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Moreira L, Guimarães NM, Santos RS, Loureiro JA, Pereira MDC, Azevedo NF. Oligonucleotide probes for imaging and diagnosis of bacterial infections. Crit Rev Biotechnol 2024:1-20. [PMID: 38830823 DOI: 10.1080/07388551.2024.2344574] [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: 02/15/2023] [Accepted: 06/17/2023] [Indexed: 06/05/2024]
Abstract
The rise of infectious diseases as a public health concern has necessitated the development of rapid and precise diagnostic methods. Imaging techniques like nuclear and optical imaging provide the ability to diagnose infectious diseases within the body, eliminating delays caused by sampling and pre-enrichments of clinical samples and offering spatial information that can aid in a more informed diagnosis. Traditional molecular probes are typically created to image infected tissue without accurately identifying the pathogen. In contrast, oligonucleotides can be tailored to target specific RNA sequences, allowing for the identification of pathogens, and even generating antibiotic susceptibility profiles by focusing on drug resistance genes. Despite the benefits that nucleic acid mimics (NAMs) have provided in terms of stabilizing oligonucleotides, the inadequate delivery of these relatively large molecules into the cytoplasm of bacteria remains a challenge for widespread use of this technology. This review summarizes the key advancements in the field of oligonucleotide probes for in vivo imaging, highlighting the most promising delivery systems described in the literature for developing optical imaging through in vivo hybridization.
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Affiliation(s)
- Luís Moreira
- LEPABE - Laboratory for Process Engineering, Environment, Biotechnology and Energy, Faculty of Engineering, University of Porto, Porto, Portugal
- ALiCE - Associate Laboratory in Chemical Engineering, Faculty of Engineering, University of Porto, Porto, Portugal
| | - Nuno Miguel Guimarães
- LEPABE - Laboratory for Process Engineering, Environment, Biotechnology and Energy, Faculty of Engineering, University of Porto, Porto, Portugal
- ALiCE - Associate Laboratory in Chemical Engineering, Faculty of Engineering, University of Porto, Porto, Portugal
| | - Rita Sobral Santos
- LEPABE - Laboratory for Process Engineering, Environment, Biotechnology and Energy, Faculty of Engineering, University of Porto, Porto, Portugal
- ALiCE - Associate Laboratory in Chemical Engineering, Faculty of Engineering, University of Porto, Porto, Portugal
| | - Joana Angélica Loureiro
- LEPABE - Laboratory for Process Engineering, Environment, Biotechnology and Energy, Faculty of Engineering, University of Porto, Porto, Portugal
- ALiCE - Associate Laboratory in Chemical Engineering, Faculty of Engineering, University of Porto, Porto, Portugal
| | - Maria do Carmo Pereira
- LEPABE - Laboratory for Process Engineering, Environment, Biotechnology and Energy, Faculty of Engineering, University of Porto, Porto, Portugal
- ALiCE - Associate Laboratory in Chemical Engineering, Faculty of Engineering, University of Porto, Porto, Portugal
| | - Nuno Filipe Azevedo
- LEPABE - Laboratory for Process Engineering, Environment, Biotechnology and Energy, Faculty of Engineering, University of Porto, Porto, Portugal
- ALiCE - Associate Laboratory in Chemical Engineering, Faculty of Engineering, University of Porto, Porto, Portugal
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2
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Janett E, Diep KL, Fromm KM, Bochet CG. A Simple Reaction for DNA Sensing and Chemical Delivery. ACS Sens 2020; 5:2338-2343. [PMID: 32804492 DOI: 10.1021/acssensors.0c00988] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Reactions templated by nucleic acids are currently at the heart of applications in biosensing and drug release. The number of chemical reactions selectively occurring only in the presence of the template, in aqueous solutions, and at room temperature and able to release a chemical moiety is still very limited. Here, we report the use of the p-nitrophenyl carbonate (NPC) as a new reactive moiety for DNA templated reactions releasing a colored reporter by reaction with a simple amine. The easily synthesized p-nitrophenyl carbonate was integrated in an oligonucleotide and showed a very good stability as well as a high reactivity toward amines, without the need for any supplementary reagent, quantitatively releasing the red p-nitrophenolate with a half-life of about 1 h.
