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Kumar R, Maity J, Mathur D, Verma A, Rana N, Kumar M, Kumar S, Prasad AK. Green synthesis of triazolo-nucleoside conjugates via azide–alkyne C–N bond formation. PHYSICAL SCIENCES REVIEWS 2022. [DOI: 10.1515/psr-2021-0090] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022]
Abstract
Abstract
Modified nucleosides are the core precursors for the synthesis of artificial nucleic acids, and are important in the field of synthetic and medicinal chemistry. In order to synthesize various triazolo-compounds, copper and ruthenium catalysed azide–alkyne 1,3-dipolar cycloaddition reactions also known as click reaction have emerged as a facile and efficient tool due to its simplicity and convenient conditions. Introduction of a triazole ring in nucleosides enhances their therapeutic value and various photophysical properties. This review primarily focuses on the plethora of synthetic methodologies being employed to synthesize sugar modified triazolyl nucleosides, their therapeutic importance and various other applications.
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Affiliation(s)
- Rajesh Kumar
- Department of Chemistry , R.D.S. College, B.R.A. Bihar University , Muzaffarpur , India
| | - Jyotirmoy Maity
- Department of Chemistry , St. Stephen’s College, University of Delhi , Delhi , India
| | - Divya Mathur
- Department of Chemistry , Daulat Ram College, University of Delhi , Delhi , India
| | - Abhishek Verma
- Department of Chemistry , Bioorganic Laboratory, University of Delhi , Delhi , India
| | - Neha Rana
- Department of Chemistry , Bioorganic Laboratory, University of Delhi , Delhi , India
| | - Manish Kumar
- Department of Chemistry , Bioorganic Laboratory, University of Delhi , Delhi , India
| | - Sandeep Kumar
- Department of Chemistry , Bioorganic Laboratory, University of Delhi , Delhi , India
| | - Ashok K. Prasad
- Department of Chemistry , Bioorganic Laboratory, University of Delhi , Delhi , India
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2
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Walunj MB, Srivatsan SG. Posttranscriptional Suzuki-Miyaura Cross-Coupling Yields Labeled RNA for Conformational Analysis and Imaging. Methods Mol Biol 2021; 2166:473-486. [PMID: 32710426 DOI: 10.1007/978-1-0716-0712-1_27] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Abstract
Chemical labeling of RNA by using chemoselective reactions that work under biologically benign conditions is increasingly becoming valuable in the in vitro and in vivo analysis of RNA. Here, we describe a modular RNA labeling method based on a posttranscriptional Suzuki-Miyaura coupling reaction, which works under mild conditions and enables the direct installation of various biophysical reporters and tags. This two-part procedure involves the incorporation of a halogen-modified UTP analog (5-iodouridine-5'-triphosphate) by a transcription reaction. Subsequent posttranscriptional coupling with boronic acid/ester substrates in the presence of a palladium catalyst provides access to RNA labeled with (a) fluorogenic environment-sensitive nucleosides for probing nucleic acid structure and recognition, (b) fluorescent probes for microscopy, and (3) affinity tags for pull-down and immunoassays. It is expected that this method could also become useful for imaging nascent RNA transcripts in cells if the nucleotide analog can be metabolically incorporated and coupled with reporters by metal-assisted cross-coupling reactions.
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Affiliation(s)
- Manisha B Walunj
- Department of Chemistry, Indian Institute of Science Education and Research (IISER), Pune, India
| | - Seergazhi G Srivatsan
- Department of Chemistry, Indian Institute of Science Education and Research (IISER), Pune, India.
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3
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Advances in oligonucleotide-based detection coupled with fluorescence resonance energy transfer. Trends Analyt Chem 2020. [DOI: 10.1016/j.trac.2019.115756] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/01/2023]
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4
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Martínez-Negro M, Sánchez-Arribas N, Guerrero-Martínez A, Moyá ML, Tros de Ilarduya C, Mendicuti F, Aicart E, Junquera E. A Non-Viral Plasmid DNA Delivery System Consisting on a Lysine-Derived Cationic Lipid Mixed with a Fusogenic Lipid. Pharmaceutics 2019; 11:E632. [PMID: 31783620 PMCID: PMC6956073 DOI: 10.3390/pharmaceutics11120632] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2019] [Revised: 11/18/2019] [Accepted: 11/25/2019] [Indexed: 12/18/2022] Open
Abstract
The insertion of biocompatible amino acid moieties in non-viral gene nanocarriers is an attractive approach that has been recently gaining interest. In this work, a cationic lipid, consisting of a lysine-derived moiety linked to a C12 chain (LYCl) was combined with a common fusogenic helper lipid (DOPE) and evaluated as a potential vehicle to transfect two plasmid DNAs (encoding green fluorescent protein GFP and luciferase) into COS-7 cells. A multidisciplinary approach has been followed: (i) biophysical characterization based on zeta potential, gel electrophoresis, small-angle X-ray scattering (SAXS), and cryo-transmission electronic microscopy (cryo-TEM); (ii) biological studies by fluorescence assisted cell sorting (FACS), luminometry, and cytotoxicity experiments; and (iii) a computational study of the formation of lipid bilayers and their subsequent stabilization with DNA. The results indicate that LYCl/DOPE nanocarriers are capable of compacting the pDNAs and protecting them efficiently against DNase I degradation, by forming Lα lyotropic liquid crystal phases, with an average size of ~200 nm and low polydispersity that facilitate the cellular uptake process. The computational results confirmed that the LYCl/DOPE lipid bilayers are stable and also capable of stabilizing DNA fragments via lipoplex formation, with dimensions consistent with experimental values. The optimum formulations (found at 20% of LYCl content) were able to complete the transfection process efficiently and with high cell viabilities, even improving the outcomes of the positive control Lipo2000*.
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Affiliation(s)
- María Martínez-Negro
- Departamento de Química Física, Facultad de Ciencias Químicas, Universidad Complutense de Madrid, 28040 Madrid, Spain; (M.M.-N.); (N.S.-A.); (A.G.-M.); (E.A.)
| | - Natalia Sánchez-Arribas
- Departamento de Química Física, Facultad de Ciencias Químicas, Universidad Complutense de Madrid, 28040 Madrid, Spain; (M.M.-N.); (N.S.-A.); (A.G.-M.); (E.A.)
| | - Andrés Guerrero-Martínez
- Departamento de Química Física, Facultad de Ciencias Químicas, Universidad Complutense de Madrid, 28040 Madrid, Spain; (M.M.-N.); (N.S.-A.); (A.G.-M.); (E.A.)
| | - María Luisa Moyá
- Grupo de Química Coloidal y Catálisis Micelar, Departamento de Química Física, Facultad de Química, Universidad de Sevilla, 41012 Sevilla, Spain;
| | - Conchita Tros de Ilarduya
- Departamento de Tecnología y Química Farmacéuticas, Facultad de Farmacia y Nutrición, Universidad de Navarra, Instituto de Investigación Sanitaria de Navarra (IdiSNA), 31080 Pamplona, Spain;
| | - Francisco Mendicuti
- Departmento de Química Analítica, Química Física e Ingeniería Química and Instituto de Investigación Quimica Andrés M. del Rio, Universidad de Alcalá, 28871 Alcalá de Henares, Spain;
| | - Emilio Aicart
- Departamento de Química Física, Facultad de Ciencias Químicas, Universidad Complutense de Madrid, 28040 Madrid, Spain; (M.M.-N.); (N.S.-A.); (A.G.-M.); (E.A.)
| | - Elena Junquera
- Departamento de Química Física, Facultad de Ciencias Químicas, Universidad Complutense de Madrid, 28040 Madrid, Spain; (M.M.-N.); (N.S.-A.); (A.G.-M.); (E.A.)
