1
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Bouvarel T, Camperi J, Guillarme D. Multi-dimensional technology - Recent advances and applications for biotherapeutic characterization. J Sep Sci 2024; 47:e2300928. [PMID: 38471977 DOI: 10.1002/jssc.202300928] [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: 12/18/2023] [Revised: 01/23/2024] [Accepted: 01/24/2024] [Indexed: 03/14/2024]
Abstract
This review provides an overview of the latest advancements and applications in multi-dimensional liquid chromatography coupled with mass spectrometry (mD-LC-MS), covering aspects such as inter-laboratory studies, digestion strategy, trapping column, and multi-level analysis. The shift from an offline to an online workflow reduces sample processing artifacts, analytical variability, analysis time, and the labor required for data acquisition. Over the past few years, this technique has demonstrated sufficient maturity for application across a diverse range of complex products. Moreover, there is potential for this strategy to evolve into an integrated process analytical technology tool for the real-time monitoring of monoclonal antibody quality. This review also identifies emerging trends, including its application to new modalities, the possibility of evaluating biological activity within the mD-LC set-up, and the consideration of multi-dimensional capillary electrophoresis as an alternative to mD-LC. As mD-LC-MS continues to evolve and integrate emerging trends, it holds the potential to shape the next generation of analytical tools, offering exciting possibilities for enhanced characterization and monitoring of complex biopharmaceutical products.
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Affiliation(s)
- Thomas Bouvarel
- Protein Analytical Chemistry, Genentech, South San Francisco, California, USA
| | - Julien Camperi
- Cell Therapy Engineering and Development, Genentech, South San Francisco, California, USA
| | - Davy Guillarme
- Institute of Pharmaceutical Sciences of Western Switzerland, University of Geneva, Geneva, Switzerland
- School of Pharmaceutical Sciences, University of Geneva, Geneva, Switzerland
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2
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Sharma VK, Mangla P, Singh SK, Prasad AK. Triazole-linked Nucleic Acids: Synthesis, Therapeutics and Synthetic Biology Applications. Curr Org Synth 2024; 21:436-455. [PMID: 37138439 DOI: 10.2174/1570179420666230502123950] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2022] [Revised: 02/27/2023] [Accepted: 03/10/2023] [Indexed: 05/05/2023]
Abstract
This article covers the triazole-linked nucleic acids where the triazole linkage (TL) replaces the natural phosphate backbone. The replacement is done at either a few selected linkages or all the phosphate linkages. Two triazole linkages, the four-atom TL1 and the six-atom TL2, have been discussed in detail. These triazole-modified oligonucleotides have found a wide range of applications, from therapeutics to synthetic biology. For example, the triazole-linked oligonucleotides have been used in the antisense oligonucleotide (ASO), small interfering RNA (siRNA) and clustered regularly interspaced short palindromic repeats (CRISPR)-Cas9 technology as therapeutic agents. Due to the ease of the synthesis and a wide range of biocompatibility, the triazole linkage TL2 has been used to assemble a functional 300-mer DNA from alkyne- and azide-functionalized 100-mer oligonucleotides as well as an epigenetically modified variant of a 335 base-pair gene from ten short oligonucleotides. These outcomes highlight the potential of triazole-linked nucleic acids and open the doors for other TL designs and artificial backbones to fully exploit the vast potential of artificial nucleic acids in therapeutics, synthetic biology and biotechnology.
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Affiliation(s)
- Vivek K Sharma
- Department of Medicine, University of Massachusetts Chan Medical School, Mattapan, MA 02126, USA
- MassBiologics of the University of Massachusetts Chan Medical School, Mattapan, MA 02126, USA
| | - Priyanka Mangla
- Oligonucleotide Discovery, Discovery Sciences, BioPharmaceuticals R&D, AstraZeneca, Gothenburg, Sweden
| | - Sunil K Singh
- Department of Chemistry, Kirori Mal College, University of Delhi, Delhi, 110 007, India
| | - Ashok K Prasad
- Department of Chemistry, Bioorganic Laboratory, University of Delhi, Delhi, 110 007, India
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3
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Zhang Y, Takaki Y, Yoshida-Takashima Y, Hiraoka S, Kurosawa K, Nunoura T, Takai K. A sequential one-pot approach for rapid and convenient characterization of putative restriction-modification systems. mSystems 2023; 8:e0081723. [PMID: 37843256 PMCID: PMC10734518 DOI: 10.1128/msystems.00817-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2023] [Accepted: 09/05/2023] [Indexed: 10/17/2023] Open
Abstract
IMPORTANCE The elucidation of the molecular basis of virus-host coevolutionary interactions is boosted with state-of-the-art sequencing technologies. However, the sequence-only information is often insufficient to output a conclusive argument without biochemical characterizations. We proposed a 1-day and one-pot approach to confirm the exact function of putative restriction-modification (R-M) genes that presumably mediate microbial coevolution. The experiments mainly focused on a series of putative R-M enzymes from a deep-sea virus and its host bacterium. The results quickly unveiled unambiguous substrate specificities, superior catalytic performance, and unique sequence preferences for two new restriction enzymes (capable of cleaving DNA) and two new methyltransferases (capable of modifying DNA with methyl groups). The reality of the functional R-M system reinforced a model of mutually beneficial interactions with the virus in the deep-sea microbial ecosystem. The cell culture-independent approach also holds great potential for exploring novel and biotechnologically significant R-M enzymes from microbial dark matter.
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Affiliation(s)
- Yi Zhang
- SUGAR Program, X-star, Japan Agency for Marine-Earth Science and Technology (JAMSTEC), Yokosuka, Japan
| | - Yoshihiro Takaki
- SUGAR Program, X-star, Japan Agency for Marine-Earth Science and Technology (JAMSTEC), Yokosuka, Japan
| | - Yukari Yoshida-Takashima
- SUGAR Program, X-star, Japan Agency for Marine-Earth Science and Technology (JAMSTEC), Yokosuka, Japan
| | - Satoshi Hiraoka
- Research Center for Bioscience and Nanoscience (CeBN), MRU, Japan Agency for Marine-Earth Science and Technology (JAMSTEC), Yokosuka, Japan
| | - Kanako Kurosawa
- SUGAR Program, X-star, Japan Agency for Marine-Earth Science and Technology (JAMSTEC), Yokosuka, Japan
| | - Takuro Nunoura
- Research Center for Bioscience and Nanoscience (CeBN), MRU, Japan Agency for Marine-Earth Science and Technology (JAMSTEC), Yokosuka, Japan
| | - Ken Takai
- SUGAR Program, X-star, Japan Agency for Marine-Earth Science and Technology (JAMSTEC), Yokosuka, Japan
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4
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Karami A, Hasani M. Methods to functionalize gold nanoparticles with tandem-phosphorothioate DNA: role of physicochemical properties of the phosphorothioate backbone in DNA adsorption to gold nanoparticles. ANALYTICAL METHODS : ADVANCING METHODS AND APPLICATIONS 2023; 15:4104-4113. [PMID: 37551768 DOI: 10.1039/d3ay00960b] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 08/09/2023]
Abstract
Perception of the differences in the physicochemical properties of phosphorothioate DNA (PS-DNA) and phosphodiester DNA (PO-DNA) greatly aids in understanding the AuNP-DNA binding process. Replacing one non-bridging oxygen atom of the anionic phosphodiester backbone with a sulfur atom leads to a major change in the DNA adsorption mechanism of AuNPs. In this work, we investigated and compared salt-aging, low pH-assisted, and freeze-thaw methods for conjugating phosphorothioate-modified oligonucleotides to AuNPs. The results obtained clearly demonstrate that only the pH-assisted method can successfully bind tandem phosphorothioate DNA to gold nanoparticles and sufficiently maintain the colloidal stability of AuNPs. When a phosphate group is converted to a phosphorothioate group, the negative charge of the phosphate group is located on the sulfur atom. Due to the soft nature of sulfur (a very weak H-bond acceptor), the negative charge on the sulfur atom cannot be shielded even with the gradual addition of salt to increase the ionic strength, so, the pH-assisted based method is the best for the functionalization of AuNPs with tandem-PS DNA.
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Affiliation(s)
- Abbas Karami
- Faculty of Chemistry, Bu-Ali Sina University, Hamedan 65174, Iran.
| | - Masoumeh Hasani
- Faculty of Chemistry, Bu-Ali Sina University, Hamedan 65174, Iran.
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5
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Kawamoto Y, Wu Y, Takahashi Y, Takakura Y. Development of nucleic acid medicines based on chemical technology. Adv Drug Deliv Rev 2023; 199:114872. [PMID: 37244354 DOI: 10.1016/j.addr.2023.114872] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2023] [Revised: 05/01/2023] [Accepted: 05/12/2023] [Indexed: 05/29/2023]
Abstract
Oligonucleotide-based therapeutics have attracted attention as an emerging modality that includes the modulation of genes and their binding proteins related to diseases, allowing us to take action on previously undruggable targets. Since the late 2010s, the number of oligonucleotide medicines approved for clinical uses has dramatically increased. Various chemistry-based technologies have been developed to improve the therapeutic properties of oligonucleotides, such as chemical modification, conjugation, and nanoparticle formation, which can increase nuclease resistance, enhance affinity and selectivity to target sites, suppress off-target effects, and improve pharmacokinetic properties. Similar strategies employing modified nucleobases and lipid nanoparticles have been used for developing coronavirus disease 2019 mRNA vaccines. In this review, we provide an overview of the development of chemistry-based technologies aimed at using nucleic acids for developing therapeutics over the past several decades, with a specific emphasis on the structural design and functionality of chemical modification strategies.
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Affiliation(s)
- Yusuke Kawamoto
- Department of Biopharmaceutics and Drug Metabolism, Graduate School of Pharmaceutical Sciences, Kyoto University, Sakyo, Kyoto 606-8501, Japan.
| | - You Wu
- Department of Biopharmaceutics and Drug Metabolism, Graduate School of Pharmaceutical Sciences, Kyoto University, Sakyo, Kyoto 606-8501, Japan
| | - Yuki Takahashi
- Department of Biopharmaceutics and Drug Metabolism, Graduate School of Pharmaceutical Sciences, Kyoto University, Sakyo, Kyoto 606-8501, Japan
| | - Yoshinobu Takakura
- Department of Biopharmaceutics and Drug Metabolism, Graduate School of Pharmaceutical Sciences, Kyoto University, Sakyo, Kyoto 606-8501, Japan.
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6
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Roussis SG, Rentel C. Exploring the use of the desirability function to optimize the separation of oligonucleotide impurities by ion pair-RP LCMS. J Chromatogr B Analyt Technol Biomed Life Sci 2023; 1220:123666. [PMID: 36921438 DOI: 10.1016/j.jchromb.2023.123666] [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: 01/17/2023] [Revised: 03/03/2023] [Accepted: 03/06/2023] [Indexed: 03/11/2023]
Abstract
The use of small alkyl amines as ion pair reagents permits enhanced separation of impurities of phosphate diester oligonucleotides, which can be beneficial to quality control applications, and aid elucidation of the mechanisms of impurity formation. In general, however, separation of the individual components that comprise the majority of oligonucleotide impurities requires development of several independent chromatographic methods. Ideally, a single method capable of separating the individual components of all impurity classes would be developed. The mathematical concept of the desirability function has been explored here for its ability to determine the combination of experimental factors that result in a single, globally optimized chromatographic method. The optimized mobile phase, consisting of 1 mM propylamine (PA), 30 mM ammonium bicarbonate (ABC), and 1 mM octanoic acid (C8A), produced excellent agreement between measured and predicted peak resolution values for a set of n - 1 impurities. The relative importance of the mobile phase constituents on the mechanism of separation has been discussed. The approach holds great promise for the improved separation of components in complex chromatographic systems.
