1
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Mizuuchi R, Ichihashi N. Minimal RNA self-reproduction discovered from a random pool of oligomers. Chem Sci 2023; 14:7656-7664. [PMID: 37476714 PMCID: PMC10355099 DOI: 10.1039/d3sc01940c] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2023] [Accepted: 06/18/2023] [Indexed: 07/22/2023] Open
Abstract
The emergence of RNA self-reproduction from prebiotic components would have been crucial in developing a genetic system during the origins of life. However, all known self-reproducing RNA molecules are complex ribozymes, and how they could have arisen from abiotic materials remains unclear. Therefore, it has been proposed that the first self-reproducing RNA may have been short oligomers that assemble their components as templates. Here, we sought such minimal RNA self-reproduction in prebiotically accessible short random RNA pools that undergo spontaneous ligation and recombination. By examining enriched RNA families with common motifs, we identified a 20-nucleotide (nt) RNA variant that self-reproduces via template-directed ligation of two 10 nt oligonucleotides. The RNA oligomer contains a 2'-5' phosphodiester bond, which typically forms during prebiotically plausible RNA synthesis. This non-canonical linkage helps prevent the formation of inactive complexes between self-complementary oligomers while decreasing the ligation efficiency. The system appears to possess an autocatalytic property consistent with exponential self-reproduction despite the limitation of forming a ternary complex of the template and two substrates, similar to the behavior of a much larger ligase ribozyme. Such a minimal, ribozyme-independent RNA self-reproduction may represent the first step in the emergence of an RNA-based genetic system from primordial components. Simultaneously, our examination of random RNA pools highlights the likelihood that complex species interactions were necessary to initiate RNA reproduction.
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Affiliation(s)
- Ryo Mizuuchi
- Department of Electrical Engineering and Bioscience, Faculty of Science and Engineering, Waseda University Shinjuku Tokyo 162-8480 Japan
- JST, FOREST Kawaguchi Saitama 332-0012 Japan
| | - Norikazu Ichihashi
- Komaba Institute for Science, The University of Tokyo Meguro Tokyo 153-8902 Japan
- Department of Life Science, Graduate School of Arts and Science, The University of Tokyo Meguro Tokyo 153-8902 Japan
- Universal Biology Institute, The University of Tokyo Meguro Tokyo 153-8902 Japan
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2
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Wrist A, Sun W, Summers RM. The Theophylline Aptamer: 25 Years as an Important Tool in Cellular Engineering Research. ACS Synth Biol 2020; 9:682-697. [PMID: 32142605 DOI: 10.1021/acssynbio.9b00475] [Citation(s) in RCA: 32] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
The theophylline aptamer was isolated from an oligonucleotide library in 1994. Since that time, the aptamer has found wide utility, particularly in synthetic biology, cellular engineering, and diagnostic applications. The primary application of the theophylline aptamer is in the construction and characterization of synthetic riboswitches for regulation of gene expression. These riboswitches have been used to control cellular motility, regulate carbon metabolism, construct logic gates, screen for mutant enzymes, and control apoptosis. Other applications of the theophylline aptamer in cellular engineering include regulation of RNA interference and genome editing through CRISPR systems. Here we describe the uses of the theophylline aptamer for cellular engineering over the past 25 years. In so doing, we also highlight important synthetic biology applications to control gene expression in a ligand-dependent manner.
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Affiliation(s)
- Alexandra Wrist
- Department of Chemical and Biological Engineering, The University of Alabama, Tuscaloosa, Alabama 35487, United States
| | - Wanqi Sun
- Department of Chemical and Biological Engineering, The University of Alabama, Tuscaloosa, Alabama 35487, United States
| | - Ryan M. Summers
- Department of Chemical and Biological Engineering, The University of Alabama, Tuscaloosa, Alabama 35487, United States
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3
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An RNA polymerase ribozyme that synthesizes its own ancestor. Proc Natl Acad Sci U S A 2020; 117:2906-2913. [PMID: 31988127 DOI: 10.1073/pnas.1914282117] [Citation(s) in RCA: 49] [Impact Index Per Article: 12.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022] Open
Abstract
The RNA-based organisms from which modern life is thought to have descended would have depended on an RNA polymerase ribozyme to copy functional RNA molecules, including copying the polymerase itself. Such a polymerase must have been capable of copying structured RNAs with high efficiency and high fidelity to maintain genetic information across successive generations. Here the class I RNA polymerase ribozyme was evolved in vitro for the ability to synthesize functional ribozymes, resulting in the markedly improved ability to synthesize complex RNAs using nucleoside 5'-triphosphate (NTP) substrates. The polymerase is descended from the class I ligase, which contains the same catalytic core as the polymerase. The class I ligase can be synthesized by the improved polymerase as three separate RNA strands that assemble to form a functional ligase. The polymerase also can synthesize the complement of each of these three strands. Despite this remarkable level of activity, only a very small fraction of the assembled ligases retain catalytic activity due to the presence of disabling mutations. Thus, the fidelity of RNA polymerization should be considered a major impediment to the construction of a self-sustained, RNA-based evolving system. The propagation of heritable information requires both efficient and accurate synthesis of genetic molecules, a requirement relevant to both laboratory systems and the early history of life on Earth.
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4
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Development of a histamine aptasensor for food safety monitoring. Sci Rep 2019; 9:16659. [PMID: 31723193 PMCID: PMC6853955 DOI: 10.1038/s41598-019-52876-1] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2019] [Accepted: 10/16/2019] [Indexed: 12/13/2022] Open
Abstract
Histamine produced by bacteria through decarboxylation of histidine in spoiled foods such as fish is known to cause food poisoning. Therefore, accurate and facile measurement of histamine is of practical importance. Using the recently discovered RNA aptamer that specifically recognizes histamine (A1-949 aptamer), we developed an aptasensor based on the structure-switching mechanism. Specifically, the aptamer A1-949 was fluorescently labeled at the 5′ end and hybridized with a short quencher DNA strand that is partially complementary to the aptamer. The quencher strand was modified with a fluorescence quencher at its 3′ terminus. Displacement of the quencher strand upon histamine binding results in an increased fluorescence. After optimizing the assay condition, the enantiomeric version of the aptasensor (L-RNA and L-DNA) was synthesized which could detect the achiral analyte with identical sensitivity and improved biochemical stability. The aptasensor performance was validated by measuring fish samples spiked with known concentrations of histamine. Finally, histamine content in spoiled fish samples was measured, and the results were compared with the measurements using a commercial enzymatic assay kit.