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5
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Escudier JM, Payrastre C, Gerland B, Tarrat N. Convertible and conformationally constrained nucleic acids (C 2NAs). Org Biomol Chem 2019; 17:6386-6397. [PMID: 31210235 DOI: 10.1039/c9ob01150a] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Abstract
We introduce the concept of Convertible and Constrained Nucleic Acids (C2NAs). By means of the synthesis of a stereocontrolled N-propargyl dioxo-1,3,2-oxaza-phosphorinane as an internucleotidic linkage, the torsional angles α and β can adopt either the canonical (g-, t) set of values able to increase DNA duplex stability or the non-canonical (g+, t) set that stabilized the hairpin structure when installed within the loop moiety. With an appended propargyl function on the nitrogen atom of the six-membered ring, the copper catalysed Huisgen's cycloaddition (CuAAC click chemistry) allows for the introduction of new functionalities at any location on the nucleic acid chain while maintaining the properties brought by the geometrical constraint and the neutral internucleotidic linkage.
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Affiliation(s)
- Jean-Marc Escudier
- Laboratoire de Synthèse et Physico-Chimie de Molécules d'Intérêt Biologique, UMR CNRS 5068, Université Paul Sabatier, 118 route de Narbonne, 31062 Toulouse, France.
| | - Corinne Payrastre
- Laboratoire de Synthèse et Physico-Chimie de Molécules d'Intérêt Biologique, UMR CNRS 5068, Université Paul Sabatier, 118 route de Narbonne, 31062 Toulouse, France.
| | - Béatrice Gerland
- Laboratoire de Synthèse et Physico-Chimie de Molécules d'Intérêt Biologique, UMR CNRS 5068, Université Paul Sabatier, 118 route de Narbonne, 31062 Toulouse, France.
| | - Nathalie Tarrat
- CEMES, Université de Toulouse, CNRS, 29 rue Jeanne Marvig, Toulouse 31055, France
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6
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Tomaszewska-Antczak A, Jastrzębska K, Maciaszek A, Mikołajczyk B, Guga P. P-Stereodefined phosphorothioate analogs of glycol nucleic acids-synthesis and structural properties. RSC Adv 2018; 8:24942-24952. [PMID: 35542141 PMCID: PMC9082371 DOI: 10.1039/c8ra05568h] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2018] [Accepted: 07/02/2018] [Indexed: 11/21/2022] Open
Abstract
Enantiomerically pure, protected acyclic nucleosides of the GNA type (glycol nucleic acids) (GN′), obtained from (R)-(+)- and (S)-(−)-glycidols and the four canonical DNA nucleobases (Ade, Cyt, Gua and Thy), were transformed into 3′-O-DMT-protected 2-thio-4,4-pentamethylene-1,3,2-oxathiaphospholane derivatives (OTP-GN′) containing a second stereogenic center at the phosphorus atom. These monomers were chromatographically separated into P-diastereoisomers, which were further used for the synthesis of P-stereodefined “dinucleoside” phosphorothioates GNPST (GN = GA, GC, GG, GT). The absolute configuration at the phosphorus atom for all eight GNPST was established enzymatically and verified chemically, and correlated with chromatographic mobility of the OTP-GN′ monomers on silica gel. The GNPS units (derived from (R)-(+)-glycidol) were introduced into self-complementary PS-(DNA/GNA) octamers of preselected, uniform absolute configuration at P-atoms. Thermal dissociation experiments showed that the thermodynamic stability of the duplexes depends on the stereochemistry of the phosphorus centers and relative arrangement of the GN units in the oligonucleotide strands. These results correlate with the changes of conformation assessed from circular dichroism spectra. The stability of P-stereodefined PS-(DNA/GNA) duplexes depends on the stereochemistry of the phosphorus centers and arrangement of –GNPS– units in the strands.![]()
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Affiliation(s)
- Agnieszka Tomaszewska-Antczak
- Centre of Molecular and Macromolecular Studies, Polish Academy of Sciences, Department of Bioorganic Chemistry Sienkiewicza 112 90-363 Łódź Poland
| | - Katarzyna Jastrzębska
- Centre of Molecular and Macromolecular Studies, Polish Academy of Sciences, Department of Bioorganic Chemistry Sienkiewicza 112 90-363 Łódź Poland
| | - Anna Maciaszek
- Centre of Molecular and Macromolecular Studies, Polish Academy of Sciences, Department of Bioorganic Chemistry Sienkiewicza 112 90-363 Łódź Poland
| | - Barbara Mikołajczyk
- Centre of Molecular and Macromolecular Studies, Polish Academy of Sciences, Department of Bioorganic Chemistry Sienkiewicza 112 90-363 Łódź Poland
| | - Piotr Guga
- Centre of Molecular and Macromolecular Studies, Polish Academy of Sciences, Department of Bioorganic Chemistry Sienkiewicza 112 90-363 Łódź Poland
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7
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Martínez-Negro M, Guerrero-Martínez A, García-Río L, Domènech Ò, Aicart E, Tros de Ilarduya C, Junquera E. Multidisciplinary Approach to the Transfection of Plasmid DNA by a Nonviral Nanocarrier Based on a Gemini-Bolaamphiphilic Hybrid Lipid. ACS OMEGA 2018; 3:208-217. [PMID: 30023772 PMCID: PMC6044976 DOI: 10.1021/acsomega.7b01657] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 10/27/2017] [Accepted: 12/26/2017] [Indexed: 06/08/2023]
Abstract
A multidisciplinary strategy, including both biochemical and biophysical studies, was proposed here to evaluate the potential of lipid nanoaggregates consisting of a mixture of a gemini-bolaamphiphilic lipid (C6C22C6) and the well-known helper lipid 1,2-dioleoyl-sn-glycero-3-phosphatidylethanolamine (DOPE) to transfect plasmid DNA into living cells in an efficient and safe way. For that purpose, several experimental techniques were employed, such as zeta potential (phase analysis light scattering methodology), agarose gel electrophoresis (pDNA compaction and pDNA protection assays), small-angle X-ray scattering, cryo-transmission electron microscopy, atomic force microscopy, fluorescence-assisted cell sorting, luminometry, and cytotoxicity assays. The results revealed that the cationic lipid and plasmid offer only 70 and 30% of their nominal positive () and negative charges (), respectively. Upon mixing with DOPE, they form lipoplexes that self-aggregate in typical multilamellar Lα lyotropic liquid-crystal nanostructures with sizes in the range of 100-200 nm and low polydispersities, very suitably fitted to remain in the bloodstream and cross the cell membrane. Interestingly, these nanoaggregates were able to compact, protect (from the degrading effect of DNase I), and transfect two DNA plasmids (pEGFP-C3, encoding the green fluorescent protein, and pCMV-Luc, encoding luciferase) into COS-7 cells, with an efficiency equal or even superior to that of the universal control Lipo2000*, as long as the effective +/- charge ratio was maintained higher than 1 but reasonably close to electroneutrality. Moreover, this transfection process was not cytotoxic because the viability of COS-7 cells remained at high levels, greater than 80%. All of these features make the C6C22C6/DOPE nanosystem an optimal nonviral gene nanocarrier in vitro and a potentially interesting candidate for future in vivo experiments.