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Affiliation(s)
| | - Claus Rentel
- Ionis Pharmaceuticals, Carlsbad, CA 92010, United States
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7
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Abstract
Polymerase chain reaction (PCR) has been a powerful molecular biology tool since the mid-1980s. Millions of copies of specific sequence regions of DNA can be generated to allow the study of these regions. Fields that use this technology range from forensics to the experimental study of human biology. Standards for performing PCR and information tools to help design PCR protocols aid in successful implementation of PCR.
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Affiliation(s)
- Page B McKinzie
- Division of Genetic and Molecular Toxicology, National Center for Toxicological Research, U.S. Food and Drug Administration, Jefferson, AR, USA.
| | - Meagan B Myers
- Division of Genetic and Molecular Toxicology, National Center for Toxicological Research, U.S. Food and Drug Administration, Jefferson, AR, USA.
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8
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Separation of phosphorothioate oligonucleotide impurities by WAX HPLC under high organic content elution conditions. Anal Biochem 2022; 659:114956. [PMID: 36270331 DOI: 10.1016/j.ab.2022.114956] [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: 06/28/2022] [Revised: 10/11/2022] [Accepted: 10/12/2022] [Indexed: 12/14/2022]
Abstract
The separation of impurities in phosphorothioate diester (PS) oligonucleotides is complicated by (1) the presence of a very large number of diastereoisomers, e.g., 219 for a 20-mer oligonucleotide, (2) peak broadening due to the hydrophobic character of the sulfur atom, and (3) the chemical similarity of the impurities to the parent oligonucleotide and each other. Further difficulties arise due to the chemical nature of oligonucleotides, which display a complex mixture of ionic, hydrophobic, H-bonding, and other functionalities. To minimize hydrophobic interactions and peak broadening due to the PS modification, we have developed a novel method that combines a weak anion exchange (WAX) column with a mobile phase elution system designed to maximize separation by a single ionic/electrostatic interaction. We found that although chaotropes are helpful, the most significant beneficial effect of the hydrophilic WAX column is that high-organic, low-salt mobile phase is required for product elution. Separations are also benefitted by pH gradient effects on stationary phase electrostatic potential and analyte ionization. An extraordinary degree of separation is achieved by the new WAX method in comparison to SAX (strong anion exchange) chromatography. For the first time, the extent of deamination of PS oligonucleotides is directly determined by a chromatography-only method. The approach, representative results, and the mechanisms of separation are discussed.
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9
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Bege M, Borbás A. The Medicinal Chemistry of Artificial Nucleic Acids and Therapeutic Oligonucleotides. Pharmaceuticals (Basel) 2022; 15:ph15080909. [PMID: 35893733 PMCID: PMC9330994 DOI: 10.3390/ph15080909] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/04/2022] [Revised: 07/17/2022] [Accepted: 07/20/2022] [Indexed: 02/04/2023] Open
Abstract
Nucleic acids play a central role in human biology, making them suitable and attractive tools for therapeutic applications. While conventional drugs generally target proteins and induce transient therapeutic effects, nucleic acid medicines can achieve long-lasting or curative effects by targeting the genetic bases of diseases. However, native oligonucleotides are characterized by low in vivo stability due to nuclease sensitivity and unfavourable physicochemical properties due to their polyanionic nature, which are obstacles to their therapeutic use. A myriad of synthetic oligonucleotides have been prepared in the last few decades and it has been shown that proper chemical modifications to either the nucleobase, the ribofuranose unit or the phosphate backbone can protect the nucleic acids from degradation, enable efficient cellular uptake and target localization ensuring the efficiency of the oligonucleotide-based therapy. In this review, we present a summary of structure and properties of artificial nucleic acids containing nucleobase, sugar or backbone modifications, and provide an overview of the structure and mechanism of action of approved oligonucleotide drugs including gene silencing agents, aptamers and mRNA vaccines.
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Affiliation(s)
- Miklós Bege
- Department of Pharmaceutical Chemistry, University of Debrecen, Egyetem tér 1, 4032 Debrecen, Hungary;
- Institute of Healthcare Industry, University of Debrecen, Nagyerdei körút 98, 4032 Debrecen, Hungary
- MTA-DE Molecular Recognition and Interaction Research Group, University of Debrecen, Egyetem tér 1, 4032 Debrecen, Hungary
| | - Anikó Borbás
- Department of Pharmaceutical Chemistry, University of Debrecen, Egyetem tér 1, 4032 Debrecen, Hungary;
- National Laboratory of Virology, University of Pécs, Ifjúság útja 20, 7624 Pécs, Hungary
- Correspondence:
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10
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Zhu G, Song P, Wu J, Luo M, Chen Z, Chen T. Application of Nucleic Acid Frameworks in the Construction of Nanostructures and Cascade Biocatalysts: Recent Progress and Perspective. Front Bioeng Biotechnol 2022; 9:792489. [PMID: 35071205 PMCID: PMC8777461 DOI: 10.3389/fbioe.2021.792489] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2021] [Accepted: 12/10/2021] [Indexed: 12/12/2022] Open
Abstract
Nucleic acids underlie the storage and retrieval of genetic information literally in all living organisms, and also provide us excellent materials for making artificial nanostructures and scaffolds for constructing multi-enzyme systems with outstanding performance in catalyzing various cascade reactions, due to their highly diverse and yet controllable structures, which are well determined by their sequences. The introduction of unnatural moieties into nucleic acids dramatically increased the diversity of sequences, structures, and properties of the nucleic acids, which undoubtedly expanded the toolbox for making nanomaterials and scaffolds of multi-enzyme systems. In this article, we first introduce the molecular structures and properties of nucleic acids and their unnatural derivatives. Then we summarized representative artificial nanomaterials made of nucleic acids, as well as their properties, functions, and application. We next review recent progress on constructing multi-enzyme systems with nucleic acid structures as scaffolds for cascade biocatalyst. Finally, we discuss the future direction of applying nucleic acid frameworks in the construction of nanomaterials and multi-enzyme molecular machines, with the potential contribution that unnatural nucleic acids may make to this field highlighted.
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Affiliation(s)
- Gan Zhu
- MOE International Joint Research Laboratory on Synthetic Biology and Medicines, School of Biology and Biological Engineering, South China University of Technology, Guangzhou, China
| | - Ping Song
- MOE International Joint Research Laboratory on Synthetic Biology and Medicines, School of Biology and Biological Engineering, South China University of Technology, Guangzhou, China
| | - Jing Wu
- MOE International Joint Research Laboratory on Synthetic Biology and Medicines, School of Biology and Biological Engineering, South China University of Technology, Guangzhou, China
| | - Minglan Luo
- MOE International Joint Research Laboratory on Synthetic Biology and Medicines, School of Biology and Biological Engineering, South China University of Technology, Guangzhou, China
| | - Zhipeng Chen
- MOE International Joint Research Laboratory on Synthetic Biology and Medicines, School of Biology and Biological Engineering, South China University of Technology, Guangzhou, China
| | - Tingjian Chen
- MOE International Joint Research Laboratory on Synthetic Biology and Medicines, School of Biology and Biological Engineering, South China University of Technology, Guangzhou, China
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11
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Leguizamon SC, Scott TF. Mimicking DNA Functions with Abiotic, Sequence-Defined Polymers. POLYM REV 2021. [DOI: 10.1080/15583724.2021.2014519] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
Affiliation(s)
- Samuel C. Leguizamon
- Department of Chemical Engineering, University of Michigan, Ann Arbor, Michigan, USA
| | - Timothy F. Scott
- Department of Chemical Engineering, Monash University, Clayton, VIC, Australia
- Department of Materials Science and Engineering, Monash University, Clayton, VIC, Australia
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12
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Roussis SG, Cedillo I, Rentel C. Characterizing the Diastereoisomeric Distribution of Phosphorothioate Oligonucleotides by Metal Ion Complexation Chromatography, In-Series Reversed Phase-Strong Anion Exchange Chromatography, and 31P NMR. Anal Chem 2021; 93:16035-16042. [PMID: 34813705 DOI: 10.1021/acs.analchem.1c03593] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Replacement of a non-bridging oxygen atom of the phosphate diester linkage of an oligonucleotide by sulfur conveys pharmacokinetic benefits, such as increased nuclease resistance and enhanced protein binding. Substitution renders the internucleotide linkages chiral, and so phosphorothioate diester (PS) oligonucleotides comprise complex mixtures of diastereoisomers. Currently, chromatographic separation of individual diastereoisomers is limited to oligonucleotides that contain no more than about four or five PS linkages. The development of therapeutic PS oligonucleotides, which often contain >15 PS linkages, would be greatly aided by methods useful for assessing batch-to-batch stereo-reproducibility. To this effect, the relative sensitivities of metal ion complexation chromatography (MICC), in-series reversed phase-strong anion exchange chromatography (RP-SAX), and 31P NMR toward changes in the diastereoisomeric distributions of therapeutic PS oligonucleotides were compared. Model oligonucleotides synthesized under conditions known to impact PS stereochemistry were used to evaluate the method performance, and all three methods showed excellent sensitivity toward changes in the diastereoisomeric composition. Interactions via the solvent-accessible areas and a combination of hydrophobic and electrostatic forces may be responsible for the selectivity demonstrated by MICC and in-series RP-SAX, respectively.
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Affiliation(s)
- Stilianos G Roussis
- Ionis Pharmaceuticals, 2855 Gazelle Ct., Carlsbad, California 92010, United States
| | - Isaiah Cedillo
- Ionis Pharmaceuticals, 2855 Gazelle Ct., Carlsbad, California 92010, United States
| | - Claus Rentel
- Ionis Pharmaceuticals, 2855 Gazelle Ct., Carlsbad, California 92010, United States
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13
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Ba S, Gao G, Li T, Zhang H. Tricking enzymes in living cells: a mechanism-based strategy for design of DNA topoisomerase biosensors. J Nanobiotechnology 2021; 19:407. [PMID: 34876137 PMCID: PMC8650243 DOI: 10.1186/s12951-021-01155-1] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2021] [Accepted: 11/21/2021] [Indexed: 12/30/2022] Open
Abstract
Most activity-based molecular probes are designed to target enzymes that catalyze the breaking of chemical bonds and the conversion of a unimolecular substrate into bimolecular products. However, DNA topoisomerases are a class of enzymes that alter DNA topology without producing any molecular segments during catalysis, which hinders the development of practical methods for diagnosing these key biomarkers in living cells. Here, we established a new strategy for the effective sensing of the expression levels and catalytic activities of topoisomerases in cell-free systems and human cells. Using our newly designed biosensors, we tricked DNA topoisomerases within their catalytic cycles to switch on fluorescence and resume new rounds of catalysis. Considering that human topoisomerases have been widely recognized as biomarkers for multiple cancers and identified as promising targets for several anticancer drugs, we believe that these DNA-based biosensors and our design strategy would greatly benefit the future development of clinical tools for cancer diagnosis and treatment. ![]()
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Affiliation(s)
- Sai Ba
- School of Chemistry and Chemical Engineering, Northwestern Polytechnical University, Xi'an, 710072, China.,Division of Chemistry and Biological Chemistry, School of Physical and Mathematical Sciences, Nanyang Technological University, Singapore, 637371, Singapore
| | - Guangpeng Gao
- School of Chemistry and Chemical Engineering, Northwestern Polytechnical University, Xi'an, 710072, China
| | - Tianhu Li
- School of Chemistry and Chemical Engineering, Northwestern Polytechnical University, Xi'an, 710072, China.
| | - Hao Zhang
- School of Chemistry and Chemical Engineering, Northwestern Polytechnical University, Xi'an, 710072, China. .,Division of Chemistry and Biological Chemistry, School of Physical and Mathematical Sciences, Nanyang Technological University, Singapore, 637371, Singapore.