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5
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Luo X, Chen Z, Li H, Li W, Cui L, Huang J. Exploiting the application of l-aptamer with excellent stability: an efficient sensing platform for malachite green in fish samples. Analyst 2019; 144:4204-4209. [PMID: 31187804 DOI: 10.1039/c9an00332k] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
Effective monitoring of the content of malachite green (MG) in aquaculture is of great importance for food safety. Traditional methods for MG assay, such as chromatography and spectroscopy, have been criticized for expensive instrumentation and complicated pretreatments. An MG RNA aptamer (MGA) is a powerful tool for immediate and rapid detection of MG. However, RNA is easily degraded by nucleases and is unstable in the environment, making accurate and reliable detection of MG difficult. In order to address the problems, an innovative levo (l)-MGA with excellent stability is designed to perform the specific recognition function. Interestingly, the gel electrophoresis and fluorescence measurement results indicate that this unnaturally occurring l-aptamer is resistant to nuclease degradation and it can be kept intact in the standard buffer solution under room temperature for quite a long time. A label-free, simple, and efficient method has been developed for sensitive detection of MG in fish tissue, which holds promising potential in food analysis and environmental monitoring.
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Affiliation(s)
- Xiaowei Luo
- Guangdong Provincial Key Laboratory of Construction and Detection in Tissue Engineering, Guangdong Provincial Key Laboratory of Medical Image Processing, Biomaterials Research Center, School of Biomedical Engineering, Southern Medical University, Guangzhou 510515, China. and Department of Chemistry, University of Washington, Washington 98195, USA
| | - Zhifeng Chen
- Guangdong Provincial Key Laboratory of Construction and Detection in Tissue Engineering, Guangdong Provincial Key Laboratory of Medical Image Processing, Biomaterials Research Center, School of Biomedical Engineering, Southern Medical University, Guangzhou 510515, China.
| | - Hongfeng Li
- Guangdong Provincial Key Laboratory of Construction and Detection in Tissue Engineering, Guangdong Provincial Key Laboratory of Medical Image Processing, Biomaterials Research Center, School of Biomedical Engineering, Southern Medical University, Guangzhou 510515, China.
| | - Wenqin Li
- Guangdong Provincial Key Laboratory of Construction and Detection in Tissue Engineering, Guangdong Provincial Key Laboratory of Medical Image Processing, Biomaterials Research Center, School of Biomedical Engineering, Southern Medical University, Guangzhou 510515, China.
| | - Liang Cui
- Department of Chemistry, Zhejiang Sci-Tech University, Hangzhou 310008, China.
| | - Jiahao Huang
- Guangdong Provincial Key Laboratory of Construction and Detection in Tissue Engineering, Guangdong Provincial Key Laboratory of Medical Image Processing, Biomaterials Research Center, School of Biomedical Engineering, Southern Medical University, Guangzhou 510515, China.
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6
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Röthlisberger P, Hollenstein M. Aptamer chemistry. Adv Drug Deliv Rev 2018; 134:3-21. [PMID: 29626546 DOI: 10.1016/j.addr.2018.04.007] [Citation(s) in RCA: 215] [Impact Index Per Article: 35.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2018] [Revised: 03/28/2018] [Accepted: 04/03/2018] [Indexed: 12/12/2022]
Abstract
Aptamers are single-stranded DNA or RNA molecules capable of tightly binding to specific targets. These functional nucleic acids are obtained by an in vitro Darwinian evolution method coined SELEX (Systematic Evolution of Ligands by EXponential enrichment). Compared to their proteinaceous counterparts, aptamers offer a number of advantages including a low immunogenicity, a relative ease of large-scale synthesis at affordable costs with little or no batch-to-batch variation, physical stability, and facile chemical modification. These alluring properties have propelled aptamers into the forefront of numerous practical applications such as the development of therapeutic and diagnostic agents as well as the construction of biosensing platforms. However, commercial success of aptamers still proceeds at a weak pace. The main factors responsible for this delay are the susceptibility of aptamers to degradation by nucleases, their rapid renal filtration, suboptimal thermal stability, and the lack of functional group diversity. Here, we describe the different chemical methods available to mitigate these shortcomings. Particularly, we describe the chemical post-SELEX processing of aptamers to include functional groups as well as the inclusion of modified nucleoside triphosphates into the SELEX protocol. These methods will be illustrated with successful examples of chemically modified aptamers used as drug delivery systems, in therapeutic applications, and as biosensing devices.
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7
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Kosikova T, Philp D. Exploring the emergence of complexity using synthetic replicators. Chem Soc Rev 2018; 46:7274-7305. [PMID: 29099123 DOI: 10.1039/c7cs00123a] [Citation(s) in RCA: 59] [Impact Index Per Article: 9.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
A significant number of synthetic systems capable of replicating themselves or entities that are complementary to themselves have appeared in the last 30 years. Building on an understanding of the operation of synthetic replicators in isolation, this field has progressed to examples where catalytic relationships between replicators within the same network and the extant reaction conditions play a role in driving phenomena at the level of the whole system. Systems chemistry has played a pivotal role in the attempts to understand the origin of biological complexity by exploiting the power of synthetic chemistry, in conjunction with the molecular recognition toolkit pioneered by the field of supramolecular chemistry, thereby permitting the bottom-up engineering of increasingly complex reaction networks from simple building blocks. This review describes the advances facilitated by the systems chemistry approach in relating the expression of complex and emergent behaviour in networks of replicators with the connectivity and catalytic relationships inherent within them. These systems, examined within well-stirred batch reactors, represent conceptual and practical frameworks that can then be translated to conditions that permit replicating systems to overcome the fundamental limits imposed on selection processes in networks operating under closed conditions. This shift away from traditional spatially homogeneous reactors towards dynamic and non-equilibrium conditions, such as those provided by reaction-diffusion reaction formats, constitutes a key change that mimics environments within cellular systems, which possess obvious compartmentalisation and inhomogeneity.
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Affiliation(s)
- Tamara Kosikova
- School of Chemistry and EaStCHEM, University of St Andrews, North Haugh, St Andrews, Fife KY16 9ST, UK.