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Affiliation(s)
- María Martínez-Negro
- Departamento
de Química Física I, Facultad de Ciencias Químicas, Universidad Complutense de Madrid, 28040 Madrid, Spain
| | - Andrés Guerrero-Martínez
- Departamento
de Química Física I, Facultad de Ciencias Químicas, Universidad Complutense de Madrid, 28040 Madrid, Spain
| | - Luis García-Río
- Centro
Singular de Investigación en Química Biolóxica
e Materiais Moleculares (CIQUS) and Departamento de Química
Física, Universidade de Santiago, 15782 Santiago, Spain
| | - Òscar Domènech
- Departamento
de Farmacia, Tecnología Farmacéutica y Fisicoquímica,
Facultad de Farmacia y Ciencia de Los Alimentos, Universitat de Barcelona, and Institut de Nanociència i Nanotecnologia
IN2UB, Barcelona, Catalonia 08028, Spain
| | - Emilio Aicart
- Departamento
de Química Física I, Facultad de Ciencias Químicas, Universidad Complutense de Madrid, 28040 Madrid, Spain
| | - Conchita Tros de Ilarduya
- Departamento
de Farmacia y Tecnología Farmacéutica, Facultad de Farmacia, Universidad de Navarra, Instituto de Investigación
Sanitaria de Navarra, 31008 Pamplona, Spain
| | - Elena Junquera
- Departamento
de Química Física I, Facultad de Ciencias Químicas, Universidad Complutense de Madrid, 28040 Madrid, Spain
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8
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Smith AL, Kolpashchikov DM. Divide and Control: Comparison of Split and Switch Hybridization Sensors. ChemistrySelect 2017; 2:5427-5431. [PMID: 29372178 PMCID: PMC5777618 DOI: 10.1002/slct.201701179] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/25/2023]
Abstract
Hybridization probes have been intensively used for nucleic acid analysis in medicine, forensics and fundamental research. Instantaneous hybridization probes (IHPs) enable signalling immediately after binding to a targeted DNA or RNA sequences without the need to isolate the probe-target complex (e. g. by gel electrophoresis). The two most common strategies for IHP design are conformational switches and split approach. A conformational switch changes its conformation and produces signal upon hybridization to a target. Split approach uses two (or more) strands that independently or semi independently bind the target and produce an output signal only if all components associate. Here, we compared the performance of split vs switch designs for deoxyribozyme (Dz) hybridization probes under optimal conditions for each of them. The split design was represented by binary Dz (BiDz) probes; while catalytic molecular beacon (CMB) probes represented the switch design. It was found that BiDz were significantly more selective than CMBs in recognition of single base substitution. CMBs produced high background signal when operated at 55°C. An important advantage of BiDz over CMB is more straightforward design and simplicity of assay optimization.
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Affiliation(s)
- Alexandra L Smith
- Chemistry Department, University of Central Florida, 4000 N. Central Florida Ave, Orlando, FL 32826
| | - Dmitry M Kolpashchikov
- Chemistry Department, Burnett School of Biomedical Sciences, National Center for Forensic Science, University of Central Florida, 4000 N. Central Florida Ave, Orlando, FL 32826
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9
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Romanucci V, Zarrelli A, Guaragna A, Di Marino C, Di Fabio G. New phosphorylating reagents for deoxyribonucleosides and oligonucleotides. Tetrahedron Lett 2017. [DOI: 10.1016/j.tetlet.2017.02.034] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/20/2022]
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10
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Nuthanakanti A, Boerneke MA, Hermann T, Srivatsan SG. Structure of the Ribosomal RNA Decoding Site Containing a Selenium-Modified Responsive Fluorescent Ribonucleoside Probe. Angew Chem Int Ed Engl 2017; 56:2640-2644. [PMID: 28156044 PMCID: PMC5397316 DOI: 10.1002/anie.201611700] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2016] [Revised: 01/17/2017] [Indexed: 12/22/2022]
Abstract
Comprehensive understanding of the structure–function relationship of RNA both in real time and at atomic level will have a profound impact in advancing our understanding of RNA functions in biology. Here, we describe the first example of a multifunctional nucleoside probe, containing a conformation‐sensitive fluorophore and an anomalous X‐ray diffraction label (5‐selenophene uracil), which enables the correlation of RNA conformation and recognition under equilibrium and in 3D. The probe incorporated into the bacterial ribosomal RNA decoding site, fluorescently reports antibiotic binding and provides diffraction information in determining the structure without distorting native RNA fold. Further, by comparing solution binding data and crystal structure, we gained insight on how the probe senses ligand‐induced conformational change in RNA. Taken together, our nucleoside probe represents a new class of biophysical tool that would complement available tools for functional RNA investigations.