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14
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Karami A, Hasani M, Azizi Jalilian F, Ezati R. Hairpin-Spherical Nucleic Acids for Diagnosing COVID-19: a Simple Method to Generalize the Conventional PCR for Molecular Assays. Anal Chem 2021; 93:9250-9257. [PMID: 34156834 PMCID: PMC8247783 DOI: 10.1021/acs.analchem.1c01515] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2021] [Accepted: 06/08/2021] [Indexed: 12/24/2022]
Abstract
The COVID-19 pandemic revealed during the first global wave of this infectious disease that mass diagnostic testing was necessary to more rapidly detect infection in patients and control the pandemic. Therefore, extra research efforts to develop reliable and more accessible techniques for disease diagnosis are of supreme importance. Here, a target-responsive assembly of gold nanoparticle-core hairpin-spherical nucleic acids (AuNP-core H-SNAs) was implemented to modify the conventional polymerase chain reaction (PCR) assay for the "naked-eye" colorimetric detection of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) RNA. Two hairpin DNA ligands are designed based on the two highly conserved regions within N and E genes of SARS-CoV-2 RNA by positioning two short palindromic arms (stem) on either side of a recognition sequence (loop). In the presence of a sequence-specific probe (activator), hairpin DNAs anchored to the surface of AuNPs unfold and expose the palindromic ends to the DNA-directed assembly of AuNPs. The sequence of the activator probes was chosen to be identical to the TaqMan probe in a real-time reverse transcription PCR (RT-PCR) assay for specifically targeting the N and E genes of SARS-CoV-2 RNA. They may either be degraded by the 5'-exonuclease activity of DNA polymerase during PCR cycles or stay intact depending on the presence or absence of the target template in the sample, respectively. Post-addition of H-SNA solutions to the final PCR products of some preconfirmed clinical samples for COVID-19 generated naked-eye-observable red and blue colors for positive and negative cases, respectively, with similar sensitivity to that of the real-time RT-PCR method.
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Affiliation(s)
- Abbas Karami
- Faculty
of Chemistry, Bu-Ali Sina University, Hamedan 65174, Iran
| | - Masoumeh Hasani
- Faculty
of Chemistry, Bu-Ali Sina University, Hamedan 65174, Iran
| | - Farid Azizi Jalilian
- Department
of Medical Virology, Faculty of Medicine, Hamedan University of Medical Sciences, Hamedan 6517619654, Iran
| | - Razieh Ezati
- Department
of Molecular Diagnosis, Farzan Molecular
and Pathobiology Laboratory, Hamedan 6515638377, Iran
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15
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Dziuba D, Didier P, Ciaco S, Barth A, Seidel CAM, Mély Y. Fundamental photophysics of isomorphic and expanded fluorescent nucleoside analogues. Chem Soc Rev 2021; 50:7062-7107. [PMID: 33956014 DOI: 10.1039/d1cs00194a] [Citation(s) in RCA: 29] [Impact Index Per Article: 9.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
Fluorescent nucleoside analogues (FNAs) are structurally diverse mimics of the natural essentially non-fluorescent nucleosides which have found numerous applications in probing the structure and dynamics of nucleic acids as well as their interactions with various biomolecules. In order to minimize disturbance in the labelled nucleic acid sequences, the FNA chromophoric groups should resemble the natural nucleobases in size and hydrogen-bonding patterns. Isomorphic and expanded FNAs are the two groups that best meet the criteria of non-perturbing fluorescent labels for DNA and RNA. Significant progress has been made over the past decades in understanding the fundamental photophysics that governs the spectroscopic and environmentally sensitive properties of these FNAs. Herein, we review recent advances in the spectroscopic and computational studies of selected isomorphic and expanded FNAs. We also show how this information can be used as a rational basis to design new FNAs, select appropriate sequences for optimal spectroscopic response and interpret fluorescence data in FNA applications.
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Affiliation(s)
- Dmytro Dziuba
- Laboratoire de Bioimagerie et Pathologies, UMR 7021, Université de Strasbourg, 74 route du Rhin, 67401 Illkirch, France.
| | - Pascal Didier
- Laboratoire de Bioimagerie et Pathologies, UMR 7021, Université de Strasbourg, 74 route du Rhin, 67401 Illkirch, France.
| | - Stefano Ciaco
- Laboratoire de Bioimagerie et Pathologies, UMR 7021, Université de Strasbourg, 74 route du Rhin, 67401 Illkirch, France. and Department of Biotechnology, Chemistry and Pharmacy, University of Siena, via Aldo Moro 2, 53100 Siena, Italy
| | - Anders Barth
- Institut für Physikalische Chemie, Lehrstuhl für Molekulare Physikalische Chemie, Heinrich-Heine-Universität, 40225 Düsseldorf, Germany
| | - Claus A M Seidel
- Institut für Physikalische Chemie, Lehrstuhl für Molekulare Physikalische Chemie, Heinrich-Heine-Universität, 40225 Düsseldorf, Germany
| | - Yves Mély
- Laboratoire de Bioimagerie et Pathologies, UMR 7021, Université de Strasbourg, 74 route du Rhin, 67401 Illkirch, France.
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Warminski M, Kowalska J, Jemielity J. Solid-Phase Synthesis of RNA 5'-Azides and Their Application for Labeling, Ligation, and Cyclization Via Click Chemistry. ACTA ACUST UNITED AC 2021; 82:e112. [PMID: 32716612 DOI: 10.1002/cpnc.112] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023]
Abstract
RNAs with 5' functional groups have been gaining interest as molecular probes and reporter molecules. Copper-catalyzed azide-alkyne cycloaddition is one of the most straightforward methods to access such molecules; however, RNA functionalization with azide group has been posing a synthetic challenge. This article describes a simple and efficient protocol for azide functionalization of oligoribonucleotides 5'-end in solid-phase. An azide moiety is attached directly to the C5'-end in two steps: (i) -OH to -I conversion using methyltriphenoxyphosphonium iodide, and (ii) -I to -N3 substitution using sodium azide. The reactivity of the resulting compounds is exemplified by fluorescent labeling using both copper(I)-catalyzed (CuAAC) and strain-promoted (SPAAC) azide-alkyne cycloaddition reactions, ligation of two RNA fragments, and cyclization of short bifunctionalized oligonucleotides. The protocol makes use of oligoribonucleotides synthesized by standard phosphoramidite approach on solid support, using commercially available 2'-O-PivOM-protected monomers. Such a protection strategy eliminates the interference between the iodination reagent and silyl protecting groups (TBDMS, TOM) commonly used in RNA synthesis by phosphoramidite approach. © 2020 Wiley Periodicals LLC. Basic Protocol 1: Solid-phase synthesis of oligoribonucleotide 5'-azides Basic Protocol 2: CuAAC labeling of oligoribonucleotide 5'-azides in solution Alternate Protocol 1: CuAAC labeling of oligoribonucleotide 5'-azides on solid support Basic Protocol 3: SPAAC labeling of oligoribonucleotide 5'-azides Basic Protocol 4: CuAAC ligation of oligoribonucleotide 5'-azides Basic Protocol 5: CuAAC cyclization of oligoribonucleotide 5'-azides Support Protocol: HPLC Purification.
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Affiliation(s)
- Marcin Warminski
- Division of Biophysics, Institute of Experimental Physics, Faculty of Physics, University of Warsaw, Warsaw, Poland
| | - Joanna Kowalska
- Division of Biophysics, Institute of Experimental Physics, Faculty of Physics, University of Warsaw, Warsaw, Poland
| | - Jacek Jemielity
- Centre of New Technologies, University of Warsaw, Warsaw, Poland
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17
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Binzel DW, Li X, Burns N, Khan E, Lee WJ, Chen LC, Ellipilli S, Miles W, Ho YS, Guo P. Thermostability, Tunability, and Tenacity of RNA as Rubbery Anionic Polymeric Materials in Nanotechnology and Nanomedicine-Specific Cancer Targeting with Undetectable Toxicity. Chem Rev 2021; 121:7398-7467. [PMID: 34038115 DOI: 10.1021/acs.chemrev.1c00009] [Citation(s) in RCA: 37] [Impact Index Per Article: 12.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
RNA nanotechnology is the bottom-up self-assembly of nanometer-scale architectures, resembling LEGOs, composed mainly of RNA. The ideal building material should be (1) versatile and controllable in shape and stoichiometry, (2) spontaneously self-assemble, and (3) thermodynamically, chemically, and enzymatically stable with a long shelf life. RNA building blocks exhibit each of the above. RNA is a polynucleic acid, making it a polymer, and its negative-charge prevents nonspecific binding to negatively charged cell membranes. The thermostability makes it suitable for logic gates, resistive memory, sensor set-ups, and NEM devices. RNA can be designed and manipulated with a level of simplicity of DNA while displaying versatile structure and enzyme activity of proteins. RNA can fold into single-stranded loops or bulges to serve as mounting dovetails for intermolecular or domain interactions without external linking dowels. RNA nanoparticles display rubber- and amoeba-like properties and are stretchable and shrinkable through multiple repeats, leading to enhanced tumor targeting and fast renal excretion to reduce toxicities. It was predicted in 2014 that RNA would be the third milestone in pharmaceutical drug development. The recent approval of several RNA drugs and COVID-19 mRNA vaccines by FDA suggests that this milestone is being realized. Here, we review the unique properties of RNA nanotechnology, summarize its recent advancements, describe its distinct attributes inside or outside the body and discuss potential applications in nanotechnology, medicine, and material science.