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Affiliation(s)
- Elia Janett
- Department of Chemistry, University of Fribourg, Chemin du Musée 9, CH-1700 Fribourg, Switzerland
| | - Kim-Long Diep
- Department of Chemistry, University of Fribourg, Chemin du Musée 9, CH-1700 Fribourg, Switzerland
| | - Katharina M. Fromm
- Department of Chemistry, University of Fribourg, Chemin du Musée 9, CH-1700 Fribourg, Switzerland
| | - Christian G. Bochet
- Department of Chemistry, University of Fribourg, Chemin du Musée 9, CH-1700 Fribourg, Switzerland
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3
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Kim KT, Winssinger N. Enhanced SNP-sensing using DNA-templated reactions through confined hybridization of minimal substrates (CHOMS). Chem Sci 2020; 11:4150-4157. [PMID: 34122878 PMCID: PMC8152519 DOI: 10.1039/d0sc00741b] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2020] [Accepted: 03/24/2020] [Indexed: 12/11/2022] Open
Abstract
DNA or RNA templated reactions are attractive for nucleic acid sensing and imaging. As for any hybridization-based sensing, there is a tradeoff between sensitivity (detection threshold) and resolution (single nucleotide discrimination). Longer probes afford better sensitivity but compromise single nucleotide resolution due to the small thermodynamic penalty of a single mismatch. Herein we report a design that overcomes this tradeoff. The reaction is leveraged on the hybridization of a minimal substrate (covering 4 nucleotides) which is confined by two guide DNAs functionalized respectively with a ruthenium photocatalyst. The use of a catalytic reaction is essential to bypass the exchange of guide DNAs while achieving signal amplification through substrate turnover. The guide DNAs restrain the reaction to a unique site and enhance the hybridization of short substrates by providing two π-stacking interactions. The reaction was shown to enable the detection of SNPs and SNVs down to 50 pM with a discrimination factor ranging from 24 to 309 (median 82, 27 examples from 3 oncogenes). The clinical diagnostic potential of the technology was demonstrated with the analysis of RAS amplicons obtained directly from cell culture.
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Affiliation(s)
- Ki Tae Kim
- Department of Organic Chemistry, NCCR Chemical Biology, Faculty of Science, University of Geneva 30 quai Ernest Ansermet 1211 Geneva Switzerland
| | - Nicolas Winssinger
- Department of Organic Chemistry, NCCR Chemical Biology, Faculty of Science, University of Geneva 30 quai Ernest Ansermet 1211 Geneva Switzerland
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Al Sulaiman D, Chang JYH, Ladame S. Subnanomolar Detection of Oligonucleotides through Templated Fluorogenic Reaction in Hydrogels: Controlling Diffusion to Improve Sensitivity. Angew Chem Int Ed Engl 2017; 56:5247-5251. [PMID: 28382640 PMCID: PMC5502887 DOI: 10.1002/anie.201701356] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2017] [Revised: 03/02/2017] [Indexed: 02/06/2023]
Abstract
Oligonucleotide-templated reactions are valuable tools for nucleic acid sensing both in vitro and in vivo. They are typically carried out under conditions that make any reaction in the absence of template highly unfavorable (most commonly by using a low concentration of reactants), which has a negative impact on the detection sensitivity. Herein, we report a novel platform for fluorogenic oligonucleotide-templated reactions between peptide nucleic acid probes embedded within permeable agarose and alginate hydrogels. We demonstrate that under conditions of restricted mobility (that is, limited diffusion), non-specific interactions between probes are prevented, thus leading to lower background signals. When applied to nucleic acid sensing, this accounts for a significant increase in sensitivity (that is, lower limit of detection). Optical nucleic acid sensors based on fluorogenic peptide nucleic acid probes embedded in permeable, physically crosslinked, alginate beads were also engineered and proved capable of detecting DNA concentrations as low as 100 pm.