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Affiliation(s)
- Ashok Nuthanakanti
- Department of Chemistry, Indian Institute of Science Education and Research, Dr. Homi Bhabha Road, Pashan, Pune, 411008, India
| | - Mark A Boerneke
- Department of Chemistry and Biochemistry, Center for Drug Discovery Innovation, University of California, San Diego, 9500 Gilman Drive, La Jolla, CA, 92093, USA
| | - Thomas Hermann
- Department of Chemistry and Biochemistry, Center for Drug Discovery Innovation, University of California, San Diego, 9500 Gilman Drive, La Jolla, CA, 92093, USA
| | - Seergazhi G Srivatsan
- Department of Chemistry, Indian Institute of Science Education and Research, Dr. Homi Bhabha Road, Pashan, Pune, 411008, India
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11
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Nuthanakanti A, Boerneke MA, Hermann T, Srivatsan SG. Structure of the Ribosomal RNA Decoding Site Containing a Selenium-Modified Responsive Fluorescent Ribonucleoside Probe. Angew Chem Int Ed Engl 2017. [DOI: 10.1002/ange.201611700] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Affiliation(s)
- Ashok Nuthanakanti
- Department of Chemistry; Indian Institute of Science Education and Research; Dr. Homi Bhabha Road, Pashan Pune 411008 India
| | - Mark A. Boerneke
- Department of Chemistry and Biochemistry; Center for Drug Discovery Innovation; University of California, San Diego; 9500 Gilman Drive La Jolla CA 92093 USA
| | - Thomas Hermann
- Department of Chemistry and Biochemistry; Center for Drug Discovery Innovation; University of California, San Diego; 9500 Gilman Drive La Jolla CA 92093 USA
| | - Seergazhi G. Srivatsan
- Department of Chemistry; Indian Institute of Science Education and Research; Dr. Homi Bhabha Road, Pashan Pune 411008 India
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12
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Passays J, Rubay C, Marcélis L, Elias B. Synthesis and Photophysical Properties of Triazolyl Ir
III
Nucleosides. Eur J Inorg Chem 2017. [DOI: 10.1002/ejic.201601227] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Affiliation(s)
- Johan Passays
- Institute of Condensed Matter and Nanosciences (IMCN) Université catholique de Louvain (UCL) Place Louis Pasteur 1/L4.01.02 1348 Louvain‐la‐Neuve Belgium
| | - Christophe Rubay
- Institute of Condensed Matter and Nanosciences (IMCN) Université catholique de Louvain (UCL) Place Louis Pasteur 1/L4.01.02 1348 Louvain‐la‐Neuve Belgium
| | - Lionel Marcélis
- Institute of Condensed Matter and Nanosciences (IMCN) Université catholique de Louvain (UCL) Place Louis Pasteur 1/L4.01.02 1348 Louvain‐la‐Neuve Belgium
| | - Benjamin Elias
- Institute of Condensed Matter and Nanosciences (IMCN) Université catholique de Louvain (UCL) Place Louis Pasteur 1/L4.01.02 1348 Louvain‐la‐Neuve Belgium
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13
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Ma DL, Wang M, Liu C, Miao X, Kang TS, Leung CH. Metal complexes for the detection of disease-related protein biomarkers. Coord Chem Rev 2016. [DOI: 10.1016/j.ccr.2016.07.010] [Citation(s) in RCA: 45] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
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14
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Kikuchi N, Kolpashchikov DM. Split Spinach Aptamer for Highly Selective Recognition of DNA and RNA at Ambient Temperatures. Chembiochem 2016; 17:1589-92. [PMID: 27305425 DOI: 10.1002/cbic.201600323] [Citation(s) in RCA: 36] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2016] [Indexed: 12/25/2022]
Abstract
Split spinach aptamer (SSA) probes for fluorescent analysis of nucleic acids were designed and tested. In SSA design, two RNA or RNA/DNA strands hybridized to a specific nucleic acid analyte and formed a binding site for low-fluorescent 3,5-difluoro-4-hydroxybenzylidene imidazolinone (DFHBI) dye, which resulted in up to a 270-fold increase in fluorescence. The major advantage of the SSA over state-of-the art fluorescent probes is high selectivity: it produces only background fluorescence in the presence of a single-base-mismatched analyte, even at room temperature. SSA is therefore a promising tool for label-free analysis of nucleic acids at ambient temperatures.
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Affiliation(s)
- Nanami Kikuchi
- Chemistry Department, University of Central Florida, 4000 Central Florida Boulevard, Orlando, FL, 32816-2366, USA
| | - Dmitry M Kolpashchikov
- Chemistry Department, University of Central Florida, 4000 Central Florida Boulevard, Orlando, FL, 32816-2366, USA.
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15
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Sridharan K, Gogtay NJ. Therapeutic nucleic acids: current clinical status. Br J Clin Pharmacol 2016; 82:659-72. [PMID: 27111518 DOI: 10.1111/bcp.12987] [Citation(s) in RCA: 152] [Impact Index Per Article: 19.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/31/2015] [Revised: 04/20/2016] [Accepted: 04/21/2016] [Indexed: 02/06/2023] Open
Abstract
Deoxyribonucleic acid (DNA) and ribonucleic acid (RNA) are simple linear polymers that have been the subject of considerable research in the last two decades and have now moved into the realm of being stand-alone therapeutic agents. Much of this has stemmed from the appreciation that they carry out myriad functions that go beyond mere storage of genetic information and protein synthesis. Therapy with nucleic acids either uses unmodified DNA or RNA or closely related compounds. From both a development and regulatory perspective, they fall somewhere between small molecules and biologics. Several of these compounds are in clinical development and many have received regulatory approval for human use. This review addresses therapeutic uses of DNA based on antisense oligonucleotides, DNA aptamers and gene therapy; and therapeutic uses of RNA including micro RNAs, short interfering RNAs, ribozymes, RNA decoys and circular RNAs. With their specificity, functional diversity and limited toxicity, therapeutic nucleic acids hold enormous promise. However, challenges that need to be addressed include targeted delivery, mass production at low cost, sustaining efficacy and minimizing off-target toxicity. Technological developments will hold the key to this and help accelerate drug approvals in the years to come.
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Affiliation(s)
- Kannan Sridharan
- Department of Health Sciences, College of Medicine, Nursing and Health Sciences, Fiji National University, Suva, Fiji
| | - Nithya Jaideep Gogtay
- Department of Clinical Pharmacology, Seth GS Medical College and KEM Hospital, Mumbai, India
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16
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Ma DL, Wang W, Mao Z, Yang C, Chen XP, Lu JJ, Han QB, Leung CH. A tutorial review for employing enzymes for the construction of G-quadruplex-based sensing platforms. Anal Chim Acta 2016; 913:41-54. [DOI: 10.1016/j.aca.2016.01.043] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2015] [Revised: 01/11/2016] [Accepted: 01/19/2016] [Indexed: 01/31/2023]
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17
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Xu L, Wang W, Chong J, Shin JH, Xu J, Wang D. RNA polymerase II transcriptional fidelity control and its functional interplay with DNA modifications. Crit Rev Biochem Mol Biol 2015; 50:503-19. [PMID: 26392149 DOI: 10.3109/10409238.2015.1087960] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
Abstract
Accurate genetic information transfer is essential for life. As a key enzyme involved in the first step of gene expression, RNA polymerase II (Pol II) must maintain high transcriptional fidelity while it reads along DNA template and synthesizes RNA transcript in a stepwise manner during transcription elongation. DNA lesions or modifications may lead to significant changes in transcriptional fidelity or transcription elongation dynamics. In this review, we will summarize recent progress toward understanding the molecular basis of RNA Pol II transcriptional fidelity control and impacts of DNA lesions and modifications on Pol II transcription elongation.