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Affiliation(s)
- Daniel W Binzel
- Center for RNA Nanobiotechnology and Nanomedicine, College of Pharmacy, Dorothy M. Davis Heart and Lung Research Institute, James Comprehensive Cancer Center, College of Medicine, The Ohio State University, Columbus, Ohio 43210, United States
| | - Xin Li
- Center for RNA Nanobiotechnology and Nanomedicine, College of Pharmacy, Dorothy M. Davis Heart and Lung Research Institute, James Comprehensive Cancer Center, College of Medicine, The Ohio State University, Columbus, Ohio 43210, United States
| | - Nicolas Burns
- Center for RNA Nanobiotechnology and Nanomedicine, College of Pharmacy, Dorothy M. Davis Heart and Lung Research Institute, James Comprehensive Cancer Center, College of Medicine, The Ohio State University, Columbus, Ohio 43210, United States
| | - Eshan Khan
- Department of Cancer Biology and Genetics, The Ohio State University Comprehensive Cancer Center, College of Medicine, Center for RNA Biology, The Ohio State University, Columbus, Ohio 43210, United States
| | - Wen-Jui Lee
- TMU Research Center of Cancer Translational Medicine, School of Medical Laboratory Science and Biotechnology, College of Medical Science and Technology, Graduate Institute of Medical Sciences, College of Medicine, Taipei Medical University, Department of Laboratory Medicine, Taipei Medical University Hospital, Taipei 110, Taiwan
| | - Li-Ching Chen
- TMU Research Center of Cancer Translational Medicine, School of Medical Laboratory Science and Biotechnology, College of Medical Science and Technology, Graduate Institute of Medical Sciences, College of Medicine, Taipei Medical University, Department of Laboratory Medicine, Taipei Medical University Hospital, Taipei 110, Taiwan
| | - Satheesh Ellipilli
- Center for RNA Nanobiotechnology and Nanomedicine, College of Pharmacy, Dorothy M. Davis Heart and Lung Research Institute, James Comprehensive Cancer Center, College of Medicine, The Ohio State University, Columbus, Ohio 43210, United States
| | - Wayne Miles
- Department of Cancer Biology and Genetics, The Ohio State University Comprehensive Cancer Center, College of Medicine, Center for RNA Biology, The Ohio State University, Columbus, Ohio 43210, United States
| | - Yuan Soon Ho
- TMU Research Center of Cancer Translational Medicine, School of Medical Laboratory Science and Biotechnology, College of Medical Science and Technology, Graduate Institute of Medical Sciences, College of Medicine, Taipei Medical University, Department of Laboratory Medicine, Taipei Medical University Hospital, Taipei 110, Taiwan
| | - Peixuan Guo
- Center for RNA Nanobiotechnology and Nanomedicine, College of Pharmacy, Dorothy M. Davis Heart and Lung Research Institute, James Comprehensive Cancer Center, College of Medicine, The Ohio State University, Columbus, Ohio 43210, United States
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18
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Ahn SY, Liu J, Vellampatti S, Wu Y, Um SH. DNA Transformations for Diagnosis and Therapy. ADVANCED FUNCTIONAL MATERIALS 2021; 31:2008279. [PMID: 33613148 PMCID: PMC7883235 DOI: 10.1002/adfm.202008279] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/28/2020] [Revised: 11/22/2020] [Indexed: 05/03/2023]
Abstract
Due to its unique physical and chemical characteristics, DNA, which is known only as genetic information, has been identified and utilized as a new material at an astonishing rate. The role of DNA has increased dramatically with the advent of various DNA derivatives such as DNA-RNA, DNA-metal hybrids, and PNA, which can be organized into 2D or 3D structures by exploiting their complementary recognition. Due to its intrinsic biocompatibility, self-assembly, tunable immunogenicity, structural programmability, long stability, and electron-rich nature, DNA has generated major interest in electronic and catalytic applications. Based on its advantages, DNA and its derivatives are utilized in several fields where the traditional methodologies are ineffective. Here, the present challenges and opportunities of DNA transformations are demonstrated, especially in biomedical applications that include diagnosis and therapy. Natural DNAs previously utilized and transformed into patterns are not found in nature due to lack of multiplexing, resulting in low sensitivity and high error frequency in multi-targeted therapeutics. More recently, new platforms have advanced the diagnostic ability and therapeutic efficacy of DNA in biomedicine. There is confidence that DNA will play a strong role in next-generation clinical technology and can be used in multifaceted applications.
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Affiliation(s)
- So Yeon Ahn
- School of Chemical EngineeringSungkyunkwan University2066, Seobu‐ro, Jangan‐guSuwonGyeonggi‐do16419Korea
| | - Jin Liu
- Hubei Key Laboratory of Bioinorganic Chemistry and Materia MedicaSchool of Chemistry and Chemical Engineering Huazhong University of Science and Technology1037 Luoyu LoadWuhan430074China
| | - Srivithya Vellampatti
- Institute of Convergent Chemical Engineering and TechnologySungkyunkwan University2066, Seobu‐ro, Jangan‐guSuwonGyeonggi‐do16419Korea
- Present address:
Progeneer, Inc.#1002, 12, Digital‐ro 31‐gil, Guro‐guSeoul08380Korea
| | - Yuzhou Wu
- Hubei Key Laboratory of Bioinorganic Chemistry and Materia MedicaSchool of Chemistry and Chemical Engineering Huazhong University of Science and Technology1037 Luoyu LoadWuhan430074China
| | - Soong Ho Um
- School of Chemical EngineeringSKKU Advanced Institute of Nanotechnology (SAINT)Biomedical Institute for Convergence at SKKU (BICS) and Institute of Quantum Biophysics (IQB)Sungkyunkwan University2066, Seobu‐ro, Jangan‐guSuwonGyeonggi‐do16419Korea
- Progeneer Inc.#1002, 12, Digital‐ro 31‐gil, Guro‐guSeoul08380Korea
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19
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Clavé G, Reverte M, Vasseur JJ, Smietana M. Modified internucleoside linkages for nuclease-resistant oligonucleotides. RSC Chem Biol 2021; 2:94-150. [PMID: 34458777 PMCID: PMC8341215 DOI: 10.1039/d0cb00136h] [Citation(s) in RCA: 31] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2020] [Accepted: 10/16/2020] [Indexed: 12/21/2022] Open
Abstract
In the past few years, several drugs derived from nucleic acids have been approved for commercialization and many more are in clinical trials. The sensitivity of these molecules to nuclease digestion in vivo implies the need to exploit resistant non-natural nucleotides. Among all the possible modifications, the one concerning the internucleoside linkage is of particular interest. Indeed minor changes to the natural phosphodiester may result in major modifications of the physico-chemical properties of nucleic acids. As this linkage is a key element of nucleic acids' chemical structures, its alteration can strongly modulate the plasma stability, binding properties, solubility, cell penetration and ultimately biological activity of nucleic acids. Over the past few decades, many research groups have provided knowledge about non-natural internucleoside linkage properties and participated in building biologically active nucleic acid derivatives. The recent renewing interest in nucleic acids as drugs, demonstrated by the emergence of new antisense, siRNA, aptamer and cyclic dinucleotide molecules, justifies the review of all these studies in order to provide new perspectives in this field. Thus, in this review we aim at providing the reader insights into modified internucleoside linkages that have been described over the years whose impact on annealing properties and resistance to nucleases have been evaluated in order to assess their potential for biological applications. The syntheses of modified nucleotides as well as the protocols developed for their incorporation within oligonucleotides are described. Given the intended biological applications, the modifications described in the literature that have not been tested for their resistance to nucleases are not reported.
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Affiliation(s)
| | - Maeva Reverte
- IBMM, Univ. Montpellier, CNRS, ENSCM Montpellier France
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20
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Samanta D, Ebrahimi SB, Mirkin CA. Nucleic-Acid Structures as Intracellular Probes for Live Cells. ADVANCED MATERIALS (DEERFIELD BEACH, FLA.) 2020; 32:e1901743. [PMID: 31271253 PMCID: PMC6942251 DOI: 10.1002/adma.201901743] [Citation(s) in RCA: 90] [Impact Index Per Article: 22.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/19/2019] [Revised: 05/08/2019] [Indexed: 05/02/2023]
Abstract
The chemical composition of cells at the molecular level determines their growth, differentiation, structure, and function. Probing this composition is powerful because it provides invaluable insight into chemical processes inside cells and in certain cases allows disease diagnosis based on molecular profiles. However, many techniques analyze fixed cells or lysates of bulk populations, in which information about dynamics and cellular heterogeneity is lost. Recently, nucleic-acid-based probes have emerged as a promising platform for the detection of a wide variety of intracellular analytes in live cells with single-cell resolution. Recent advances in this field are described and common strategies for probe design, types of targets that can be identified, current limitations, and future directions are discussed.
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Affiliation(s)
- Devleena Samanta
- Department of Chemistry and International Institute for Nanotechnology, Northwestern University, 2145 Sheridan Road, Evanston, IL, 60208, USA
| | - Sasha B Ebrahimi
- Department of Chemical and Biological Engineering, Northwestern University, 2145 Sheridan Road, Evanston, IL, 60208, USA
| | - Chad A Mirkin
- Department of Chemistry and International Institute for Nanotechnology, Northwestern University, 2145 Sheridan Road, Evanston, IL, 60208, USA
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21
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Yamashita S, Nishida K, Osawa T, Nakanishi A, Ito Y, Hari Y. Synthesis of Oligonucleotides Containing 2'- N-alkylaminocarbonyl-2'-amino-LNA (2'-urea-LNA) Moieties Using Post-Synthetic Modification Strategy. Molecules 2020; 25:molecules25020346. [PMID: 31952133 PMCID: PMC7024358 DOI: 10.3390/molecules25020346] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2019] [Revised: 01/10/2020] [Accepted: 01/14/2020] [Indexed: 11/16/2022] Open
Abstract
The post-synthetic modification of an oligonucleotide is a powerful strategy for the synthesis of various analogs of the oligonucleotide, aiming to achieve the desired functions. In this study, we synthesized the thymidine phosphoramidite of 2′-N-pentafluorophenoxycarbonyl-2′-amino-LNA, which was introduced into oligonucleotides. Oligonucleotides containing a 2′-N-pentafluorophenoxycarbonyl-2′-amino-LNA unit could be isolated under ultra-mild deprotection conditions (50 mM K2CO3 in MeOH at room temperature for 4 h). Moreover, by treatment with various amines as a post-synthetic modification, the oligonucleotides were successfully converted into the corresponding 2′-N-alkylaminocarbonyl-2′-amino-LNA (2′-urea-LNA) derivatives. The duplex- and triplex-forming abilities of the synthesized oligonucleotides were evaluated by UV-melting experiments, which showed that 2′-urea-LNAs could stabilize the nucleic acid complexes, similar to the proto-type, 2′-amino-LNA. Thus, 2′-urea-LNAs could be promising units for the modification of oligonucleotides; the design of a substituent on urea may aid the formation of useful oligonucleotides. In addition, pentafluorophenoxycarbonyl, an amino moiety, acted as a precursor of the substituted urea, which may be applicable to the synthesis of oligonucleotide conjugates.