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Affiliation(s)
- Dana Al Sulaiman
- Department of Bioengineering, Imperial College London, South Kensington Campus, London, SW7 2AZ, UK
| | - Jason Y H Chang
- Department of Bioengineering, Imperial College London, South Kensington Campus, London, SW7 2AZ, UK
| | - Sylvain Ladame
- Department of Bioengineering, Imperial College London, South Kensington Campus, London, SW7 2AZ, UK
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5
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Al Sulaiman D, Chang JYH, Ladame S. Subnanomolar Detection of Oligonucleotides through Templated Fluorogenic Reaction in Hydrogels: Controlling Diffusion to Improve Sensitivity. Angew Chem Int Ed Engl 2017. [DOI: 10.1002/ange.201701356] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Affiliation(s)
- Dana Al Sulaiman
- Department of Bioengineering; Imperial College London; South Kensington Campus London SW7 2AZ UK
| | - Jason Y. H. Chang
- Department of Bioengineering; Imperial College London; South Kensington Campus London SW7 2AZ UK
| | - Sylvain Ladame
- Department of Bioengineering; Imperial College London; South Kensington Campus London SW7 2AZ UK
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6
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Metcalf GAD, Shibakawa A, Patel H, Sita-Lumsden A, Zivi A, Rama N, Bevan CL, Ladame S. Amplification-Free Detection of Circulating microRNA Biomarkers from Body Fluids Based on Fluorogenic Oligonucleotide-Templated Reaction between Engineered Peptide Nucleic Acid Probes: Application to Prostate Cancer Diagnosis. Anal Chem 2016; 88:8091-8. [PMID: 27498854 DOI: 10.1021/acs.analchem.6b01594] [Citation(s) in RCA: 46] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
Highly abundant in cells, microRNAs (or miRs) play a key role as regulators of gene expression. A proportion of them are also detectable in biofluids making them ideal noninvasive biomarkers for pathologies in which miR levels are aberrantly expressed, such as cancer. Peptide nucleic acids (PNAs) are engineered uncharged oligonucleotide analogues capable of hybridizing to complementary nucleic acids with high affinity and high specificity. Herein, novel PNA-based fluorogenic biosensors have been designed and synthesized that target miR biomarkers for prostate cancer (PCa). The sensing strategy is based on oligonucleotide-templated reactions where the only miR of interest serves as a matrix to catalyze an otherwise highly unfavorable fluorogenic reaction. Validated in vitro using synthetic RNAs, these newly developed biosensors were then shown to detect endogenous concentrations of miR in human blood samples without the need for any amplification step and with minimal sample processing. This low-cost, quantitative, and versatile sensing technology has been technically validated using gold-standard RT-qPCR. Compared to RT-qPCR however, this enzyme-free, isothermal blood test is amenable to incorporation into low-cost portable devices and could therefore be suitable for widespread public screening.
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Affiliation(s)
- Gavin A D Metcalf
- Department of Bioengineering, Imperial College London , South Kensington Campus, London SW72AZ, U.K.,Department of Surgery and Cancer, Imperial College London , Hammersmith Hospital Campus, London W120NN, U.K
| | - Akifumi Shibakawa
- Department of Surgery and Cancer, Imperial College London , Hammersmith Hospital Campus, London W120NN, U.K
| | - Hinesh Patel
- Department of Bioengineering, Imperial College London , South Kensington Campus, London SW72AZ, U.K
| | - Ailsa Sita-Lumsden
- Department of Surgery and Cancer, Imperial College London , Hammersmith Hospital Campus, London W120NN, U.K
| | - Andrea Zivi
- Department of Surgery and Cancer, Imperial College London , Hammersmith Hospital Campus, London W120NN, U.K
| | - Nona Rama
- Department of Surgery and Cancer, Imperial College London , Hammersmith Hospital Campus, London W120NN, U.K
| | - Charlotte L Bevan
- Department of Surgery and Cancer, Imperial College London , Hammersmith Hospital Campus, London W120NN, U.K
| | - Sylvain Ladame
- Department of Bioengineering, Imperial College London , South Kensington Campus, London SW72AZ, U.K
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Rombouts K, Braeckmans K, Remaut K. Fluorescent Labeling of Plasmid DNA and mRNA: Gains and Losses of Current Labeling Strategies. Bioconjug Chem 2015; 27:280-97. [PMID: 26670733 DOI: 10.1021/acs.bioconjchem.5b00579] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/12/2023]
Abstract
Live-cell imaging has provided the life sciences with insights into the cell biology and dynamics. Fluorescent labeling of target molecules proves to be indispensable in this regard. In this Review, we focus on the current fluorescent labeling strategies for nucleic acids, and in particular mRNA (mRNA) and plasmid DNA (pDNA), which are of interest to a broad range of scientific fields. By giving a background of the available techniques and an evaluation of the pros and cons, we try to supply scientists with all the information needed to come to an informed choice of nucleic acid labeling strategy aimed at their particular needs.