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8
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Chovelon B, Fiore E, Faure P, Peyrin E, Ravelet C. Mirror-image aptamer kissing complex for arginine-vasopressin sensing. Anal Chim Acta 2017; 1001:143-150. [PMID: 29291797 DOI: 10.1016/j.aca.2017.11.043] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2017] [Revised: 11/03/2017] [Accepted: 11/13/2017] [Indexed: 12/31/2022]
Abstract
The recently reported aptamer kissing complex (AKC) strategy has allowed for the development of a new kind of sandwich-like sensing tools. Currently AKC assays have been only applied to low molecular weight molecules and their functionality in complex matrices remains challenging. The objective of the present study broken down into two sub-aims; exploring the propensity to broaden the scope of detectable analytes and designing a more robust system for potential applications to realistic samples. An all L-configuration aptaswitch module derived from a hairpin spiegelmer specific to a larger target, i.e. the arginine-vasopressin (AVP) hormone, was elaborated. The target-induced AKC formation in presence of a specific mirror-image RNA hairpin (L-aptakiss) probe were analyzed by using fluorescence anisotropy. The mirror-image kissing complex was successfully formed when the L-AVP target bound to the engineered L-aptaswitch element. It was also established that the use of methanol as cosolvent significantly improved the assay sensitivity through the stabilization of the ternary complex. Finally, the capability of the mirror-image method to operate in 10-fold diluted, untreated human serum was illustrated. The current work revealed that the AKC concept can be expanded to a wider range of targets and converted to a L-configuration sensing platform especially suitable for bioanalysis purposes.
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Affiliation(s)
- Benoit Chovelon
- University Grenoble Alpes, DPM UMR 5063, F-38041 Grenoble, France; CNRS, DPM UMR 5063, F-38041 Grenoble, France; Département de Biochimie, Toxicologie et Pharmacologie, CHU de Grenoble Site Nord - Institut de Biologie et de Pathologie, F-38041 Grenoble, France
| | - Emmanuelle Fiore
- University Grenoble Alpes, DPM UMR 5063, F-38041 Grenoble, France; CNRS, DPM UMR 5063, F-38041 Grenoble, France; Département de Biochimie, Toxicologie et Pharmacologie, CHU de Grenoble Site Nord - Institut de Biologie et de Pathologie, F-38041 Grenoble, France
| | - Patrice Faure
- Département de Biochimie, Toxicologie et Pharmacologie, CHU de Grenoble Site Nord - Institut de Biologie et de Pathologie, F-38041 Grenoble, France; University Grenoble Alpes, Laboratory of Hypoxy Physiopathology Study Inserm U1042, 38700 La Tronche, France
| | - Eric Peyrin
- University Grenoble Alpes, DPM UMR 5063, F-38041 Grenoble, France; CNRS, DPM UMR 5063, F-38041 Grenoble, France.
| | - Corinne Ravelet
- University Grenoble Alpes, DPM UMR 5063, F-38041 Grenoble, France; CNRS, DPM UMR 5063, F-38041 Grenoble, France.
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9
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Chen H, Xie S, Liang H, Wu C, Cui L, Huan SY, Zhang X. Generation of Biostable L-aptamers against Achiral Targets by Chiral Inversion of Existing D-aptamers. Talanta 2016; 164:662-667. [PMID: 28107987 DOI: 10.1016/j.talanta.2016.11.001] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2016] [Revised: 10/22/2016] [Accepted: 11/01/2016] [Indexed: 01/01/2023]
Abstract
In this paper, based on reciprocal chiral substrate specificity, taking achiral molecules, ethanolamine (EA) and malachite green (MG) as two model targets, biostable L- DNA aptamers and L-RNA aptamers were generated respectively by chiral inversion of existing D-aptamers. In the detection of EA with L-DNA aptamer-based sensors, the feasibility of our strategy was confirmed, while in the detection of MG with L-RNA aptamers, linear calibration curves were obtained in the range from 0.1 to 5µm with the detection limit of 0.065µm under optimized experimental conditions. The results demonstrated that the mirror-image L-aptamers have identical recognition capability as D-aptamers. Meanwhile, L-aptamers have superior biostability to resist nuclease digestion, protein binding interference and off-target effects, enabling their applications in complex practical samples, such as lake water and fish tissue extractions. Our work provides a simple, yet universal and efficient way to develop biostable aptamers.
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Affiliation(s)
- Huapei Chen
- Molecular Science and Biomedicine Laboratory, State Key Laboratory for Chemo/Bio Sensing and Chemometrics, College of Chemistry and Chemical Engineering, College of Biology, and Collaborative Research Center of Molecular Engineering for Theranostics, Hunan University, Changsha 410082, China
| | - Sitao Xie
- Molecular Science and Biomedicine Laboratory, State Key Laboratory for Chemo/Bio Sensing and Chemometrics, College of Chemistry and Chemical Engineering, College of Biology, and Collaborative Research Center of Molecular Engineering for Theranostics, Hunan University, Changsha 410082, China
| | - Hao Liang
- Molecular Science and Biomedicine Laboratory, State Key Laboratory for Chemo/Bio Sensing and Chemometrics, College of Chemistry and Chemical Engineering, College of Biology, and Collaborative Research Center of Molecular Engineering for Theranostics, Hunan University, Changsha 410082, China
| | - Cuichen Wu
- Attribute Sciences, Amgen, One Amgen Center Drive, Thousand Oaks, CA 91320, United States
| | - Liang Cui
- Molecular Science and Biomedicine Laboratory, State Key Laboratory for Chemo/Bio Sensing and Chemometrics, College of Chemistry and Chemical Engineering, College of Biology, and Collaborative Research Center of Molecular Engineering for Theranostics, Hunan University, Changsha 410082, China.
| | - Shuang-Yan Huan
- Molecular Science and Biomedicine Laboratory, State Key Laboratory for Chemo/Bio Sensing and Chemometrics, College of Chemistry and Chemical Engineering, College of Biology, and Collaborative Research Center of Molecular Engineering for Theranostics, Hunan University, Changsha 410082, China
| | - Xiaobing Zhang
- Molecular Science and Biomedicine Laboratory, State Key Laboratory for Chemo/Bio Sensing and Chemometrics, College of Chemistry and Chemical Engineering, College of Biology, and Collaborative Research Center of Molecular Engineering for Theranostics, Hunan University, Changsha 410082, China.