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Affiliation(s)
- Shoko Yamashita
- Faculty of Pharmaceutical Sciences, Tokushima Bunri University, Nishihama, Yamashiro-cho, Tokushima 770-8514, Japan
| | - Kodai Nishida
- Faculty of Pharmaceutical Sciences, Tokushima Bunri University, Nishihama, Yamashiro-cho, Tokushima 770-8514, Japan
| | - Takashi Osawa
- Faculty of Pharmaceutical Sciences, Tokushima Bunri University, Nishihama, Yamashiro-cho, Tokushima 770-8514, Japan
- Graduate School of Pharmaceutical Sciences, Osaka University, 1-6 Yamadaoka, Suita 565-0871, Japan
| | - Ayumi Nakanishi
- Faculty of Pharmaceutical Sciences, Tokushima Bunri University, Nishihama, Yamashiro-cho, Tokushima 770-8514, Japan
| | - Yuta Ito
- Faculty of Pharmaceutical Sciences, Tokushima Bunri University, Nishihama, Yamashiro-cho, Tokushima 770-8514, Japan
| | - Yoshiyuki Hari
- Faculty of Pharmaceutical Sciences, Tokushima Bunri University, Nishihama, Yamashiro-cho, Tokushima 770-8514, Japan
- Correspondence:
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22
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Jastrzębska K, Mikołajczyk B, Guga P. LNA units present in [ RP-PS]-(DNA#LNA) chimeras enhance the thermal stability of parallel duplexes and triplexes formed with (2′-OMe)-RNA strands. RSC Adv 2020; 10:22370-22376. [PMID: 35514591 PMCID: PMC9054617 DOI: 10.1039/d0ra03934a] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2020] [Accepted: 05/28/2020] [Indexed: 11/21/2022] Open
Abstract
The results of CD measurements indicate that 2-4 LNA units distributed along 12 nt P-stereodefined phosphorothioate [RP-PS]-(DNA#LNA) chimeras impose a C3′-endo conformation on the 2′-deoxyribonucleosides. Under neutral and slightly acidic conditions homopurine [Rp-PS]-(DNA#LNA) hybridizes with 9–12 nt Hoogsteen-paired (2′-OMe)-RNA strands to form parallel duplexes, which are thermally more stable than the reported earlier analogous complexes containing LNA-free [RP-PS]-DNA oligomers (ΔTm = 7 °C per LNA unit at pH 5.4). Upon addition of the corresponding Watson–Crick-paired (2′-OMe)-RNA strands, parallel triplexes are formed with further increased thermal stability. 3′-O-(2-Thio-1,3,2-oxathiaphospholane) derivatives of 5′-O-DMT-LNA-nucleosides were used to prepare P-stereodefined (RP-PS)-DNA#LNA chimeras, which form thermally stable parallel complexes with (2′-OMe)-RNA matrices.![]()
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Affiliation(s)
- Katarzyna Jastrzębska
- Department of Bioorganic Chemistry
- Centre of Molecular and Macromolecular Studies
- Polish Academy of Sciences
- 90-363 Łódź
- Poland
| | - Barbara Mikołajczyk
- Department of Bioorganic Chemistry
- Centre of Molecular and Macromolecular Studies
- Polish Academy of Sciences
- 90-363 Łódź
- Poland
| | - Piotr Guga
- Department of Bioorganic Chemistry
- Centre of Molecular and Macromolecular Studies
- Polish Academy of Sciences
- 90-363 Łódź
- Poland
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23
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24
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Simulescu V, Ilia G. Solid-phase Synthesis of Phosphorus Derivatives. CURR ORG CHEM 2019. [DOI: 10.2174/1385272823666190213112019] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
The solid-phase synthesis (SPS) of phosphorus-containing compounds is based mainly on the fact that the chemical process is conducted in a two-phase system. One of the components is connected via covalent bonds to a solid support, which is in general an insoluble polymer, representing the solid phase of the process. The other components involved into the process are solubilized in a solution. The method is suitable to be applied to almost any organic compounds. A common example of using solid-phase synthesis is for obtaining products nucleotide containing, similar to nucleic acids. During the whole process, the nucleotide is always on the solid phase, after the condensation reaction, except for the last step, when the synthesis is already finished. Then, the product is released and separated very easily by filtration. The obtained polymer-oligonucleotide product can participate further in condensation reactions as well. Other important biomolecules synthesized by solid-phase approach during the last decades are nucleoside di- and triphosphates, nucleoside diphosphate sugars and dinucleoside polyphosphates. Those products are precursors of deoxysugars, aminodeoxysugars, uronic acids or glycoconjugates, and are also necessary for DNA and RNA synthesis. The use of the solid-phase method in the context of immobilized oligomers is of great interest nowadays. The solid-phase synthesis offers many advantages in comparison with the conventional solution-phase method, because it takes much less time, it is highly stereoselective, the products are separated and purified usually by a simple filtration or decantation, solvents with high boiling points could be used, the whole process is based on solid polymer support and the obtained compounds should not be isolated.
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Affiliation(s)
- Vasile Simulescu
- Institute of Chemistry Timisoara of Romanian Academy, 24 Mihai Viteazul Bvd., 300223 Timisoara, Romania
| | - Gheorghe Ilia
- Institute of Chemistry Timisoara of Romanian Academy, 24 Mihai Viteazul Bvd., 300223 Timisoara, Romania
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25
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Burns JR, Howorka S. Structural and Functional Stability of DNA Nanopores in Biological Media. NANOMATERIALS 2019; 9:nano9040490. [PMID: 30934927 PMCID: PMC6523550 DOI: 10.3390/nano9040490] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/12/2019] [Revised: 03/22/2019] [Accepted: 03/23/2019] [Indexed: 01/20/2023]
Abstract
DNA nanopores offer a unique nano-scale foothold at the membrane interface that can help advance the life sciences as biophysical research tools or gate-keepers for drug delivery. Biological applications require sufficient physiological stability and membrane activity for viable biological action. In this report, we determine essential parameters for efficient nanopore folding and membrane binding in biocompatible cell media. The parameters are identified for an archetypal DNA nanopore composed of six interwoven strands carrying cholesterol lipid anchors. Using gel electrophoresis and fluorescence spectroscopy, the nanostructures are found to assemble efficiently in cell media, such as LB and DMEM, and remain structurally stable at physiological temperatures. Furthermore, the pores’ oligomerization state is monitored using fluorescence spectroscopy and confocal microscopy. The pores remain predominately water-soluble over 24 h in all buffer systems, and were able to bind to lipid vesicles after 24 h to confirm membrane activity. However, the addition of fetal bovine serum to DMEM causes a significant reduction in nanopore activity. Serum proteins complex rapidly to the pore, most likely via ionic interactions, to reduce the effective nanopore concentration in solution. Our findings outline crucial conditions for maintaining lipidated DNA nanodevices, structurally and functionally intact in cell media, and pave the way for biological studies in the future.
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Affiliation(s)
- Jonathan R Burns
- Department of Chemistry, Institute of Structural Molecular Biology, University College London, London WC1H 0AJ, UK.
| | - Stefan Howorka
- Department of Chemistry, Institute of Structural Molecular Biology, University College London, London WC1H 0AJ, UK.
- Institute of Biophysics, Johannes Kepler University, A-4020 Linz, Austria.
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26
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Roussis SG, Cedillo I, Rentel C. Semi-quantitative determination of co-eluting impurities in oligonucleotide drugs using ion-pair reversed-phase liquid chromatography mass spectrometry. J Chromatogr A 2018; 1584:106-114. [PMID: 30473112 DOI: 10.1016/j.chroma.2018.11.034] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2018] [Revised: 10/24/2018] [Accepted: 11/18/2018] [Indexed: 01/13/2023]
Abstract
Continued improvements in understanding RNA biology have led to significant success in the development of antisense oligonucleotide therapeutics, and several oligonucleotide drugs have now been approved. Manufacturing of oligonucleotides may be associated with the production of impurities. Current methods for quantification of impurities that co-elute with the main drug component rely on manual ion extraction and integration of the characteristic mass signal of each impurity. For certain applications however, especially those involving large sets of samples such as those generated in the optimization of oligonucleotide manufacturing processes, a rapid method that provides semi-quantitative determination of impurity levels would be sufficient. In this work, an automated approach has been developed to rapidly determine the relative amounts of co-eluting impurities in oligonucleotide samples. The most abundant mass in the isotopic distribution is automatically calculated from the impurity formula and used to detect the presence of the impurities. The principles of the approach are described, and representative examples are given. Impurities determined in different manufacturing lots are compared directly, and by principal component analysis. The ability of the method to determine impurity levels across large sample sets is illustrated for an oligonucleotide drug purification study.
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Affiliation(s)
| | - Isaiah Cedillo
- Ionis Pharmaceuticals, Carlsbad, CA 92010, United States
| | - Claus Rentel
- Ionis Pharmaceuticals, Carlsbad, CA 92010, United States
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27
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Ghosh N, Katare R. Molecular mechanism of diabetic cardiomyopathy and modulation of microRNA function by synthetic oligonucleotides. Cardiovasc Diabetol 2018; 17:43. [PMID: 29566757 PMCID: PMC5863891 DOI: 10.1186/s12933-018-0684-1] [Citation(s) in RCA: 42] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/06/2018] [Accepted: 03/10/2018] [Indexed: 02/06/2023] Open
Abstract
Diabetic cardiomyopathy (DCM) is a chronic complication in individuals with diabetes and is characterized by ventricular dilation and hypertrophy, diastolic dysfunction, decreased or preserved systolic function and reduced ejection fraction eventually resulting in heart failure. Despite being well characterized, the fundamental mechanisms leading to DCM are still elusive. Recent studies identified the involvement of small non-coding small RNA molecules such as microRNAs (miRs) playing a key role in the etiology of DCM. Therefore, miRs associated with DCM represents a new class of targets for the development of mechanistic therapeutics, which may yield marked benefits compared to other therapeutic approaches. Indeed, few miRs currently under active clinical investigation, with many expressing cautious optimism that miRs based therapies will succeed in the coming years. The major caution in using miRs based therapy is the need to improve the stability and specificity following systemic injection, which can be achieved through chemical and structural modification. In this review, we first discuss the established role of miRs in DCM and the advances in miRs based therapeutic strategies for the prevention/treatment of DCM. We next discuss the currently employed chemical modification of miR oligonucleotides and their utility in therapies specifically focusing on the DCM. Finally, we summarize the commonly used delivery system and approaches for assessment of miRNA modulation and potential off-target effects.
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Affiliation(s)
- Nilanjan Ghosh
- Department of Physiology-HeartOtago, University of Otago, 270, Great King Street, Dunedin, 9010 New Zealand
| | - Rajesh Katare
- Department of Physiology-HeartOtago, University of Otago, 270, Great King Street, Dunedin, 9010 New Zealand
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28
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Wilson MJ, Fenati RA, Williams EGL, Ellis AV. Synthesis of a deoxyguanosine monophosphate rich propyl methacrylate oligomer. NEW J CHEM 2018. [DOI: 10.1039/c8nj00989a] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Propyl methacrylate oligomers with pendant guanosine monophosphate nucleotides can self-assemble in the presence of monovalent cations.
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Affiliation(s)
- Michael J. Wilson
- Flinders Centre for Nanoscale Science and Technology
- Flinders University
- Bedford Park
- Australia
- School of Chemical and Biomedical Engineering
| | - Renzo A. Fenati
- Flinders Centre for Nanoscale Science and Technology
- Flinders University
- Bedford Park
- Australia
- School of Chemical and Biomedical Engineering
| | | | - Amanda V. Ellis
- School of Chemical and Biomedical Engineering
- University of Melbourne
- Victoria 3010
- Australia
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29
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Yeldell SB, Ruble BK, Dmochowski IJ. Oligonucleotide modifications enhance probe stability for single cell transcriptome in vivo analysis (TIVA). Org Biomol Chem 2017; 15:10001-10009. [PMID: 29052679 PMCID: PMC5718921 DOI: 10.1039/c7ob02353g] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
Single cell transcriptomics provides a powerful discovery tool for identifying new cell types and functions as well as a means to probe molecular features of the etiology and treatment of human diseases, including cancer. However, such analyses are limited by the difficulty of isolating mRNA from single cells within biological samples. We recently introduced a photochemical method for isolating mRNA from single living cells, Transcriptome In Vivo Analysis (TIVA). The TIVA probe is a "caged" polyU : polyA oligonucleotide hairpin designed to enter live tissue, where site-specific activation with 405 nm laser reveals the polyU-biotin strand to bind mRNA in a target cell, enabling subsequent mRNA isolation and sequencing. The TIVA method is well suited for analysis of living cells in resected tissue, but has not yet been applied to living cells in whole organisms. Adapting TIVA to this more challenging environment requires a probe with higher thermal stability, more robust caging, and greater nuclease resistance. In this paper we present modifications to the original TIVA probe with multiple aspects of enhanced stability. These newer probes utilize an extended 22mer polyU capture strand with two 9mer polyA blocking strands ("22/9/9") for higher thermal stability pre-photolysis and improved mRNA capture affinity post-photolysis. The "22/9/9 GC" probe features a terminal GC pair to reduce pre-photolysis interactions with mRNA by more than half. The "PS-22/9/9" probe features a phosphorothioated backbone, which extends serum stability from <1 h to at least 48 h, and also mediates uptake into cultured human fibroblasts.