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Affiliation(s)
- K Rombouts
- Laboratory of general biochemistry and physical pharmacy, Faculty of pharmacy and ‡Centre for Nano- and Biophotonics, Ghent University , Ghent 9000, Belgium
| | - K Braeckmans
- Laboratory of general biochemistry and physical pharmacy, Faculty of pharmacy and ‡Centre for Nano- and Biophotonics, Ghent University , Ghent 9000, Belgium
| | - K Remaut
- Laboratory of general biochemistry and physical pharmacy, Faculty of pharmacy and ‡Centre for Nano- and Biophotonics, Ghent University , Ghent 9000, Belgium
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Quantification of plasma HIV RNA using chemically engineered peptide nucleic acids. Nat Commun 2014; 5:5079. [PMID: 25283173 PMCID: PMC4187110 DOI: 10.1038/ncomms6079] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2014] [Accepted: 08/26/2014] [Indexed: 11/08/2022] Open
Abstract
The remarkable stability of peptide nucleic acids (PNAs) toward enzymatic degradation makes this class of molecules ideal to develop as part of a diagnostic device. Here we report the development of chemically-engineered PNAs for the quantitative detection of HIV RNA at clinically relevant levels that are competitive with current PCR-based assays. Using a sandwich hybridization approach, chemical groups were systematically introduced into a surface PNA probe and a reporter PNA probe to achieve quantitative detection for HIV RNA as low as 20 copies per milliliter of plasma. For the surface PNA probe, four cyclopentane groups were incorporated to promote stronger binding to the target HIV RNA compared to PNA without the cyclopentanes. For the reporter PNA probe, 25 biotin groups were attached to promote strong signal amplification after binding to the target HIV RNA. These general approaches to engineer PNA probes may be used to detect other RNA target sequences.
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Choi Y, Metcalf G, Sleiman MH, Vair-Turnbull D, Ladame S. Oligonucleotide-templated reactions based on Peptide Nucleic Acid (PNA) probes: concept and biomedical applications. Bioorg Med Chem 2014; 22:4395-8. [PMID: 24957880 DOI: 10.1016/j.bmc.2014.05.071] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2014] [Revised: 05/28/2014] [Accepted: 05/30/2014] [Indexed: 12/12/2022]
Abstract
Sensing technologies based on Peptide Nucleic Acids (PNAs) and oligonucleotide-templated chemistry are perfectly suited for biomedical applications (e.g., diagnosis, prognosis and stratification of diseases) and could compete well with more traditional amplification technologies using expensive dual-labelled oligonucleotide probes. PNAs can be easily synthesised and functionalised, are more stable and are more responsive to point-mutations than their DNA counterpart. For these reasons, fluorogenic PNAs represent an interesting alternative to DNA-based molecular beacons for sensing applications in a cell-free environment, where cellular uptake is not required.
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Affiliation(s)
- Youngeun Choi
- Department of Bioengineering, Imperial College London, London SW7 2AZ, UK
| | - Gavin Metcalf
- Department of Bioengineering, Imperial College London, London SW7 2AZ, UK
| | - Mazen Haj Sleiman
- Department of Bioengineering, Imperial College London, London SW7 2AZ, UK
| | | | - Sylvain Ladame
- Department of Bioengineering, Imperial College London, London SW7 2AZ, UK.