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Affiliation(s)
- Liang Xu
- a Skaggs School of Pharmacy and Pharmaceutical Sciences, The University of California San Diego , La Jolla , CA , USA
| | - Wei Wang
- a Skaggs School of Pharmacy and Pharmaceutical Sciences, The University of California San Diego , La Jolla , CA , USA
| | - Jenny Chong
- a Skaggs School of Pharmacy and Pharmaceutical Sciences, The University of California San Diego , La Jolla , CA , USA
| | - Ji Hyun Shin
- a Skaggs School of Pharmacy and Pharmaceutical Sciences, The University of California San Diego , La Jolla , CA , USA
| | - Jun Xu
- a Skaggs School of Pharmacy and Pharmaceutical Sciences, The University of California San Diego , La Jolla , CA , USA
| | - Dong Wang
- a Skaggs School of Pharmacy and Pharmaceutical Sciences, The University of California San Diego , La Jolla , CA , USA
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18
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Fakhfakh K, Hughesman CB, Louise Creagh A, Kao V, Haynes C. Calorimetric and Spectroscopic Analysis of the Thermal Stability of Short Duplex DNA-Containing Sugar and Base-Modified Nucleotides. Methods Enzymol 2015; 567:97-127. [PMID: 26794352 DOI: 10.1016/bs.mie.2015.08.001] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
Abstract
Base- and sugar-modified analogs of DNA and RNA are finding ever expanding use in medicine and biotechnology as tools to better tailor structured oligonucleotides by altering their thermal stability, nuclease resistance, base-pairing specificity, antisense activity, or cellular uptake. Proper deployment of these chemical modifications generally requires knowledge of how each affects base-pairing properties and thermal stabilities. Here, we describe in detail how differential scanning calorimetry and UV spectroscopy may be used to quantify the melting thermodynamics of short dsDNA containing chemically modified nucleosides in one or both strands. Insights are provided into why and how the presence of highly stable base pairs containing modified nucleosides can alter the nature of calorimetry or melting spectroscopy data, and how each experiment must therefore be conducted to ensure high-quality melting thermodynamics data are obtained. Strengths and weaknesses of the two methods when applied to chemically modified duplexes are also addressed.
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Affiliation(s)
- Kareem Fakhfakh
- Michael Smith Laboratories, University of British Columbia, Vancouver, British Columbia, Canada; Department of Chemical and Biological Engineering, University of British Columbia, Vancouver, British Columbia, Canada
| | - Curtis B Hughesman
- Michael Smith Laboratories, University of British Columbia, Vancouver, British Columbia, Canada
| | - A Louise Creagh
- Michael Smith Laboratories, University of British Columbia, Vancouver, British Columbia, Canada; Department of Chemical and Biological Engineering, University of British Columbia, Vancouver, British Columbia, Canada
| | - Vincent Kao
- Department of Chemical and Biological Engineering, University of British Columbia, Vancouver, British Columbia, Canada
| | - Charles Haynes
- Michael Smith Laboratories, University of British Columbia, Vancouver, British Columbia, Canada; Department of Chemical and Biological Engineering, University of British Columbia, Vancouver, British Columbia, Canada; RES'EAU Water Research Network, Department of Chemical and Biological Engineering, University of British Columbia, Vancouver, British Columbia, Canada.
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19
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Fakhfakh K, Marais O, Cheng XBJ, Castañeda JR, Hughesman CB, Haynes C. Molecular thermodynamics of LNA:LNA base pairs and the hyperstabilizing effect of 5′-proximal LNA:DNA base pairs. AIChE J 2015. [DOI: 10.1002/aic.14916] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Affiliation(s)
- Kareem Fakhfakh
- Michael Smith Laboratories, University of British Columbia; Vancouver BC Canada
- Dept. of Chemical and Biological Engineering; University of British Columbia; Vancouver BC Canada
| | - Olivia Marais
- Dept. of Chemical and Biological Engineering; University of British Columbia; Vancouver BC Canada
| | - Xin Bo Justin Cheng
- Dept. of Chemical and Biological Engineering; University of British Columbia; Vancouver BC Canada
| | - Jorge Real Castañeda
- Dept. of Chemical and Biological Engineering; University of British Columbia; Vancouver BC Canada
| | - Curtis B. Hughesman
- Michael Smith Laboratories, University of British Columbia; Vancouver BC Canada
| | - Charles Haynes
- Michael Smith Laboratories, University of British Columbia; Vancouver BC Canada
- Dept. of Chemical and Biological Engineering; University of British Columbia; Vancouver BC Canada
- RES'EAU Water Research Network, Dept. of Chemical and Biological Engineering; University of British Columbia; Vancouver BC Canada
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20
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Huang H, Shi S, Zheng X, Yao T. Sensitive detection for coralyne and mercury ions based on homo-A/T DNA by exonuclease signal amplification. Biosens Bioelectron 2015; 71:439-444. [PMID: 25950941 DOI: 10.1016/j.bios.2015.04.076] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2015] [Revised: 04/13/2015] [Accepted: 04/23/2015] [Indexed: 12/27/2022]
Abstract
Based on specific homo-A/T DNA binding properties, a strategy for coralyne and mercury ions detection was realised by exonuclease-aided signal amplification. Coralyne could specifically bind homo-A DNA and protect it from the hydrolysis of exonuclease I. The coralyne-protected DNA was subsequently used as a trigger strand to hydrolyze DNA2 in exonuclease-aided signal amplification process. Thiazole orange was used to quantify the remainder DNA2. Under the optimal condition, the fluorescence intensity was linearly proportional to the concentration of coralyne in the range of 0.2-100 nM with a limit of detection (LOD) of 0.31 nM, which presented the lowest LOD for coralyne among all reported. With homo-T and Hg(2+) taking the place of homo-A DNA and coralyne, respectively, the system could also be used for Hg(2+) detection. The experiments in real samples also showed good results. This method was label-free, low-cost, easy-operating and highly repeatable for the detection of coralyne and mercury ions. It could also be extended to detect various analytes, such as other metal ions, proteins and small molecules by using appropriate aptamers.
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Affiliation(s)
- Hailiang Huang
- Department of Chemistry, and Shanghai Key Lab of Chemical Assessment and Sustainability, Tongji University, Shanghai 200092, China
| | - Shuo Shi
- Department of Chemistry, and Shanghai Key Lab of Chemical Assessment and Sustainability, Tongji University, Shanghai 200092, China.
| | - Xuyue Zheng
- Department of Chemistry, and Shanghai Key Lab of Chemical Assessment and Sustainability, Tongji University, Shanghai 200092, China
| | - Tianming Yao
- Department of Chemistry, and Shanghai Key Lab of Chemical Assessment and Sustainability, Tongji University, Shanghai 200092, China.
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21
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Pawar MG, Nuthanakanti A, Srivatsan SG. Heavy atom containing fluorescent ribonucleoside analog probe for the fluorescence detection of RNA-ligand binding. Bioconjug Chem 2014; 24:1367-77. [PMID: 23841942 DOI: 10.1021/bc400194g] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
Abstract
Although numerous biophysical tools have provided effective systems to study nucleic acids, our current knowledge on how RNA structure complements its function is limited. Therefore, development of robust tools to study the structure–function relationship of RNA is highly desired. Toward this endeavor, we have developed a new ribonucleoside analog, based on a (selenophen-2-yl)pyrimidine core, which could serve as a fluorescence probe to study the function of RNA in real time and as an anomalous scattering label (selenium atom) for the phase determination in X-ray crystallography. The fluorescent selenophene-modified uridine analog is minimally perturbing and exhibits probe-like properties such as sensitivity to microenvironment and conformation changes. Utilizing these properties and amicability of the corresponding ribonucleotide analog to enzymatic incorporation, we have synthesized a fluorescent bacterial ribosomal decoding site (A-site) RNA construct and have developed a fluorescence binding assay to effectively monitor the binding of aminoglycoside antibiotics to the A-site. Our results demonstrate that this simple approach of building a dual probe could provide new avenues to study the structure–function relationship of not only nucleic acids, but also other biomacromolecules.