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Affiliation(s)
- S B Yeldell
- Department of Chemistry, University of Pennsylvania, 231 South 34th Street, Philadelphia, PA 19104-6323, USA.
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Fluorescent nucleobases as tools for studying DNA and RNA. Nat Chem 2017; 9:1043-1055. [PMID: 29064490 DOI: 10.1038/nchem.2859] [Citation(s) in RCA: 208] [Impact Index Per Article: 29.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2017] [Accepted: 07/11/2017] [Indexed: 02/07/2023]
Abstract
Understanding the diversity of dynamic structures and functions of DNA and RNA in biology requires tools that can selectively and intimately probe these biomolecules. Synthetic fluorescent nucleobases that can be incorporated into nucleic acids alongside their natural counterparts have emerged as a powerful class of molecular reporters of location and environment. They are enabling new basic insights into DNA and RNA, and are facilitating a broad range of new technologies with chemical, biological and biomedical applications. In this Review, we will present a brief history of the development of fluorescent nucleobases and explore their utility as tools for addressing questions in biophysics, biochemistry and biology of nucleic acids. We provide chemical insights into the two main classes of these compounds: canonical and non-canonical nucleobases. A point-by-point discussion of the advantages and disadvantages of both types of fluorescent nucleobases is made, along with a perspective into the future challenges and outlook for this burgeoning field.
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Yang X. Solid-Phase Synthesis of RNA Analogs Containing Phosphorodithioate Linkages. ACTA ACUST UNITED AC 2017; 70:4.77.1-4.77.13. [PMID: 28921494 DOI: 10.1002/cpnc.40] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/22/2023]
Abstract
The oligoribonucleotide phosphorodithioate (PS2-RNA) modification uses two sulfur atoms to replace two non-bridging oxygen atoms at an internucleotide phosphorodiester backbone linkage. Like a natural phosphodiester RNA backbone linkage, a PS2-modified backbone linkage is achiral at phosphorus. PS2-RNAs are highly stable to nucleases and several in vitro assays have demonstrated their biological activity. For example, PS2-RNAs silenced mRNA in vitro and bound to protein targets in the form of PS2-aptamers (thioaptamers). Thus, the interest in and promise of PS2-RNAs has drawn attention to synthesizing, isolating, and characterizing these compounds. RNA-thiophosphoramidite monomers are commercially available from AM Biotechnologies and this unit describes an effective methodology for solid-phase synthesis, deprotection, and purification of RNAs having PS2 internucleotide linkages. © 2017 by John Wiley & Sons, Inc.
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Komiyama M, Yoshimoto K, Sisido M, Ariga K. Chemistry Can Make Strict and Fuzzy Controls for Bio-Systems: DNA Nanoarchitectonics and Cell-Macromolecular Nanoarchitectonics. BULLETIN OF THE CHEMICAL SOCIETY OF JAPAN 2017. [DOI: 10.1246/bcsj.20170156] [Citation(s) in RCA: 238] [Impact Index Per Article: 34.0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Affiliation(s)
- Makoto Komiyama
- World Premier International (WPI) Research Centre for Materials Nanoarchitectonics (MANA), National Institute for Materials Science (NIMS), 1-1 Namiki, Tsukuba, Ibaraki 305-0044
- Life Science Center of Tsukuba Advanced Research Alliance, University of Tsukuba, 1-1-1 Ten-noudai, Tsukuba, Ibaraki 305-8577
| | - Keitaro Yoshimoto
- Department of Life Sciences, Graduate School of Arts and Science, The University of Tokyo, 3-8-1 Komaba, Meguro-ku, Tokyo 153-8902
| | - Masahiko Sisido
- Professor Emeritus, Research Core for Interdisciplinary Sciences, Okayama University, 3-1-1 Tsushima-naka, Kita-ku, Okayama 700-8530
| | - Katsuhiko Ariga
- World Premier International (WPI) Research Centre for Materials Nanoarchitectonics (MANA), National Institute for Materials Science (NIMS), 1-1 Namiki, Tsukuba, Ibaraki 305-0044
- Graduate School of Frontier Sciences, The University of Tokyo, Kashiwa, Chiba 277-0827
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Ramaswamy A, Smyrnova D, Froeyen M, Maiti M, Herdewijn P, Ceulemans A. Molecular Dynamics of Double Stranded Xylo-Nucleic Acid. J Chem Theory Comput 2017; 13:5028-5038. [PMID: 28742346 DOI: 10.1021/acs.jctc.7b00309] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
Xylo-nucleic acid (XyloNA) is a synthetic analogue of ribo-nucleic acid (RNA), where the ribose sugar has been replaced by xylose. We present a molecular dynamics study of the conformational evolution of XyloNA double strand oligomers derived from A-RNA through the substitution of β-d-ribofuranose by β-d-xylofuranose and having lengths of 8, 16, and 29 base pairs, using a set of independent all-atom simulations performed at various time scales ranging from 55 to 100 ns, with one long 500 ns simulation of the 29-mer. In order to validate the robustness of XyloNA conformation, a set of simulations using various cutoff distances and solvation box dimensions has also been performed. These independent simulations reveal the uncoiling or elongation of the initial conformation to form an open ladder type transient state conformation and the subsequent formation of a highly flexible duplex with a tendency to coil in a left-handed fashion. The observed open ladder conformation is in line with recently obtained NMR data on the XyloNA 8-mer derived using 5'-d(GUGUACAC)-3'. The observed negative interbase pair twist leads to the observed highly flexible left-handed duplex, which is significantly less rigid than the stable left-handed dXyloNA duplex having a strong negative twist. A comparison between the xylo-analogues of DNA and RNA shows a clear distinction between the helical parameters, with implications for the pairing mechanism.
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Affiliation(s)
- Amutha Ramaswamy
- Laboratory for Quantum Chemistry, KULeuven , Celestijnenlaan 200F, B-3001 Leuven, Belgium.,Centre for Bioinformatics, School of Life Sciences, Pondicherry University , Puducherry 605014, India
| | - Daryna Smyrnova
- Laboratory for Quantum Chemistry, KULeuven , Celestijnenlaan 200F, B-3001 Leuven, Belgium
| | - Mathy Froeyen
- Laboratory for Medicinal Chemistry, KULeuven , Herestraat 49, B-3000 Leuven, Belgium
| | - Mohitosh Maiti
- Laboratory for Medicinal Chemistry, KULeuven , Herestraat 49, B-3000 Leuven, Belgium
| | - Piet Herdewijn
- Laboratory for Medicinal Chemistry, KULeuven , Herestraat 49, B-3000 Leuven, Belgium
| | - Arnout Ceulemans
- Laboratory for Quantum Chemistry, KULeuven , Celestijnenlaan 200F, B-3001 Leuven, Belgium
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Kant R, Maiti B, Agarwal A. Synthesis, characterization, Hirshfeld surfaces and DFT computation of novel benzyl N -(1,3-benzothiazol-2-yl)- N -benzylcarbamate. J Mol Struct 2017. [DOI: 10.1016/j.molstruc.2017.04.061] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/19/2022]
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35
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Warminski M, Kowalska J, Jemielity J. Synthesis of RNA 5'-Azides from 2'-O-Pivaloyloxymethyl-Protected RNAs and Their Reactivity in Azide-Alkyne Cycloaddition Reactions. Org Lett 2017. [PMID: 28636394 DOI: 10.1021/acs.orglett.7b01591] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
Commercially available 2'-O-pivaloyloxymethyl (PivOM) phosphoramidites were employed in an SPS protocol for RNA 5' azides. The utility of the N3-RNAs in CuAAC and SPAAC was demonstrated by RNA 5' labeling, chemical ligation including fragment joining and cyclization, and bioconjugation. As a result, several new RNA conjugates that may be valuable tools for studies on biological events such as innate immune response (cyclic dinucleotides), post-transcriptional gene regulation (circular RNAs), or mRNA turnover (m7G capped RNAs) were obtained.
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Affiliation(s)
- Marcin Warminski
- Division of Biophysics, Institute of Experimental Physics, Faculty of Physics, University of Warsaw , Pasteura 5, 02-093 Warsaw, Poland
| | - Joanna Kowalska
- Division of Biophysics, Institute of Experimental Physics, Faculty of Physics, University of Warsaw , Pasteura 5, 02-093 Warsaw, Poland
| | - Jacek Jemielity
- Centre of New Technologies, University of Warsaw , Banacha 2c, 02-097 Warsaw, Poland
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Maio G, Enweronye O, Zumrut HE, Batool S, Van N, Mallikaratchy P. Systematic optimization and modification of a DNA aptamer with 2'-O-methyl RNA analogues. ChemistrySelect 2017; 2:2335-2340. [PMID: 29226219 DOI: 10.1002/slct.201700359] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/21/2023]
Abstract
Nucleic acid aptamers (NAAs) are short synthetic DNA or RNA molecules that specifically fold into distinct three-dimensional structures able to specifically recognize a target. While NAAs show unprecedented promise in a variety of applications, including sensing, therapeutics and diagnostics, one major limitation involves the lack of stability towards omnipresent nucleases. Therefore, we herein report a systematic truncation and incorporation of 2'-O-methyl bases to a DNA aptamer, which results in increased stability without affecting affinity. One of the newly designed analogues is stable up to 24 hours, demonstrating that 2'-O-methyl RNA is an attractive modification to DNA aptamers, especially when therapeutic applications are intended.
