, 69120 Heidelberg, Germany.
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23
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Narita A, Ogawa K, Sando S, Aoyama Y. Visible sensing of nucleic acid sequences with a genetically encodable unmodified RNA probe. Angew Chem Int Ed Engl 2007; 45:2879-83. [PMID: 16550617 DOI: 10.1002/anie.200503836] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Affiliation(s)
- Atsushi Narita
- Department of Synthetic Chemistry and Biological Chemistry, Graduate School of Engineering, Kyoto University, Katsura, Nishikyo-ku, Kyoto 615-8510, Japan
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24
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Ogawa A, Maeda M. Aptazyme-based riboswitches as label-free and detector-free sensors for cofactors. Bioorg Med Chem Lett 2007; 17:3156-60. [PMID: 17391960 DOI: 10.1016/j.bmcl.2007.03.033] [Citation(s) in RCA: 47] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2007] [Revised: 03/07/2007] [Accepted: 03/10/2007] [Indexed: 11/20/2022]
Abstract
We constructed a label-free and detector-free aptazyme-based riboswitch sensor for detecting the cofactor of the aptazyme. This riboswitch, which usually suppresses the gene expression with its anti-RBS sequence bound to the RBS of its own mRNA (OFF), activates the translation only when a cofactor is added to release the anti-RBS sequence from itself as a result of cofactor-induced self-cleavage by the aptazyme (ON). The rationally optimized one with beta-galactosidase as a reporter gene enabled us to detect the cofactor of the aptazyme visibly with high ON/OFF efficiency.
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Affiliation(s)
- Atsushi Ogawa
- Bioengineering Laboratory, RIKEN (The Institute of Physical and Chemical Research), 2-1 Hirosawa, Wako, Saitama 351-0198, Japan.
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25
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Abstract
RNA molecules play important and diverse regulatory roles in the cell by virtue of their interaction with other nucleic acids, proteins and small molecules. Inspired by this natural versatility, researchers have engineered RNA molecules with new biological functions. In the last two years efforts in synthetic biology have produced novel, synthetic RNA components capable of regulating gene expression in vivo largely in bacteria and yeast, setting the stage for scalable and programmable cellular behavior. Immediate challenges for this emerging field include determining how computational and directed-evolution techniques can be implemented to increase the complexity of engineered RNA systems, as well as determining how such systems can be broadly extended to mammalian systems. Further challenges include designing RNA molecules to be sensors of intracellular and environmental stimuli, probes to explore the behavior of biological networks and components of engineered cellular control systems.
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Affiliation(s)
- Farren J Isaacs
- Department of Genetics, Harvard Medical School, Boston, Massachusetts 02115, USA.
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26
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Graf N, Göritz M, Krämer R. Eine Metallionen freisetzende Sonde für den DNA-Nachweis durch katalytische Signalverstärkung. Angew Chem Int Ed Engl 2006. [DOI: 10.1002/ange.200504319] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
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27
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Narita A, Ogawa K, Sando S, Aoyama Y. Visible Sensing of Nucleic Acid Sequences with a Genetically Encodable Unmodified RNA Probe. Angew Chem Int Ed Engl 2006. [DOI: 10.1002/ange.200503836] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
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28
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Abstract
In this article we unify a series of recent studies on bio- and chemosensors under a single signaling strategy: signal amplification by allosteric catalysis (SAAC). The SAAC strategy mimics biological signal transduction processes, where molecular recognition between an external signal and a protein receptor is allosterically transduced into catalytically amplified chemical information (usually second messengers). Several recent biosensing and chemosensing studies apply this nature-inspired strategy by using engineered allosteric enzymes, ribozymes, or regulatable organic catalysts. The factors pertinent to achieving high sensitivity and specificity in SAAC strategies are analyzed. The authors believe that these early studies from a variety of research groups have opened up a new venue for the development of sensing technologies where molecular recognition and catalysis can be coupled for practical purposes.
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Affiliation(s)
- Lei Zhu
- Department of Chemistry and Biochemistry, University of Texas at Austin, Austin, TX 78712, USA
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29
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