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22
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Xu L, Butler KV, Chong J, Wengel J, Kool ET, Wang D. Dissecting the chemical interactions and substrate structural signatures governing RNA polymerase II trigger loop closure by synthetic nucleic acid analogues. Nucleic Acids Res 2014; 42:5863-70. [PMID: 24692664 PMCID: PMC4027217 DOI: 10.1093/nar/gku238] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/03/2023] Open
Abstract
The trigger loop (TL) of RNA polymerase II (Pol II) is a conserved structural motif that is crucial for Pol II catalytic activity and transcriptional fidelity. The TL remains in an inactive open conformation when the mismatched substrate is bound. In contrast, TL switches from an inactive open state to a closed active state to facilitate nucleotide addition upon the binding of the cognate substrate to the Pol II active site. However, a comprehensive understanding of the specific chemical interactions and substrate structural signatures that are essential to this TL conformational change remains elusive. Here we employed synthetic nucleotide analogues as ‘chemical mutation’ tools coupling with α-amanitin transcription inhibition assay to systematically dissect the key chemical interactions and structural signatures governing the substrate-coupled TL closure in Saccharomyces cerevisiae Pol II. This study reveals novel insights into understanding the molecular basis of TL conformational transition upon substrate binding during Pol II transcription. This synthetic chemical biology approach may be extended to understand the mechanisms of other RNA polymerases as well as other nucleic acid enzymes in future studies.
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Affiliation(s)
- Liang Xu
- Skaggs School of Pharmacy and Pharmaceutical Sciences, The University of California, San Diego, La Jolla, CA 92093-0625, USA
| | | | - Jenny Chong
- Skaggs School of Pharmacy and Pharmaceutical Sciences, The University of California, San Diego, La Jolla, CA 92093-0625, USA
| | - Jesper Wengel
- Nucleic Acid Center and Biomolecular Nanoscale Engineering Center, Department of Physics, Chemistry and Pharmacy, University of Southern Denmark, Campusvej 55, 5230 Odense M, Denmark
| | - Eric T Kool
- Department of Chemistry, Stanford University, Stanford, CA 94305-5080, USA
| | - Dong Wang
- Skaggs School of Pharmacy and Pharmaceutical Sciences, The University of California, San Diego, La Jolla, CA 92093-0625, USA
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23
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Patzke V, McCaskill JS, von Kiedrowski G. DNA mit 3′-5′-Disulfid-Verknüpfung - schnelle chemische Ligation durch isosteren Ersatz. Angew Chem Int Ed Engl 2014. [DOI: 10.1002/ange.201310644] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
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24
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Patzke V, McCaskill JS, von Kiedrowski G. DNA with 3'-5'-disulfide links--rapid chemical ligation through isosteric replacement. Angew Chem Int Ed Engl 2014; 53:4222-6. [PMID: 24623660 DOI: 10.1002/anie.201310644] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2013] [Revised: 01/28/2014] [Indexed: 11/11/2022]
Abstract
Efforts to chemically ligate oligonucleotides, without resorting to biochemical enzymes, have led to a multitude of synthetic analogues, and have extended oligomer ligation to reactions of novel oligonucleotides, peptides, and hybrids such as PNA.1 Key requirements for potential diagnostic tools not based on PCR include a fast templated chemical DNA ligation method that exhibits high pairing selectivity, and a sensitive detection method. Here we report on a solid-phase synthesis of oligonucleotides containing 5'- or 3'-mercapto-dideoxynucleotides and their chemical ligations, yielding 3'-5'-disulfide bonds as a replacement for 3'-5'-phosphodiester units. Employing a system designed for fluorescence monitoring, we demonstrate one of the fastest ligation reactions with half-lives on the order of seconds. The nontemplated ligation reaction is efficiently suppressed by the choice of DNA modification and the 3'-5' orientation of the activation site. The influence of temperature on the templated reaction is shown.
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Affiliation(s)
- Volker Patzke
- Lehrstuhl für Bioorganische Chemie, Ruhr-Universität Bochum, 44780 Bochum (Germany).
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25
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Ma DL, He HZ, Leung KH, Zhong HJ, Chan DSH, Leung CH. Label-free luminescent oligonucleotide-based probes. Chem Soc Rev 2013; 42:3427-40. [PMID: 23348604 DOI: 10.1039/c2cs35472a] [Citation(s) in RCA: 180] [Impact Index Per Article: 16.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Abstract
Breakthrough advances in chemistry and biology over the last two decades have vastly expanded the repertoire of nucleic acid structure and function with potential application in multiple areas of science and technology, including sensing and analytical applications. DNA oligonucleotides represent popular tools for the development of sensing platforms due to their low cost, rich structural polymorphism, and their ability to bind to cognate ligands with sensitivity and specificity rivaling those for protein enzymes and antibodies. In this review, we give an overview of the "label-free" approach that has been a particular focus of our group and others for the construction of luminescent DNA-based sensing platforms. The label-free strategy aims to overcome some of the drawbacks associated with the use of covalently-labeled oligonucleotides prevalent in electrochemical and optical platforms. Label-free DNA-based probes harness the selective interaction between luminescent dyes and functional oligonucleotides that exhibit a "structure-switching" response upon binding to analytes. Based on the numerous examples of label-free luminescent DNA-based probes reported recently, we envisage that this field would continue to thrive and mature in the years to come.
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Affiliation(s)
- Dik-Lung Ma
- Department of Chemistry, Hong Kong Baptist University, Kowloon Tong, Hong Kong, China.
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26
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Rios AC, Tor Y. On the Origin of the Canonical Nucleobases: An Assessment of Selection Pressures across Chemical and Early Biological Evolution. Isr J Chem 2013; 53:469-483. [PMID: 25284884 PMCID: PMC4181368 DOI: 10.1002/ijch.201300009] [Citation(s) in RCA: 62] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023]
Abstract
The native bases of RNA and DNA are prominent examples of the narrow selection of organic molecules upon which life is based. How did nature "decide" upon these specific heterocycles? Evidence suggests that many types of heterocycles could have been present on the early Earth. It is therefore likely that the contemporary composition of nucleobases is a result of multiple selection pressures that operated during early chemical and biological evolution. The persistence of the fittest heterocycles in the prebiotic environment towards, for example, hydrolytic and photochemical assaults, may have given some nucleobases a selective advantage for incorporation into the first informational polymers. The prebiotic formation of polymeric nucleic acids employing the native bases remains, however, a challenging problem to reconcile. Hypotheses have proposed that the emerging RNA world may have included many types of nucleobases. This is supported by the extensive utilization of non-canonical nucleobases in extant RNA and the resemblance of many of the modified bases to heterocycles generated in simulated prebiotic chemistry experiments. Selection pressures in the RNA world could have therefore narrowed the composition of the nucleic acid bases. Two such selection pressures may have been related to genetic fidelity and duplex stability. Considering these possible selection criteria, the native bases along with other related heterocycles seem to exhibit a certain level of fitness. We end by discussing the strength of the N-glycosidic bond as a potential fitness parameter in the early DNA world, which may have played a part in the refinement of the alphabetic bases.