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Affiliation(s)
- George Maio
- Department of Chemistry, Lehman College for The City University of New York, 250 Beford Park Blvd West, Bronx, New York, NY 10468
| | - Osita Enweronye
- Department of Chemistry, Lehman College for The City University of New York, 250 Beford Park Blvd West, Bronx, New York, NY 10468
| | - Hasan E Zumrut
- Ph.D. Program in Chemistry and Biochemistry, CUNY Graduate Center, 365 Fifth Avenue, New York, NY 10016, USA
| | - Sana Batool
- Department of Chemistry, Lehman College for The City University of New York, 250 Beford Park Blvd West, Bronx, New York, NY 10468
| | - Nabeela Van
- Department of Chemistry, Lehman College for The City University of New York, 250 Beford Park Blvd West, Bronx, New York, NY 10468
| | - Prabodhika Mallikaratchy
- Department of Chemistry, Lehman College for The City University of New York, 250 Beford Park Blvd West, Bronx, New York, NY 10468.,Ph.D. Program in Chemistry and Biochemistry, CUNY Graduate Center, 365 Fifth Avenue, New York, NY 10016, USA.,Ph.D. Program in Molecular, Cellular and Developmental Biology, CUNY Graduate Center, 365 Fifth Avenue, New York, NY 10016, USA
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37
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Sigel A, Operschall BP, Matera-Witkiewicz A, Świątek-Kozłowska J, Sigel H. Acid–base and metal ion-binding properties of thiopyrimidine derivatives. Coord Chem Rev 2016. [DOI: 10.1016/j.ccr.2016.02.003] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/22/2022]
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38
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Perez-Gonzalez C, Lafontaine DA, Penedo JC. Fluorescence-Based Strategies to Investigate the Structure and Dynamics of Aptamer-Ligand Complexes. Front Chem 2016; 4:33. [PMID: 27536656 PMCID: PMC4971091 DOI: 10.3389/fchem.2016.00033] [Citation(s) in RCA: 44] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2016] [Accepted: 07/11/2016] [Indexed: 12/11/2022] Open
Abstract
In addition to the helical nature of double-stranded DNA and RNA, single-stranded oligonucleotides can arrange themselves into tridimensional structures containing loops, bulges, internal hairpins and many other motifs. This ability has been used for more than two decades to generate oligonucleotide sequences, so-called aptamers, that can recognize certain metabolites with high affinity and specificity. More recently, this library of artificially-generated nucleic acid aptamers has been expanded by the discovery that naturally occurring RNA sequences control bacterial gene expression in response to cellular concentration of a given metabolite. The application of fluorescence methods has been pivotal to characterize in detail the structure and dynamics of these aptamer-ligand complexes in solution. This is mostly due to the intrinsic high sensitivity of fluorescence methods and also to significant improvements in solid-phase synthesis, post-synthetic labeling strategies and optical instrumentation that took place during the last decade. In this work, we provide an overview of the most widely employed fluorescence methods to investigate aptamer structure and function by describing the use of aptamers labeled with a single dye in fluorescence quenching and anisotropy assays. The use of 2-aminopurine as a fluorescent analog of adenine to monitor local changes in structure and fluorescence resonance energy transfer (FRET) to follow long-range conformational changes is also covered in detail. The last part of the review is dedicated to the application of fluorescence techniques based on single-molecule microscopy, a technique that has revolutionized our understanding of nucleic acid structure and dynamics. We finally describe the advantages of monitoring ligand-binding and conformational changes, one molecule at a time, to decipher the complexity of regulatory aptamers and summarize the emerging folding and ligand-binding models arising from the application of these single-molecule FRET microscopy techniques.
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Affiliation(s)
- Cibran Perez-Gonzalez
- Laboratory for Biophysics and Biomolecular Dynamics, SUPA School of Physics and Astronomy, University of St. AndrewsSt Andrews, UK
| | - Daniel A. Lafontaine
- RNA Group, Department of Biology, Faculty of Science, Université de SherbrookeSherbrooke, QC, Canada
| | - J. Carlos Penedo
- Laboratory for Biophysics and Biomolecular Dynamics, SUPA School of Physics and Astronomy, University of St. AndrewsSt Andrews, UK
- Laboratory for Biophysics and Biomolecular Dynamics, Biomedical Sciences Research Complex, School of Biology, University of St. AndrewsSt. Andrews, UK
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39
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Patil KM, Chen G. Recognition of RNA Sequence and Structure by Duplex and Triplex Formation: Targeting miRNA and Pre-miRNA. ACTA ACUST UNITED AC 2016. [DOI: 10.1007/978-3-319-34175-0_13] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
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40
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Reverte M, Vasseur JJ, Smietana M. Nuclease stability of boron-modified nucleic acids: application to label-free mismatch detection. Org Biomol Chem 2016; 13:10604-8. [PMID: 26441029 DOI: 10.1039/c5ob01815c] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Abstract
5'-End boronic acid-modified oligonucleotides were evaluated against various nucleases at single and double stranded levels. The results show that these modifications induce a high resistance to degradation by calf-spleen and snake venom phosphodiesterases. More importantly, this eventually led to the development of a new label-free enzyme-assisted fluorescence-based method for single mismatch detection.
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Affiliation(s)
- Maëva Reverte
- Institut des Biomolécules Max Mousseron (IBMM) UMR 5247 CNRS-Université de Montpellier-ENSCM, Place Bataillon, 34095 Montpellier, France.
| | - Jean-Jacques Vasseur
- Institut des Biomolécules Max Mousseron (IBMM) UMR 5247 CNRS-Université de Montpellier-ENSCM, Place Bataillon, 34095 Montpellier, France.
| | - Michael Smietana
- Institut des Biomolécules Max Mousseron (IBMM) UMR 5247 CNRS-Université de Montpellier-ENSCM, Place Bataillon, 34095 Montpellier, France.
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41
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Álvarez Porebski PW, Lynen F. Offline comprehensive liquid chromatography in combination with a Deoxyribonuclease I immobilized enzymatic reactor for selective screening of oligonucleotide mixtures. J Chromatogr A 2016; 1451:164-168. [PMID: 27208984 DOI: 10.1016/j.chroma.2016.05.021] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2016] [Revised: 05/01/2016] [Accepted: 05/04/2016] [Indexed: 10/21/2022]
Abstract
The development of a comprehensive ion-pair chromatography-immobilized enzyme reactor×ion-pair chromatography (IPC-IMER×IPC) methodology for the advanced characterization of DNA/RNA oligonucleotides (ONs) mixtures has been carried out. More in detail, a DNase I IMER has been coupled to IPC in the post column configuration, followed by the collection of the eluting fractions and reanalysis by IPC. The effect of the mobile phase over the IMER activity was qualitatively evaluated. The methodology proved to generate relevant ON degradation profiles that might be correlated with the ON stability towards nucleases. Moreover, this platform shows potential for its further implementation in selective analysis of ON mixtures and in mapping studies.
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Affiliation(s)
- Piotr Wiktor Álvarez Porebski
- Separation Science Group, Department of Organic and Macromolecular Chemistry, Universiteit Gent, Krijgslaan 281 S4-bis, 9000 Gent, Belgium.
| | - Frederic Lynen
- Separation Science Group, Department of Organic and Macromolecular Chemistry, Universiteit Gent, Krijgslaan 281 S4-bis, 9000 Gent, Belgium.
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42
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Ma DL, Wang W, Mao Z, Kang TS, Han QB, Chan PWH, Leung CH. Utilization of G-Quadruplex-Forming Aptamers for the Construction of Luminescence Sensing Platforms. Chempluschem 2016; 82:8-17. [DOI: 10.1002/cplu.201600036] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2016] [Revised: 03/07/2016] [Indexed: 01/01/2023]
Affiliation(s)
- Dik-Lung Ma
- Department of Chemistry; Hong Kong Baptist University; 224 Waterloo Road, Kowloon Tong Hong Kong 852 P. R. China
| | - Wanhe Wang
- Department of Chemistry; Hong Kong Baptist University; 224 Waterloo Road, Kowloon Tong Hong Kong 852 P. R. China
| | - Zhifeng Mao
- Department of Chemistry; Hong Kong Baptist University; 224 Waterloo Road, Kowloon Tong Hong Kong 852 P. R. China
| | - Tian-Shu Kang
- State Key Laboratory of Quality Research in Chinese Medicine; Institute of Chinese Medical Sciences; University of Macau; Macao 999078 P. R. China
| | - Quan-Bin Han
- School of Chinese Medicine; Hong Kong Baptist University; Kowloon Hong Kong 852 P. R. China
| | - Philip Wai Hong Chan
- School of Chemistry; Monash University; Clayton VIC 3800 Australia
- Department of Chemistry; University of Warwick; Coventry CV4 7AL United Kingdom
| | - Chung-Hang Leung
- State Key Laboratory of Quality Research in Chinese Medicine; Institute of Chinese Medical Sciences; University of Macau; Macao 999078 P. R. China
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43
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Bugovsky S, Balika W, Koranda M, Schnabl S, Allmaier G. Quality control of oligonucleotide synthesis by means of matrix-assisted laser desorption/ionization linear time-of-flight mass spectrometry on a nanocoated disposable target. RAPID COMMUNICATIONS IN MASS SPECTROMETRY : RCM 2016; 30:665-668. [PMID: 26842587 DOI: 10.1002/rcm.7471] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/05/2015] [Revised: 11/25/2015] [Accepted: 11/25/2015] [Indexed: 06/05/2023]
Affiliation(s)
- Stefan Bugovsky
- Institute of Chemical Technologies and Analytics, Vienna University of Technology, Vienna, A-1060, Austria
| | | | | | | | - Günter Allmaier
- Institute of Chemical Technologies and Analytics, Vienna University of Technology, Vienna, A-1060, Austria
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Wang R, Lu D, Bai H, Jin C, Yan G, Ye M, Qiu L, Chang R, Cui C, Liang H, Tan W. Using modified aptamers for site specific protein-aptamer conjugations. Chem Sci 2015; 7:2157-2161. [PMID: 28044095 PMCID: PMC5201207 DOI: 10.1039/c5sc02631h] [Citation(s) in RCA: 42] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022] Open
Abstract
We have developed a new method for the selective conjugation of target proteins at lysine residues through a protein–aptamer template-directed reaction.
Conjugation of DNA to defined locations on a protein surface will be a powerful tool for positioning functional groups and molecules in biological and biomedical studies. However, tagging protein with DNA is challenging in physiological environments, and requires a bioorthogonal approach. Here, we report a chemical solution to selectively conjugate DNA aptamers with a protein by protein–aptamer template (PAT)-directed reactions. Since protein–aptamer interactions are bioorthogonal, we exploit the PAT as a unique platform for specific DNA–protein cross-linking. We develop a series of modified oligonucleotides for PAT-directed reactions and find an F-carboxyl group as a suitable functionality for selective and site-specific conjugation. The functionality is incorporated into aptamers in our F-carboxyl phosphoramidite with an easy synthesis. We also demonstrate the necessity of a linker between the reactive functionality and the aptamer sequences.