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10
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Real-Time Detection of a Self-Replicating RNA Enzyme. Molecules 2016; 21:molecules21101310. [PMID: 27706059 PMCID: PMC5108293 DOI: 10.3390/molecules21101310] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2016] [Revised: 09/25/2016] [Accepted: 09/27/2016] [Indexed: 12/03/2022] Open
Abstract
A system was developed to detect the self-replication of an RNA enzyme in real time. The enzyme is an RNA ligase that undergoes exponential amplification at a constant temperature and can be made to operate in a ligand-dependent manner. The real-time system is based on a fluorimetric readout that directly couples the ligation event to an increase in florescence signal that can be monitored using standard instrumentation. The real-time system can also operate entirely with l-RNA, which is not susceptible to degradation by ribonucleases that are present in biological samples. The system is analogous to real-time PCR, but with the potential to detect small molecules, proteins, and other targets that can be recognized by a suitable aptamer. The ligand-dependent self-replication of RNA has potential applications in molecular diagnostics and biosensing that benefit from the rapid, precise, and real-time detection of various target molecules.
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11
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Olea C, Weidmann J, Dawson PE, Joyce GF. An L-RNA Aptamer that Binds and Inhibits RNase. ACTA ACUST UNITED AC 2016; 22:1437-1441. [PMID: 26590636 DOI: 10.1016/j.chembiol.2015.09.017] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2015] [Revised: 08/26/2015] [Accepted: 09/01/2015] [Indexed: 11/27/2022]
Abstract
L-RNA aptamers were developed that bind to barnase RNase and thereby inhibit the function of the enzyme. These aptamers were obtained by first carrying out in vitro selection of D-RNAs that bind to the full-length synthetic D-enantiomer of barnase, then reversing the mirror and preparing L-RNAs of identical sequence that similarly bind to natural L-barnase. The resulting L-aptamers bind L-barnase with an affinity of ∼100 nM and function as competitive inhibitors of enzyme cleavage of D-RNA substrates. L-RNA aptamers are resistant to degradation by ribonucleases, thus enabling them to function in biological samples, most notably for applications in molecular diagnostics and therapeutics. In addition to the irony of using RNA to inhibit RNase, L-RNA aptamers such as those described here could be used to measure the concentration or inhibit the function of RNase in the laboratory or in biological systems.
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Affiliation(s)
- Charles Olea
- Department of Chemistry and The Skaggs Institute for Chemical Biology, The Scripps Research Institute, 10550 North Torrey Pines Road, La Jolla, CA 92037, USA
| | - Joachim Weidmann
- Department of Chemistry and The Skaggs Institute for Chemical Biology, The Scripps Research Institute, 10550 North Torrey Pines Road, La Jolla, CA 92037, USA; Division of Functional Genome Analysis, Deutsches Krebsforschungszentrum, Im Neuenheimer Feld 580, 69120 Heidelberg, Germany
| | - Philip E Dawson
- Department of Chemistry and The Skaggs Institute for Chemical Biology, The Scripps Research Institute, 10550 North Torrey Pines Road, La Jolla, CA 92037, USA
| | - Gerald F Joyce
- Department of Chemistry and The Skaggs Institute for Chemical Biology, The Scripps Research Institute, 10550 North Torrey Pines Road, La Jolla, CA 92037, USA.
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12
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Front waves in the early RNA world: The Schlögl model and the logistic growth model. J Theor Biol 2016; 392:62-8. [PMID: 26739373 DOI: 10.1016/j.jtbi.2015.11.027] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2015] [Revised: 11/15/2015] [Accepted: 11/23/2015] [Indexed: 11/24/2022]
Abstract
Front wave solutions of nonlinear reaction-diffusion models describing the spatio-temporal growth of RNA populations in the early RNA world are discussed. A two-variable model for RNA enzymes and enzyme complex molecules as well as single-variable models obtained via adiabatic elimination of the complex molecules are considered. In both models, the focus is on enzyme diffusion in one spatial dimension, assuming that the diffusion of complex molecules can be neglected. It is shown that one of the single-variable models corresponds to a Schlögl model of front propagation. In general, for the single-variable models it is found that front speed corresponds to the minimal speed of traveling fronts. In contrast, the two-variable model exhibits even slower front propagation. Front propagation might be an important factor in competitive evolutionary processes in the early RNA world.
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13
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Cui L, Peng R, Fu T, Zhang X, Wu C, Chen H, Liang H, Yang C, Tan W. Biostable L-DNAzyme for Sensing of Metal Ions in Biological Systems. Anal Chem 2016; 88:1850-5. [PMID: 26691677 PMCID: PMC4892185 DOI: 10.1021/acs.analchem.5b04170] [Citation(s) in RCA: 61] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2015] [Accepted: 12/22/2015] [Indexed: 12/13/2022]
Abstract
DNAzymes, an important type of metal ion-dependent functional nucleic acid, are widely applied in bioanalysis and biomedicine. However, the use of DNAzymes in practical applications has been impeded by the intrinsic drawbacks of natural nucleic acids, such as interferences from nuclease digestion and protein binding, as well as undesired intermolecular interactions with other nucleic acids. On the basis of reciprocal chiral substrate specificity, the enantiomer of D-DNAzyme, L-DNAzyme, could initiate catalytic cleavage activity with the same achiral metal ion as a cofactor. Meanwhile, by using the advantage of nonbiological L-DNAzyme, which is not subject to the interferences of biological matrixes, as recognition units, a facile and stable L-DNAzyme sensor was proposed for sensing metal ions in complex biological samples and live cells.