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Affiliation(s)
- Andro C. Rios
- Department of Chemistry and Biochemistry, University of California, San Diego, 9500 Gilman Drive, La Jolla, CA 92093-0358 (USA), phone: (+1) 8585346401, fax: (+1) 858534 0202
| | - Yitzhak Tor
- Department of Chemistry and Biochemistry, University of California, San Diego, 9500 Gilman Drive, La Jolla, CA 92093-0358 (USA), phone: (+1) 8585346401, fax: (+1) 858534 0202
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27
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Li S, Langenegger SM, Häner R. Control of aggregation-induced emission by DNA hybridization. Chem Commun (Camb) 2013; 49:5835-7. [PMID: 23702589 DOI: 10.1039/c3cc42706d] [Citation(s) in RCA: 65] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Abstract
Aggregation-induced emission (AIE) was studied by hybridization of dialkynyl-tetraphenylethylene (DATPE) modified DNA strands. Molecular aggregation and fluorescence of DATPEs are controlled by duplex formation.
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Affiliation(s)
- Shaoguang Li
- Department of Chemistry and Biochemistry, University of Bern, Freiestrasse 3, CH-3012 Bern, Switzerland
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28
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Tanpure AA, Pawar MG, Srivatsan SG. Fluorescent Nucleoside Analogs: Probes for Investigating Nucleic Acid Structure and Function. Isr J Chem 2013. [DOI: 10.1002/ijch.201300010] [Citation(s) in RCA: 101] [Impact Index Per Article: 9.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
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29
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Nguyen HV, Zhao ZY, Sallustrau A, Horswell SL, Male L, Mulas A, Tucker JHR. A ferrocene nucleic acid oligomer as an organometallic structural mimic of DNA. Chem Commun (Camb) 2013; 48:12165-7. [PMID: 23090440 DOI: 10.1039/c2cc36428j] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
The design, synthesis and electrochemical behaviour of an oligomer consisting of linked thymine-functionalised ferrocene units are reported, which, as a so-called form of ferrocene nucleic acid (FcNA), acts as a structural mimic of DNA.
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Affiliation(s)
- Huy V Nguyen
- School of Chemistry, University of Birmingham, Edgbaston, Birmingham, B15 2TT, UK
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30
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Kaminski PA, Labesse G. Phosphodeoxyribosyltransferases, designed enzymes for deoxyribonucleotides synthesis. J Biol Chem 2013; 288:6534-41. [PMID: 23325804 DOI: 10.1074/jbc.m112.446492] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
A large number of nucleoside analogues and 2'-deoxynucleoside triphosphates (dNTP) have been synthesized to interfere with DNA metabolism. However, in vivo the concentration and phosphorylation of these analogues are key limiting factors. In this context, we designed enzymes to switch nucleobases attached to a deoxyribose monophosphate. Active chimeras were made from two distantly related enzymes: a nucleoside deoxyribosyltransferase from lactobacilli and a 5'-monophosphate-2'-deoxyribonucleoside hydrolase from rat. Then their unprecedented activity was further extended to deoxyribose triphosphate, and in vitro biosyntheses could be successfully performed with several base analogues. These new enzymes provide new tools to synthesize dNTP analogues and to deliver them into cells.
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31
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Lau PS, Li Y. Exploration of structure-switching in the design of aptamer biosensors. ADVANCES IN BIOCHEMICAL ENGINEERING/BIOTECHNOLOGY 2013; 140:69-92. [PMID: 23851586 DOI: 10.1007/10_2013_223] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
The process of "structure-switching" enables biomolecular switches to function as effective biosensing tools. Biomolecular switches can be activated or inactivated by binding to a specific target that triggers a precise conformational change in the biomolecules involved. Although many examples of aptamer-based biomolecular switches can be found in nature, substantial effort has been made in the last decade to engineer structure-switching aptamer sensors by coupling aptamers to a signal transduction method to generate a readout signal upon target binding to the aptamer domain. This chapter focuses on the progress of research on engineered structure-switching aptamer sensors. We begin by discussing the origin of the structure-switching aptamer design, highlight the key developments of structure-switching DNA aptamers for fluorescence-, electrochemistry-, and colorimetry-based detection, and introduce our recent efforts in exploring RNA aptamers to create structure-switching molecular sensors.
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Affiliation(s)
- Pui Sai Lau
- Department of Biochemistry and Biomedical Sciences, Department of Chemistry and Chemical Biology, and Michael D. DeGroote Infectious Disease Research Institute, McMaster University, 1280 Main Street West, Hamilton, ON, L8S 4K1, Canada
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32
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Leung CH, Zhong HJ, He HZ, Lu L, Chan DSH, Ma DL. Luminescent oligonucleotide-based detection of enzymes involved with DNA repair. Chem Sci 2013. [DOI: 10.1039/c3sc51228b] [Citation(s) in RCA: 47] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
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33
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Ma DL, Ma VPY, Chan DSH, Leung KH, He HZ, Leung CH. Recent advances in luminescent heavy metal complexes for sensing. Coord Chem Rev 2012. [DOI: 10.1016/j.ccr.2012.07.005] [Citation(s) in RCA: 241] [Impact Index Per Article: 20.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
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34
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Kotikam V, Fernandes M, Kumar VA. Comparing the interactions of DNA, polyamide (PNA) and polycarbamate nucleic acid (PCNA) oligomers with graphene oxide (GO). Phys Chem Chem Phys 2012; 14:15003-6. [PMID: 23038211 DOI: 10.1039/c2cp42770b] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
The fluorescently labelled short octameric oligothymine sequences of DNA, PNA and PCNA were used in fluorescence quenching studies in conjunction with dispersed graphene oxide. The measurable restoration of their fluorescence by complementary oligodeoxyadenylate was compared. This is the first study aimed at replacing the natural DNA probes with synthetic DNA mimics that show excellent properties in terms of formation of very strong duplexes with cDNA in addition to their stability towards proteases and nucleases.