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10
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Boutorine AS, Novopashina DS, Krasheninina OA, Nozeret K, Venyaminova AG. Fluorescent probes for nucleic Acid visualization in fixed and live cells. Molecules 2013; 18:15357-97. [PMID: 24335616 PMCID: PMC6270009 DOI: 10.3390/molecules181215357] [Citation(s) in RCA: 81] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2013] [Revised: 11/20/2013] [Accepted: 12/05/2013] [Indexed: 12/13/2022] Open
Abstract
This review analyses the literature concerning non-fluorescent and fluorescent probes for nucleic acid imaging in fixed and living cells from the point of view of their suitability for imaging intracellular native RNA and DNA. Attention is mainly paid to fluorescent probes for fluorescence microscopy imaging. Requirements for the target-binding part and the fluorophore making up the probe are formulated. In the case of native double-stranded DNA, structure-specific and sequence-specific probes are discussed. Among the latest, three classes of dsDNA-targeting molecules are described: (i) sequence-specific peptides and proteins; (ii) triplex-forming oligonucleotides and (iii) polyamide oligo(N-methylpyrrole/N-methylimidazole) minor groove binders. Polyamides seem to be the most promising targeting agents for fluorescent probe design, however, some technical problems remain to be solved, such as the relatively low sequence specificity and the high background fluorescence inside the cells. Several examples of fluorescent probe applications for DNA imaging in fixed and living cells are cited. In the case of intracellular RNA, only modified oligonucleotides can provide such sequence-specific imaging. Several approaches for designing fluorescent probes are considered: linear fluorescent probes based on modified oligonucleotide analogs, molecular beacons, binary fluorescent probes and template-directed reactions with fluorescence probe formation, FRET donor-acceptor pairs, pyrene excimers, aptamers and others. The suitability of all these methods for living cell applications is discussed.
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Affiliation(s)
- Alexandre S. Boutorine
- Muséum National d’Histoire Naturelle, CNRS, UMR 7196, INSERM, U565, 57 rue Cuvier, B.P. 26, Paris Cedex 05, F-75231, France; E-Mail:
| | - Darya S. Novopashina
- Institute of Chemical Biology and Fundamental Medicine, Siberian Division of Russian Academy of Sciences, Lavrentyev Ave., 8, Novosibirsk 630090, Russia; E-Mails: (D.S.N.); (O.A.K.); (A.G.V.)
| | - Olga A. Krasheninina
- Institute of Chemical Biology and Fundamental Medicine, Siberian Division of Russian Academy of Sciences, Lavrentyev Ave., 8, Novosibirsk 630090, Russia; E-Mails: (D.S.N.); (O.A.K.); (A.G.V.)
- Department of Natural Sciences, Novosibirsk State University, Pirogova Str., 2, Novosibirsk 630090, Russia
| | - Karine Nozeret
- Muséum National d’Histoire Naturelle, CNRS, UMR 7196, INSERM, U565, 57 rue Cuvier, B.P. 26, Paris Cedex 05, F-75231, France; E-Mail:
| | - Alya G. Venyaminova
- Institute of Chemical Biology and Fundamental Medicine, Siberian Division of Russian Academy of Sciences, Lavrentyev Ave., 8, Novosibirsk 630090, Russia; E-Mails: (D.S.N.); (O.A.K.); (A.G.V.)
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11
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Goldman JM, Zhang LA, Manna A, Armitage BA, Ly DH, Schneider JW. High affinity γPNA sandwich hybridization assay for rapid detection of short nucleic acid targets with single mismatch discrimination. Biomacromolecules 2013; 14:2253-61. [PMID: 23777445 DOI: 10.1021/bm400388a] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Hybridization analysis of short DNA and RNA targets presents many challenges for detection. The commonly employed sandwich hybridization approach cannot be implemented for these short targets due to insufficient probe-target binding strengths for unmodified DNA probes. Here, we present a method capable of rapid and stable sandwich hybridization detection for 22 nucleotide DNA and RNA targets. Stable hybridization is achieved using an n-alkylated, polyethylene glycol γ-carbon modified peptide nucleic acid (γPNA) amphiphile. The γPNA's exceptionally high affinity enables stable hybridization of a second DNA-based probe to the remaining bases of the short target. Upon hybridization of both probes, an electrophoretic mobility shift is measured via interaction of the n-alkane modification on the γPNA with capillary electrophoresis running buffer containing nonionic surfactant micelles. We find that sandwich hybridization of both probes is stable under multiple binding configurations and demonstrate single base mismatch discrimination. The binding strength of both probes is also stabilized via coaxial stacking on adjacent hybridization to targets. We conclude with a discussion on the implementation of the proposed sandwich hybridization assay as a high-throughput microRNA detection method.