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Affiliation(s)
- Liang Cui
- Molecular
Science and Biomedicine Laboratory, State Key Laboratory for Chemo/Bio
Sensing and Chemometrics, College of Chemistry and Chemical Engineering,
College of Biology, and Collaborative Research Center of Molecular
Engineering for Theranostics, Hunan University, Changsha 410082, China
| | - Ruizi Peng
- Molecular
Science and Biomedicine Laboratory, State Key Laboratory for Chemo/Bio
Sensing and Chemometrics, College of Chemistry and Chemical Engineering,
College of Biology, and Collaborative Research Center of Molecular
Engineering for Theranostics, Hunan University, Changsha 410082, China
| | - Ting Fu
- Molecular
Science and Biomedicine Laboratory, State Key Laboratory for Chemo/Bio
Sensing and Chemometrics, College of Chemistry and Chemical Engineering,
College of Biology, and Collaborative Research Center of Molecular
Engineering for Theranostics, Hunan University, Changsha 410082, China
| | - Xiaobing Zhang
- Molecular
Science and Biomedicine Laboratory, State Key Laboratory for Chemo/Bio
Sensing and Chemometrics, College of Chemistry and Chemical Engineering,
College of Biology, and Collaborative Research Center of Molecular
Engineering for Theranostics, Hunan University, Changsha 410082, China
| | - Cuichen Wu
- Molecular
Science and Biomedicine Laboratory, State Key Laboratory for Chemo/Bio
Sensing and Chemometrics, College of Chemistry and Chemical Engineering,
College of Biology, and Collaborative Research Center of Molecular
Engineering for Theranostics, Hunan University, Changsha 410082, China
- Department
of Chemistry and Department of Physiology and Functional Genomics,
Center for Research at the Bio/Nano Interface, Health Cancer Center, University
of Florida, Gainesville, Florida 32611-7200, United States
| | - Huapei Chen
- Molecular
Science and Biomedicine Laboratory, State Key Laboratory for Chemo/Bio
Sensing and Chemometrics, College of Chemistry and Chemical Engineering,
College of Biology, and Collaborative Research Center of Molecular
Engineering for Theranostics, Hunan University, Changsha 410082, China
| | - Hao Liang
- Molecular
Science and Biomedicine Laboratory, State Key Laboratory for Chemo/Bio
Sensing and Chemometrics, College of Chemistry and Chemical Engineering,
College of Biology, and Collaborative Research Center of Molecular
Engineering for Theranostics, Hunan University, Changsha 410082, China
| | - Chaoyong
James Yang
- State
Key Laboratory of Physical Chemistry of Solid Surfaces, Key Laboratory
for Chemical Biology of Fujian Province, The MOE Key Laboratory of
Spectrochemical Analysis & Instrumentation, Department of Chemical
Biology, College of Chemistry and Chemical Engineering, Xiamen University, Xiamen 361005, P. R. China
| | - Weihong Tan
- Molecular
Science and Biomedicine Laboratory, State Key Laboratory for Chemo/Bio
Sensing and Chemometrics, College of Chemistry and Chemical Engineering,
College of Biology, and Collaborative Research Center of Molecular
Engineering for Theranostics, Hunan University, Changsha 410082, China
- Department
of Chemistry and Department of Physiology and Functional Genomics,
Center for Research at the Bio/Nano Interface, Health Cancer Center, University
of Florida, Gainesville, Florida 32611-7200, United States
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14
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Abstract
A review covering the previous 25 years study into self-replicating systems.
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Affiliation(s)
- Gregory Clixby
- University of Sheffield
- Department of Chemistry
- Sheffield
- UK
| | - Lance Twyman
- University of Sheffield
- Department of Chemistry
- Sheffield
- UK
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15
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Nowak P, Colomb-Delsuc M, Otto S, Li J. Template-Triggered Emergence of a Self-Replicator from a Dynamic Combinatorial Library. J Am Chem Soc 2015; 137:10965-9. [PMID: 26192814 DOI: 10.1021/jacs.5b04380] [Citation(s) in RCA: 36] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
Self-assembly of a specific member of a dynamic combinatorial library (DCL) may lead to self-replication of this molecule. However, if the concentration of the potential replicator in the DCL fails to exceed its critical aggregation concentration (CAC), then self-replication will not occur. We now show how addition of a template can raise the concentration of a library member-template complex beyond its CAC, leading to the onset of self-replication. Once in existence, the replicator aggregates promote further replication also in the absence of the template that induced the initial emergence of the replicator.
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Affiliation(s)
- Piotr Nowak
- Centre for Systems Chemistry, Stratingh Insitute, University of Groningen , Nijenborgh 4, 9747 AG Groningen, The Netherlands
| | - Mathieu Colomb-Delsuc
- Centre for Systems Chemistry, Stratingh Insitute, University of Groningen , Nijenborgh 4, 9747 AG Groningen, The Netherlands
| | - Sijbren Otto
- Centre for Systems Chemistry, Stratingh Insitute, University of Groningen , Nijenborgh 4, 9747 AG Groningen, The Netherlands
| | - Jianwei Li
- Centre for Systems Chemistry, Stratingh Insitute, University of Groningen , Nijenborgh 4, 9747 AG Groningen, The Netherlands
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16
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Singhal A, Nielsen PE. Cross-catalytic peptide nucleic acid (PNA) replication based on templated ligation. Org Biomol Chem 2015; 12:6901-7. [PMID: 25057801 DOI: 10.1039/c4ob01158a] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
We report the first PNA self-replicating system based on template directed cross-catalytic ligation, a process analogous to biological replication. Using two template PNAs and four pentameric precursor PNAs, all four possible carbodiimide assisted amide ligation products were detected and identified by HPLC and MALDI-TOF analysis. We conclude that the two template complementary reaction products are generated via cross-catalysis, while the other two self-complementary (and in principle auto-catalytic) products are formed via intra-complex coupling between the two sets of complementary PNA precursors. Cross-catalytic product formation followed product inhibited kinetics, but approximately two replication rounds were observed. Analogous but less efficient replication was found for a similar tetrameric system. These results demonstrate that simpler nucleobase replication systems than natural oligonucleotides are feasible, thereby strengthening the foundation for the discussion of a possible role for PNA (like) genetic material in the prebiotic evolution of life and lay the ground for further studies into evolution of such potentially prebiotic systems.
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Affiliation(s)
- Abhishek Singhal
- Department of Cellular and Molecular Medicine, Faculty of Health Sciences, University of Copenhagen, The Panum Institute, Blegdamsvej 3c, DK-2200 Copenhagen N, Denmark.
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17
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Hoehlig K, Bethge L, Klussmann S. Stereospecificity of oligonucleotide interactions revisited: no evidence for heterochiral hybridization and ribozyme/DNAzyme activity. PLoS One 2015; 10:e0115328. [PMID: 25679211 PMCID: PMC4334536 DOI: 10.1371/journal.pone.0115328] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2014] [Accepted: 11/13/2014] [Indexed: 11/18/2022] Open
Abstract
A major challenge for the application of RNA- or DNA-oligonucleotides in biotechnology and molecular medicine is their susceptibility to abundant nucleases. One intriguing possibility to tackle this problem is the use of mirror-image (l-)oligonucleotides. For aptamers, this concept has successfully been applied to even develop therapeutic agents, so-called Spiegelmers. However, for technologies depending on RNA/RNA or RNA/DNA hybridization, like antisense or RNA interference, it has not been possible to use mirror-image oligonucleotides because Watson-Crick base pairing of complementary strands is (thought to be) stereospecific. Many scientists consider this a general principle if not a dogma. A recent publication proposing heterochiral Watson-Crick base pairing and sequence-specific hydrolysis of natural RNA by mirror-image ribozymes or DNAzymes (and vice versa) prompted us to systematically revisit the stereospecificity of oligonucleotides hybridization and catalytic activity. Using hyperchromicity measurements we demonstrate that hybridization only occurs among homochiral anti-parallel complementary oligonucleotide strands. As expected, achiral PNA hybridizes to RNA and DNA irrespective of their chirality. In functional assays we could not confirm an alleged heterochiral hydrolytic activity of ribozymes or DNAzymes. Our results confirm a strict stereospecificity of oligonucleotide hybridization and clearly argue against the possibility to use mirror-image oligonucleotides for gene silencing or antisense applications.