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Affiliation(s)
- Ruowen Wang
- Molecular Sciences and Biomedicine Laboratory, State Key Laboratory for Chemo/Biosensing and Chemometrics, College of Chemistry and Chemical Engineering and College of Biology, Collaborative Innovation Center for Molecular Engineering and Theranostics, Hunan University, Changsha 410082, China; Departments of Chemistry and Department of Physiology and Functional Genomics, Center for Research at the Bio/Nano Interface, Shands Cancer Center, UF Genetics Institute and McKnight Brain Institute, University of Florida, Gainesville, Florida32611-7200, United States
| | - Danqing Lu
- Molecular Sciences and Biomedicine Laboratory, State Key Laboratory for Chemo/Biosensing and Chemometrics, College of Chemistry and Chemical Engineering and College of Biology, Collaborative Innovation Center for Molecular Engineering and Theranostics, Hunan University, Changsha 410082, China
| | - Huarong Bai
- Molecular Sciences and Biomedicine Laboratory, State Key Laboratory for Chemo/Biosensing and Chemometrics, College of Chemistry and Chemical Engineering and College of Biology, Collaborative Innovation Center for Molecular Engineering and Theranostics, Hunan University, Changsha 410082, China
| | - Cheng Jin
- Molecular Sciences and Biomedicine Laboratory, State Key Laboratory for Chemo/Biosensing and Chemometrics, College of Chemistry and Chemical Engineering and College of Biology, Collaborative Innovation Center for Molecular Engineering and Theranostics, Hunan University, Changsha 410082, China
| | - Guobei Yan
- Molecular Sciences and Biomedicine Laboratory, State Key Laboratory for Chemo/Biosensing and Chemometrics, College of Chemistry and Chemical Engineering and College of Biology, Collaborative Innovation Center for Molecular Engineering and Theranostics, Hunan University, Changsha 410082, China
| | - Mao Ye
- Molecular Sciences and Biomedicine Laboratory, State Key Laboratory for Chemo/Biosensing and Chemometrics, College of Chemistry and Chemical Engineering and College of Biology, Collaborative Innovation Center for Molecular Engineering and Theranostics, Hunan University, Changsha 410082, China
| | - Liping Qiu
- Molecular Sciences and Biomedicine Laboratory, State Key Laboratory for Chemo/Biosensing and Chemometrics, College of Chemistry and Chemical Engineering and College of Biology, Collaborative Innovation Center for Molecular Engineering and Theranostics, Hunan University, Changsha 410082, China; Departments of Chemistry and Department of Physiology and Functional Genomics, Center for Research at the Bio/Nano Interface, Shands Cancer Center, UF Genetics Institute and McKnight Brain Institute, University of Florida, Gainesville, Florida32611-7200, United States
| | - Rongshan Chang
- Molecular Sciences and Biomedicine Laboratory, State Key Laboratory for Chemo/Biosensing and Chemometrics, College of Chemistry and Chemical Engineering and College of Biology, Collaborative Innovation Center for Molecular Engineering and Theranostics, Hunan University, Changsha 410082, China
| | - Cheng Cui
- Departments of Chemistry and Department of Physiology and Functional Genomics, Center for Research at the Bio/Nano Interface, Shands Cancer Center, UF Genetics Institute and McKnight Brain Institute, University of Florida, Gainesville, Florida32611-7200, United States
| | - Hao Liang
- Molecular Sciences and Biomedicine Laboratory, State Key Laboratory for Chemo/Biosensing and Chemometrics, College of Chemistry and Chemical Engineering and College of Biology, Collaborative Innovation Center for Molecular Engineering and Theranostics, Hunan University, Changsha 410082, China
| | - Weihong Tan
- Molecular Sciences and Biomedicine Laboratory, State Key Laboratory for Chemo/Biosensing and Chemometrics, College of Chemistry and Chemical Engineering and College of Biology, Collaborative Innovation Center for Molecular Engineering and Theranostics, Hunan University, Changsha 410082, China; Departments of Chemistry and Department of Physiology and Functional Genomics, Center for Research at the Bio/Nano Interface, Shands Cancer Center, UF Genetics Institute and McKnight Brain Institute, University of Florida, Gainesville, Florida32611-7200, United States
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Oligonucleotide therapeutics: chemistry, delivery and clinical progress. Future Med Chem 2015; 7:2221-42. [PMID: 26510815 DOI: 10.4155/fmc.15.144] [Citation(s) in RCA: 73] [Impact Index Per Article: 8.1] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
Abstract
Oligonucleotide therapeutics have the potential to become a third pillar of drug development after small molecules and protein therapeutics. However, the three approved oligonucleotide drugs over the past 17 years have not proven to be highly successful in a commercial sense. These trailblazer drugs have nonetheless laid the foundations for entire classes of drug candidates to follow. This review will examine further advances in chemistry that are earlier in the pipeline of oligonucleotide drug candidates. Finally, we consider the possible effect of delivery systems that may provide extra footholds to improve the potency and specificity of oligonucleotide drugs. Our overview focuses on strategies to imbue antisense oligonucleotides with more drug-like properties and their applicability to other nucleic acid therapeutics.
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Gaddes ER, Lee D, Gydush G, Wang Y, Dong C. Regulation of fibrin-mediated tumor cell adhesion to the endothelium using anti-thrombin aptamer. Exp Cell Res 2015; 339:417-26. [PMID: 26481421 DOI: 10.1016/j.yexcr.2015.10.010] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2015] [Revised: 09/29/2015] [Accepted: 10/09/2015] [Indexed: 12/27/2022]
Abstract
Molecular intervention during transient stages of various metastatic pathways may lead to development of promising therapeutic technologies. One of such involves soluble fibrin (sFn) that has been implicated as a cross-linker between circulating blood or tumor cells and endothelial cell receptors, promoting cell arrest on the endothelium during circulation. sFn generation is a result of thrombin-mediated fibrinogen (Fg) cleavage due to either vascular injuries or a tumor microenvironment. For cancer therapy, thrombin-mediated conversions of Fg to sFn thus serve as potential intervention points to decrease circulating tumor cell adhesion to the endothelium and subsequent metastatic events. The purpose of this work was to investigate the function of an anti-thrombin oligonucleotide aptamer in reducing tumor cell arrest. Both molecular and cellular interactions were examined to demonstrate the binding and inhibitory effects of anti-thrombin aptamer. The results show that the aptamer is capable of inhibiting thrombin-mediated Fg conversion, thereby reducing sFn-mediated tumor cell adhesion in a concentration-dependent manner. Notably, the aptamer is able to bind thrombin under dynamic flow conditions and reduce tumor cell adhesive events at various physiological shear rates. This study further indicates that oligonucleotide aptamers hold great promise as therapeutic regulators of tumor cell adhesion, and consequently, metastatic activity.
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Affiliation(s)
- Erin R Gaddes
- Department of Biomedical Engineering, The Pennsylvania State University, University Park, PA 16802, USA
| | - Deborah Lee
- Department of Biomedical Engineering, The Pennsylvania State University, University Park, PA 16802, USA
| | - Gregory Gydush
- Department of Biomedical Engineering, The Pennsylvania State University, University Park, PA 16802, USA
| | - Yong Wang
- Department of Biomedical Engineering, The Pennsylvania State University, University Park, PA 16802, USA
| | - Cheng Dong
- Department of Biomedical Engineering, The Pennsylvania State University, University Park, PA 16802, USA.
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Spitsyn MA, Shershov VE, Kuznetsova VE, Barsky VE, Egorov EE, Emelyanova MA, Kreindlin EY, Lysov YP, Guseinov TO, Fesenko DE, Lapa SA, Surzhikov SA, Abramov IS, Nasedkina TV, Zasedatelev AS, Chudinov AV. Infrared fluorescent markers for microarray DNA analysis. Mol Biol 2015. [DOI: 10.1134/s0026893315050167] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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In vitro analysis of phosphorothioate modification of DNA reveals substrate recognition by a multiprotein complex. Sci Rep 2015. [PMID: 26213215 PMCID: PMC4515589 DOI: 10.1038/srep12513] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/03/2022] Open
Abstract
A wide variety of prokaryotes possess DNA modifications consisting of sequence-specific phosphorothioates (PT) inserted by members of a five-gene cluster. Recent genome mapping studies revealed two unusual features of PT modifications: short consensus sequences and partial modification of a specific genomic site in a population of bacteria. To better understand the mechanism of target selection of PT modifications that underlies these features, we characterized the substrate recognition of the PT-modifying enzymes termed DptC, D and E in a cell extract system from Salmonella. The results revealed that double-stranded oligodeoxynucleotides underwent de novo PT modification in vitro, with the same modification pattern as in vivo, i. e., GpsAAC/GpsTTC motif. Unexpectedly, in these in vitro analyses we observed no significant effect on PT modification by sequences flanking GAAC/GTTC motif, while PT also occurred in the GAAC/GTTC motif that could not be modified in vivo. Hemi-PT DNA also served as substrate of the PT-modifying enzymes, but not single-stranded DNA. The PT-modifying enzymes were then found to function as a large protein complex, with all of three subunits in tetrameric conformations. This study provided the first demonstration of in vitro DNA PT modification by PT-modifying enzymes that function as a large protein complex.
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Roussis SG. A Novel and Intuitive Method of Displaying and Interacting with Mass Difference Information: Application to Oligonucleotide Drug Impurities. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2015; 26:1150-1164. [PMID: 25836378 DOI: 10.1007/s13361-015-1115-0] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/22/2014] [Revised: 01/26/2015] [Accepted: 02/23/2015] [Indexed: 06/04/2023]
Abstract
A new method is presented for determining relationships between components in complex analytical systems. The method uses the mass differences between peaks in high resolution electrospray ionization (ESI) mass spectra. It relates peaks that share common mass differences. The method is based on the fundamental assumption that peaks in the spectra having the same exact mass difference are related by the same chemical moiety/substructure. Moreover, the presence (or absence/loss) of the same chemical moiety from a series of molecules may reflect similarities in the mechanisms of formation of each molecule. The determined mass differences in the spectra are used to automatically differentiate the types of components in the samples. Contour plots and summary plots of the summed total ion signal as a function of the mass difference are generated, which form powerful tools for the rapid and automated determination of the components in the samples and for comparisons with other samples. For the first time, in this work a unique profile contour plot has been developed that permits the interactive interrogation of the mass range by mass difference data matrix to obtain valuable information about components that share a common mechanism of formation, and all possible mechanisms of formation linked to a selected precursor molecule. The method can be used as an additional and complementary method to the existing analytical methods to determine relationships between components in complex chemical systems.
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Hajjawi OS. Ribonucleic acid (RNA) biosynthesis in human cancer. Cancer Cell Int 2015; 15:22. [PMID: 25717284 PMCID: PMC4339644 DOI: 10.1186/s12935-015-0167-3] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2014] [Accepted: 01/20/2015] [Indexed: 12/28/2022] Open
Abstract
In many respects, the most remarkable chemical substances within the genome of eukaryotic cells are remarkable proteins which are the critical structural and functional units of living cells. The specifications for everything that goes in the cell are natural digital-to-digital decoding process in an archive sequence by deoxyribonucleic acid (DNA) and an articulate construction by ribonucleic acid (RNA). The products of DNA transcription are long polymers of ribonucleotides rather than deoxyribonucleotides and are termed ribonucleic acids. Certain deoxyribonucleotide sequences, or genes, give rise to transfer RNA (tRNA) and other ribosomal RNA (rRNA) when transcribed. The ribonucleotide sequences fold extensively and rRNA is associated with specific proteins to yield the essential cell components, ribosomes. Transcription of other special sequences yields messenger RNAs (mRNAs) that contain ribonucleotide sequences that will be ultimately translated into new types of amino acid sequences of functional cellular protein molecules. This switch to a different variety of cellular molecular sequences is complex, but each sequence of the three ribonucleotides specifies the insertion of one particular amino acid into the polypeptide chain under production. Whilst mRNA is considered the vehicle by which genetic information is transmitted from the genome and allocated in the appropriate cytoplasmic sites for translation into protein via cap-dependent mechanism, the actual translation depends also on the presence of other so-called household and luxury protein molecules. Recent evidence suggests RNA species are required at initiation, because treatment of cells with antibiotics or drugs that inhibit RNA synthesis cause a decrease in protein synthesis. The rRNA is necessary as a structural constituent of the ribosomes upon which translation takes place, whereas tRNA is necessary as an adaptor in amino acid activation and elongation protein chains to ribosomes. In this article, we review malignant tumor, with stem like properties, and recent technical advances into the phenomenon of micro-particles and micro-vesicles containing cell-free nucleic acids that circulate plasma. New areas of research have been opened into screening tumor telomerase progression, prognosis of aptamers targeting cell surface, monitoring the efficacy of anticancer therapies, oncogenic transformation of host cell, and RNA polymerases role in the cell cycle progression and differentiation.
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Affiliation(s)
- Omar S Hajjawi
- Department of Biology, Arab American University, P. O. Box 240, Jenin, Israeli Occupied Territories of Palestine
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