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Affiliation(s)
- Johnathan M Goldman
- Department of Chemical Engineering and Center for Nucleic Acids Science and Technology, Carnegie Mellon University, Pittsburgh, Pennsylvania 15213-3890, United States
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Gorska K, Winssinger N. Reactions templated by nucleic acids: more ways to translate oligonucleotide-based instructions into emerging function. Angew Chem Int Ed Engl 2013; 52:6820-43. [PMID: 23794204 DOI: 10.1002/anie.201208460] [Citation(s) in RCA: 114] [Impact Index Per Article: 10.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2012] [Indexed: 12/30/2022]
Abstract
The programmability of oligonucleotide recognition offers an attractive platform to direct the assembly of reactive partners that can engage in chemical reactions. Recently, significant progress has been made in both the breadth of chemical transformations and in the functional output of the reaction. Herein we summarize these recent progresses and illustrate their applications to translate oligonucleotide instructions into functional materials and novel architectures (conductive polymers, nanopatterns, novel oligonucleotide junctions); into fluorescent or bioactive molecule using cellular RNA; to interrogate secondary structures or oligonucelic acids; or a synthetic oligomer.
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Affiliation(s)
- Katarzyna Gorska
- Institut de Science et Ingénierie Supramoléculaires (ISIS-UMR 7006), Universite de Strasbourg-CNRS, 8 allée Gaspard Monge, 67000 Strasbourg, France
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Gorska K, Winssinger N. Reaktionen an Nucleinsäuretemplaten: mehr Methoden zur Übersetzung Oligonucleotid-basierter Informationen in neue Funktionen. Angew Chem Int Ed Engl 2013. [DOI: 10.1002/ange.201208460] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
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14
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Percivalle C, Bartolo JF, Ladame S. Oligonucleotide-templated chemical reactions: pushing the boundaries of a nature-inspired process. Org Biomol Chem 2013; 11:16-26. [PMID: 23076879 DOI: 10.1039/c2ob26163d] [Citation(s) in RCA: 43] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Widespread in nature, oligonucleotide-templated reactions of phosphodiester bond formation have inspired chemists who are now applying this elegant strategy to the catalysis of a broad range of otherwise inefficient reactions. This review highlights the increasing diversity of chemical reactions that can be efficiently catalysed by an oligonucleotide template, using Watson-Crick base-pairing to bring both reagents in close enough proximity to react, thus increasing significantly their effective molarity. The applications of this elegant concept for nucleic acid sensing and controlled organic synthesis will also be discussed.
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Affiliation(s)
- Claudia Percivalle
- Department of Bioengineering, Imperial College London, South Kensington campus, London SW7 2AZ, UK
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Photochemically relevant DNA-based molecular systems enabling chemical and signal transductions and their analytical applications. JOURNAL OF PHOTOCHEMISTRY AND PHOTOBIOLOGY C-PHOTOCHEMISTRY REVIEWS 2012. [DOI: 10.1016/j.jphotochemrev.2012.03.002] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
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16
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Chen XH, Roloff A, Seitz O. Consecutive Signal Amplification for DNA Detection Based on De Novo Fluorophore Synthesis and Host-Guest Chemistry. Angew Chem Int Ed Engl 2012; 51:4479-83. [DOI: 10.1002/anie.201108845] [Citation(s) in RCA: 43] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2011] [Indexed: 01/27/2023]
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17
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Chen XH, Roloff A, Seitz O. Konsekutive Signalverstärkung für die DNA-Detektion basierend auf einer De-novo-Fluorophorsynthese und Wirt-Gast-Chemie. Angew Chem Int Ed Engl 2012. [DOI: 10.1002/ange.201108845] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
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18
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Loakes D. Nucleotides and nucleic acids; oligo- and polynucleotides. ORGANOPHOSPHORUS CHEMISTRY 2012. [DOI: 10.1039/9781849734875-00169] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/29/2023]
Affiliation(s)
- David Loakes
- Medical Research Council Laboratory of Molecular Biology, Hills Road Cambridge CB2 2QH UK
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Gorska K, Manicardi A, Barluenga S, Winssinger N. DNA-templated release of functional molecules with an azide-reduction-triggered immolative linker. Chem Commun (Camb) 2011; 47:4364-6. [DOI: 10.1039/c1cc10222b] [Citation(s) in RCA: 76] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
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20
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Duprey JLHA, Zhao ZY, Bassani DM, Manchester J, Vyle JS, Tucker JHR. Detection of DNA base variation and cytosine methylation at a single nucleotide site using a highly sensitive fluorescent probe. Chem Commun (Camb) 2011; 47:6629-31. [DOI: 10.1039/c1cc11205h] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
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