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18
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Leonetti G, Otto S. Solvent composition dictates emergence in dynamic molecular networks containing competing replicators. J Am Chem Soc 2015; 137:2067-72. [PMID: 25584629 DOI: 10.1021/ja512644f] [Citation(s) in RCA: 38] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
Abstract
In Darwinian evolution, species that are better adapted to their environment win the competition for common resources from less well-adapted competitors. Thus, in such scenarios the nature of the environment may dictate the outcome of the competition. We investigated to what degree these biological principles acting at the level of species extend to the molecular level into systems based on fully synthetic self-replicating molecules. We now report two systems in which two replicators compete for a common building block and where the environment dictates which of the two replicators wins. We observed that subtle changes in the environment can lead to dramatic differences in the outcome of the competition.
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Affiliation(s)
- Giulia Leonetti
- Centre for Systems Chemistry, Stratingh Institute, University of Groningen , Nijenborgh 4, 9747 AG Groningen, The Netherlands
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19
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Ligand-dependent exponential amplification of self-replicating RNA enzymes. Methods Enzymol 2015. [PMID: 25605379 DOI: 10.1016/bs.mie.2014.10.030] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register]
Abstract
A general analytical method for the detection of target ligands has been developed, based on a special class of self-replicating aptazymes. These "autocatalytic aptazymes" are generated by linking an aptamer domain to the catalytic domain of a self-replicating RNA enzyme. Ligand-dependent self-replication of RNA proceeds in a self-sustained manner, undergoing exponential amplification at a constant temperature without the assistance of any proteins or other biological materials. The rate of exponential amplification is dependent on the concentration of the ligand, thus enabling quantitative ligand detection. This system has the potential to detect any ligand that can be recognized by an aptamer, including small molecules and proteins. The instability of RNA in biological samples due to the presence of ribonucleases can be overcome by employing the enantiomeric L-RNA form of the self-replicating enzyme. Methods for real-time fluorescence monitoring over the course of exponential amplification are currently being developed.
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20
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Urata S, Miyahata T, Matsuura H, Kitamura Y, Ihara T. Alteration of DNAzyme Activity by Silver Ion. CHEM LETT 2014. [DOI: 10.1246/cl.140197] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
Affiliation(s)
- Shoma Urata
- Department of Applied Chemistry and Biochemistry, Graduate School of Science and Technology, Kumamoto University
| | - Takaaki Miyahata
- Department of Applied Chemistry and Biochemistry, Graduate School of Science and Technology, Kumamoto University
| | - Hirotaka Matsuura
- Department of Applied Chemistry and Biochemistry, Graduate School of Science and Technology, Kumamoto University
| | - Yusuke Kitamura
- Department of Applied Chemistry and Biochemistry, Graduate School of Science and Technology, Kumamoto University
- CREST, Japan Science and Technology Agency
| | - Toshihiro Ihara
- Department of Applied Chemistry and Biochemistry, Graduate School of Science and Technology, Kumamoto University
- CREST, Japan Science and Technology Agency
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21
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Wyszko E, Mueller F, Gabryelska M, Bondzio A, Popenda M, Barciszewski J, Erdmann VA. Spiegelzymes® mirror-image hammerhead ribozymes and mirror-image DNAzymes, an alternative to siRNAs and microRNAs to cleave mRNAs in vivo? PLoS One 2014; 9:e86673. [PMID: 24489764 PMCID: PMC3906056 DOI: 10.1371/journal.pone.0086673] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2013] [Accepted: 12/12/2013] [Indexed: 02/02/2023] Open
Abstract
With the discovery of small non-coding RNA (ncRNA) molecules as regulators for cellular processes, it became intriguing to develop technologies by which these regulators can be applied in molecular biology and molecular medicine. The application of ncRNAs has significantly increased our knowledge about the regulation and functions of a number of proteins in the cell. It is surprising that similar successes in applying these small ncRNAs in biotechnology and molecular medicine have so far been very limited. The reasons for these observations may lie in the high complexity in which these RNA regulators function in the cells and problems with their delivery, stability and specificity. Recently, we have described mirror-image hammerhead ribozymes and DNAzymes (Spiegelzymes®) which can sequence-specifically hydrolyse mirror-image nucleic acids, such as our mirror-image aptamers (Spiegelmers) discovered earlier. In this paper, we show for the first time that Spiegelzymes are capable of recognising complementary enantiomeric substrates (D-nucleic acids), and that they efficiently hydrolyse them at submillimolar magnesium concentrations and at physiologically relevant conditions. The Spiegelzymes are very stable in human sera, and do not require any protein factors for their function. They have the additional advantages of being non-toxic and non-immunogenic. The Spiegelzymes can be used for RNA silencing and also as therapeutic and diagnostic tools in medicine. We performed extensive three-dimensional molecular modelling experiments with mirror-image hammerhead ribozymes and DNAzymes interacting with D-RNA targets. We propose a model in which L/D-double helix structures can be formed by natural Watson-Crick base pairs, but where the nucleosides of one of the two strands will occur in an anticlinal conformation. Interestingly enough, the duplexes (L-RNA/D-RNA and L-DNA/D-RNA) in these models can show either right- or left-handedness. This is a very new observation, suggesting that molecular symmetry of enantiomeric nucleic acids is broken down.