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Affiliation(s)
- Venubabu Kotikam
- Organic Chemistry Division, CSIR-National Chemical Laboratory, Pune, 411008, India
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35
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Garo F, Häner R. Influence of a GC Base Pair on Excitation Energy Transfer in DNA-Assembled Phenanthrene π-Stacks. Bioconjug Chem 2012; 23:2105-13. [DOI: 10.1021/bc300302v] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Florian Garo
- Department of Chemistry and Biochemistry, University of Bern, Freiestrasse 3, CH-3012 Bern, Switzerland
| | - Robert Häner
- Department of Chemistry and Biochemistry, University of Bern, Freiestrasse 3, CH-3012 Bern, Switzerland
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36
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Wang S, Guo J, Ono T, Kool ET. DNA polyfluorophores for real-time multicolor tracking of dynamic biological systems. Angew Chem Int Ed Engl 2012; 51:7176-80. [PMID: 22684777 DOI: 10.1002/anie.201201928] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2012] [Revised: 04/16/2012] [Indexed: 11/07/2022]
Abstract
Dye-ing to live: Spectral limitations of common organic dyes make it difficult or impossible to visualize and follow multiple biological components in rapidly moving systems. The development of a multispectral set of improved DNA-scaffolded fluorophores is described. Their use in multicolor cellular imaging (see scheme) and in tracking of biological motions on the subsecond timescale is demonstrated.
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Affiliation(s)
- Shenliang Wang
- Department of Chemistry, Stanford University, Stanford, CA 94305, USA
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37
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Wang S, Guo J, Ono T, Kool ET. DNA Polyfluorophores for Real-Time Multicolor Tracking of Dynamic Biological Systems. Angew Chem Int Ed Engl 2012. [DOI: 10.1002/ange.201201928] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
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38
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Rao H, Tanpure AA, Sawant AA, Srivatsan SG. Enzymatic incorporation of an azide-modified UTP analog into oligoribonucleotides for post-transcriptional chemical functionalization. Nat Protoc 2012; 7:1097-112. [PMID: 22576108 DOI: 10.1038/nprot.2012.046] [Citation(s) in RCA: 38] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
This protocol describes the detailed experimental procedure for the synthesis of an azide-modified uridine triphosphate analog and its effective incorporation into an oligoribonucleotide by in vitro transcription reactions. Furthermore, procedures for labeling azide-modified oligoribonucleotides post-transcriptionally with biophysical probes by copper(I)-catalyzed alkyne-azide cycloaddition (CuAAC) and Staudinger reactions are also provided. This post-transcriptional chemical modification protocol is simple and modular, and it affords labeled oligonucleotides in reasonable amounts for biophysical assays. The procedure for enzymatic incorporation of the monophosphate of azide-modified UTP into an oligoribonucleotide transcript takes ∼2 d, and subsequent post-transcriptional chemical functionalization of the transcript takes about 2 d.
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Affiliation(s)
- Harita Rao
- Department of Chemistry, Indian Institute of Science Education and Research, Pune, India
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39
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Malinovskii VL, Nussbaumer AL, Häner R. Oligopyrenotides: chiral nanoscale templates for chromophore assembly. Angew Chem Int Ed Engl 2012; 51:4905-8. [PMID: 22492542 DOI: 10.1002/anie.201201352] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2012] [Indexed: 01/29/2023]
Abstract
Getting organized: DNA-like supramolecular polymers formed of short oligopyrenotides serve as a helical scaffold for the molecular assembly of ligands. The cationic porphyrin meso-tetrakis(1-methylpyridin-4-yl)porphyrin interacts with the helical polymers in a similar way as with poly(dA:dT).
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40
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Malinovskii VL, Nussbaumer AL, Häner R. Oligopyrenotides: Chiral Nanoscale Templates for Chromophore Assembly. Angew Chem Int Ed Engl 2012. [DOI: 10.1002/ange.201201352] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
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41
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42
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Affiliation(s)
- Yin Nah Teo
- Department of Chemistry, Stanford University, California 94305, United States
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43
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Schmouth JF, Bonaguro RJ, Corso-Diaz X, Simpson EM. Modelling human regulatory variation in mouse: finding the function in genome-wide association studies and whole-genome sequencing. PLoS Genet 2012; 8:e1002544. [PMID: 22396661 PMCID: PMC3291530 DOI: 10.1371/journal.pgen.1002544] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022] Open
Abstract
An increasing body of literature from genome-wide association studies and human whole-genome sequencing highlights the identification of large numbers of candidate regulatory variants of potential therapeutic interest in numerous diseases. Our relatively poor understanding of the functions of non-coding genomic sequence, and the slow and laborious process of experimental validation of the functional significance of human regulatory variants, limits our ability to fully benefit from this information in our efforts to comprehend human disease. Humanized mouse models (HuMMs), in which human genes are introduced into the mouse, suggest an approach to this problem. In the past, HuMMs have been used successfully to study human disease variants; e.g., the complex genetic condition arising from Down syndrome, common monogenic disorders such as Huntington disease and β-thalassemia, and cancer susceptibility genes such as BRCA1. In this commentary, we highlight a novel method for high-throughput single-copy site-specific generation of HuMMs entitled High-throughput Human Genes on the X Chromosome (HuGX). This method can be applied to most human genes for which a bacterial artificial chromosome (BAC) construct can be derived and a mouse-null allele exists. This strategy comprises (1) the use of recombineering technology to create a human variant-harbouring BAC, (2) knock-in of this BAC into the mouse genome using Hprt docking technology, and (3) allele comparison by interspecies complementation. We demonstrate the throughput of the HuGX method by generating a series of seven different alleles for the human NR2E1 gene at Hprt. In future challenges, we consider the current limitations of experimental approaches and call for a concerted effort by the genetics community, for both human and mouse, to solve the challenge of the functional analysis of human regulatory variation.
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Affiliation(s)
- Jean-François Schmouth
- Centre for Molecular Medicine and Therapeutics at the Child and Family Research Institute, University of British Columbia, Vancouver, Canada
- Genetics Graduate Program, University of British Columbia, Vancouver, Canada
| | - Russell J. Bonaguro
- Centre for Molecular Medicine and Therapeutics at the Child and Family Research Institute, University of British Columbia, Vancouver, Canada
| | - Ximena Corso-Diaz
- Centre for Molecular Medicine and Therapeutics at the Child and Family Research Institute, University of British Columbia, Vancouver, Canada
- Genetics Graduate Program, University of British Columbia, Vancouver, Canada
| | - Elizabeth M. Simpson
- Centre for Molecular Medicine and Therapeutics at the Child and Family Research Institute, University of British Columbia, Vancouver, Canada
- Genetics Graduate Program, University of British Columbia, Vancouver, Canada
- Department of Medical Genetics, University of British Columbia, Vancouver, Canada
- Department of Psychiatry, University of British Columbia, Vancouver, Canada
- * E-mail:
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Probst M, Wenger D, Biner SM, Häner R. The DNA three-way junction as a mould for tripartite chromophore assembly. Org Biomol Chem 2012; 10:755-9. [DOI: 10.1039/c1ob06400b] [Citation(s) in RCA: 31] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
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Tanaka M, Kozakai R, Saito Y, Saito I. Stabilization of DNA duplex by 2-substituted adenine as a minor groove modifier. Bioorg Med Chem Lett 2011; 21:7021-4. [DOI: 10.1016/j.bmcl.2011.09.104] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2011] [Revised: 09/24/2011] [Accepted: 09/27/2011] [Indexed: 01/07/2023]
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