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Affiliation(s)
- Eliza Wyszko
- Institute of Bioorganic Chemistry of the Polish Academy of Sciences, Poznan, Poland
| | | | - Marta Gabryelska
- Institute of Bioorganic Chemistry of the Polish Academy of Sciences, Poznan, Poland
| | - Angelika Bondzio
- Institute for Biochemistry, Veterinary Medicine, Free University of Berlin, Berlin, Germany
| | - Mariusz Popenda
- Institute of Bioorganic Chemistry of the Polish Academy of Sciences, Poznan, Poland
| | - Jan Barciszewski
- Institute of Bioorganic Chemistry of the Polish Academy of Sciences, Poznan, Poland
| | - Volker A. Erdmann
- Institute for Chemistry and Biochemistry, Free University of Berlin, Berlin, Germany
- Erdmann Technologies GmbH, Berlin, Germany
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22
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Robertson MP, Joyce GF. Highly efficient self-replicating RNA enzymes. ACTA ACUST UNITED AC 2014; 21:238-45. [PMID: 24388759 DOI: 10.1016/j.chembiol.2013.12.004] [Citation(s) in RCA: 57] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2013] [Revised: 12/02/2013] [Accepted: 12/07/2013] [Indexed: 10/25/2022]
Abstract
An RNA enzyme has been developed that catalyzes the joining of oligonucleotide substrates to form additional copies of itself, undergoing self-replication with exponential growth. The enzyme also can cross-replicate with a partner enzyme, resulting in their mutual exponential growth and enabling self-sustained Darwinian evolution. The opportunity for inventive evolution within this synthetic genetic system depends on the diversity of the evolving population, which is limited by the catalytic efficiency of the enzyme. Directed evolution was used to improve the efficiency of the enzyme and increase its exponential growth rate to 0.14 min(-1), corresponding to a doubling time of 5 min. This is close to the limit of 0.21 min(-1) imposed by the rate of product release, but sufficient to enable more than 80 logs of growth per day.
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Affiliation(s)
- Michael P Robertson
- Department of Chemistry, The Scripps Research Institute, 10550 N. Torrey Pines Road, La Jolla, CA 92037, USA; Department of Molecular Biology, The Scripps Research Institute, 10550 N. Torrey Pines Road, La Jolla, CA 92037, USA; The Skaggs Institute for Chemical Biology, The Scripps Research Institute, 10550 N. Torrey Pines Road, La Jolla, CA 92037, USA
| | - Gerald F Joyce
- Department of Chemistry, The Scripps Research Institute, 10550 N. Torrey Pines Road, La Jolla, CA 92037, USA; Department of Molecular Biology, The Scripps Research Institute, 10550 N. Torrey Pines Road, La Jolla, CA 92037, USA; The Skaggs Institute for Chemical Biology, The Scripps Research Institute, 10550 N. Torrey Pines Road, La Jolla, CA 92037, USA.
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23
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Malakoutikhah M, Peyralans JJP, Colomb-Delsuc M, Fanlo-Virgós H, Stuart MCA, Otto S. Uncovering the selection criteria for the emergence of multi-building-block replicators from dynamic combinatorial libraries. J Am Chem Soc 2013; 135:18406-17. [PMID: 24219346 DOI: 10.1021/ja4067805] [Citation(s) in RCA: 81] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/22/2023]
Abstract
A family of self-replicating macrocycles was developed using dynamic combinatorial chemistry. Replication is driven by self-assembly of the replicators into fibrils and relies critically on mechanically induced fibril fragmentation. Analysis of separate dynamic combinatorial libraries made from one of six peptide-functionalized building blocks of different hydrophobicity revealed two selection criteria that govern the emergence of replicators from these systems. First, the replicators need to have a critical macrocycle size that endows them with sufficient multivalency to enable their self-assembly into fibrils. Second, efficient replication occurs only for library members that are of low abundance in the absence of a replication pathway. This work has led to spontaneous emergence of replicators with unrivalled structural complexity, being built from up to eight identical subunits and reaching a MW of up to 5.6 kDa. The insights obtained in this work provide valuable guidance that should facilitate future discovery of new complex self-replicating molecules. They may also assist in the development of new self-synthesizing materials, where self-assembly drives the synthesis of the very molecules that self-assemble. To illustrate the potential of this concept, the present system enables access to self-assembling materials made from self-synthesizing macrocycles with tunable ring size ranging from trimers to octamers.
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Affiliation(s)
- Morteza Malakoutikhah
- Centre for Systems Chemistry, Stratingh Institute, University of Groningen , Nijenborgh 4, 9747 AG Groningen, The Netherlands
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24
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Selck DA, Karymov MA, Sun B, Ismagilov RF. Increased robustness of single-molecule counting with microfluidics, digital isothermal amplification, and a mobile phone versus real-time kinetic measurements. Anal Chem 2013; 85:11129-36. [PMID: 24199852 DOI: 10.1021/ac4030413] [Citation(s) in RCA: 55] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/11/2023]
Abstract
Quantitative bioanalytical measurements are commonly performed in a kinetic format and are known to not be robust to perturbation that affects the kinetics itself or the measurement of kinetics. We hypothesized that the same measurements performed in a "digital" (single-molecule) format would show increased robustness to such perturbations. Here, we investigated the robustness of an amplification reaction (reverse-transcription loop-mediated amplification, RT-LAMP) in the context of fluctuations in temperature and time when this reaction is used for quantitative measurements of HIV-1 RNA molecules under limited-resource settings (LRS). The digital format that counts molecules using dRT-LAMP chemistry detected a 2-fold change in concentration of HIV-1 RNA despite a 6 °C temperature variation (p-value = 6.7 × 10(-7)), whereas the traditional kinetic (real-time) format did not (p-value = 0.25). Digital analysis was also robust to a 20 min change in reaction time, to poor imaging conditions obtained with a consumer cell-phone camera, and to automated cloud-based processing of these images (R(2) = 0.9997 vs true counts over a 100-fold dynamic range). Fluorescent output of multiplexed PCR amplification could also be imaged with the cell phone camera using flash as the excitation source. Many nonlinear amplification schemes based on organic, inorganic, and biochemical reactions have been developed, but their robustness is not well understood. This work implies that these chemistries may be significantly more robust in the digital, rather than kinetic, format. It also calls for theoretical studies to predict robustness of these chemistries and, more generally, to design robust reaction architectures. The SlipChip that we used here and other digital microfluidic technologies already exist to enable testing of these predictions. Such work may lead to identification or creation of robust amplification chemistries that enable rapid and precise quantitative molecular measurements under LRS. Furthermore, it may provide more general principles describing robustness of chemical and biological networks in digital formats.
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Affiliation(s)
- David A Selck
- Division of Chemistry and Chemical Engineering, California Institute of Technology , 1200 East California Boulevard, Pasadena, California 91125, United States
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25
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Ruiz-Mirazo K, Briones C, de la Escosura A. Prebiotic Systems Chemistry: New Perspectives for the Origins of Life. Chem Rev 2013; 114:285-366. [DOI: 10.1021/cr2004844] [Citation(s) in RCA: 563] [Impact Index Per Article: 51.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Affiliation(s)
- Kepa Ruiz-Mirazo
- Biophysics
Unit (CSIC-UPV/EHU), Leioa, and Department of Logic and Philosophy
of Science, University of the Basque Country, Avenida de Tolosa 70, 20080 Donostia−San Sebastián, Spain
| | - Carlos Briones
- Department
of Molecular Evolution, Centro de Astrobiología (CSIC−INTA, associated to the NASA Astrobiology Institute), Carretera de Ajalvir, Km 4, 28850 Torrejón de Ardoz, Madrid, Spain
| | - Andrés de la Escosura
- Organic
Chemistry Department, Universidad Autónoma de Madrid, Cantoblanco, 28049 Madrid, Spain
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26
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Abstract
An L-RNA aptamer was developed that binds the natural D-form of the HIV-1 trans-activation responsive (TAR) RNA. The aptamer initially was obtained as a D-aptamer against L-TAR RNA through in vitro selection. Then the corresponding L-aptamer was prepared by chemical synthesis and used to bind the desired target. The L-aptamer binds D-TAR RNA with a Kd of 100 nM. It binds D-TAR exclusively at the six-nucleotide distal loop, but does so through tertiary interactions rather than simple Watson-Crick pairing. This complex is the first example of two nucleic acids molecules of opposing chirality that interact through a mode of binding other than primary structure. Binding of the L-aptamer to D-TAR RNA inhibits formation of the Tat-TAR ribonucleoprotein complex that is essential for TAR function. This suggests that L-aptamers, which are intrinsically resistant to degradation by ribonucleases, might be pursued as an alternative to antisense oligonucleotides to target structured RNAs of biological or therapeutic interest.
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Affiliation(s)
- Jonathan T. Sczepanski
- Departments of Chemistry and Molecular Biology and The Skaggs Institute for Chemical Biology, The Scripps Research Institute, 10550 North Torrey Pines Road, La Jolla, California 92037, United States
| | - Gerald F. Joyce
- Departments of Chemistry and Molecular Biology and The Skaggs Institute for Chemical Biology, The Scripps Research Institute, 10550 North Torrey Pines Road, La Jolla, California 92037, United States
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27
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Abstract
For over 20 years, laboratories around the world have been applying the principles of Darwinian evolution to isolate DNA and RNA molecules with specific ligand-binding or catalytic activities. This area of synthetic biology, commonly referred to as in vitro genetics, is made possible by the availability of natural polymerases that can replicate genetic information in the laboratory. Moving beyond natural nucleic acids requires organic chemistry to synthesize unnatural analogues and polymerase engineering to create enzymes that recognize artificial substrates. Progress in both of these areas has led to the emerging field of synthetic genetics, which explores the structural and functional properties of synthetic genetic polymers by in vitro evolution. This review examines recent advances in the Darwinian evolution of artificial genetic polymers and their potential downstream applications in exobiology, molecular medicine, and synthetic biology.
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Affiliation(s)
- John C Chaput
- Center for Evolutionary Medicine and Informatics in the Biodesign Institute, and Department of Chemistry and Biochemistry, Arizona State University, Tempe, AZ 85287-5301, USA.
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28
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Ferretti AC, Joyce GF. Kinetic properties of an RNA enzyme that undergoes self-sustained exponential amplification. Biochemistry 2013; 52:1227-35. [PMID: 23384307 DOI: 10.1021/bi301646n] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
A special class of biochemical reactions involves a set of enzymes that generate additional copies of themselves and transfer heritable information from parent to progeny molecules, thus providing the basis for genetics and Darwinian evolution. Such a process has been realized with a pair of self-replicating RNA enzymes that undergo exponential amplification at a constant temperature. Exponential growth requires that the rate of production of new enzymes be directly proportional to the existing concentration of enzymes, which is the case for this system and provides a doubling time of ~20 min. However, the catalytic rate of the underlying enzymes is ~100-fold faster than the observed rate of replication. As in biological replication, other aspects of the system limit the generation time, chiefly the propensity of the substrate molecules to form nonproductive complexes that limit their availability for replication. An analysis of this and other kinetic properties of the self-replicating RNA enzymes reveals how exponential amplification is achieved and how the rate of amplification might be increased.
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Affiliation(s)
- Antonio C Ferretti
- Departments of Chemistry and Molecular Biology and The Skaggs Institute for Chemical Biology, The Scripps Research Institute, 10550 North Torrey Pines Road, La Jolla, CA 92037, USA
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29
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Fixation and accumulation of thermotolerant catalytic competence of a pair of ligase ribozymes through complex formation and cross ligation. J Mol Evol 2013; 76:48-58. [PMID: 23288433 DOI: 10.1007/s00239-012-9536-x] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2012] [Accepted: 12/05/2012] [Indexed: 12/11/2022]
Abstract
In the early stages of the hypothetical RNA world, some primitive RNA catalysts (ribozymes) may have emerged through self-assembly of short RNA oligomers. Although they may be unstable against temperature fluctuations and other environmental changes, ligase ribozymes (ribozymes with RNA strand-joining activity) may resolve structural instability of self-assembling RNAs by converting them to the corresponding unimolecular formats. To investigate this possibility, we constructed a model system using a cross-ligation system composed of a pair of self-assembling ligase ribozymes. Their abilities to act as catalysts, substrates, and a cross-ligation system were analyzed with or without thermal pretreatment before the reactions. A pair of self-assembling ligase ribozymes, each of which can form multiple conformations, demonstrated that thermotolerance was acquired and accumulated through complex-formation that stabilized the active forms of the bimolecular ribozymes and also cross-ligation that produced the unimolecular ribozymes.
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30
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Dieckmann A, Houk KN. Analysis of supramolecular complex energetics in artificial replicators. Chem Sci 2013. [DOI: 10.1039/c3sc51192h] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
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31
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Pinheiro VB, Loakes D, Holliger P. Synthetic polymers and their potential as genetic materials. Bioessays 2012; 35:113-22. [PMID: 23281109 DOI: 10.1002/bies.201200135] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Abstract
DNA and RNA are the only known natural genetic materials. Systematic modification of each of their chemical building blocks (nucleobase, sugar, and phosphate) has enabled the study of the key properties that make those nucleic acids genetic materials. All three moieties contribute to replication and, significantly, all three moieties can be replaced by synthetic analogs without loss of function. Synthetic nucleic acid polymers capable of storing and propagating information not only expand the central dogma, but also highlight that DNA and RNA are not unique chemical solutions for genetic information storage. By considering replication as a question of information transfer, we propose that any polymer that can be replicated could serve as a genetic material.
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Affiliation(s)
- Vitor B Pinheiro
- Medical Research Council, Laboratory of Molecular Biology, Cambridge, UK.
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