1
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Kan Y, Jin Z, Ke Y, Lin D, Yan L, Wu L, He Y. Replicative bypass studies of l-deoxyribonucleosides in Vitro and in E. coli cell. Sci Rep 2022; 12:21183. [PMID: 36476762 PMCID: PMC9729220 DOI: 10.1038/s41598-022-24802-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2022] [Accepted: 11/21/2022] [Indexed: 12/12/2022] Open
Abstract
L-nucleosides were the most important antiviral lead compounds because they can inhibit viral DNA polymerase and DNA synthesis of many viruses, whereas they may lead to mutations in DNA replication and cause genomic instability. In this study, we reported the replicative bypass of L-deoxynucleosides in recombinant DNA by restriction enzyme-mediated assays to examine their impact on DNA replication in vitro and in E. coli cells. The results showed that a template L-dC inhibited Taq DNA polymerase reaction, whereas it can be bypassed by Vent (exo-) DNA polymerase as well as in cell replication, inserting correct nucleotides opposite L-dC. L-dG can be bypassed by Taq DNA polymerase and in E. coli cells, maintaining insertion of correct incoming nucleotides, and L-dG induced mutagenic replication by Vent (exo-) DNA polymerase. In contrast, L-dA can induced mutagenic replication in vitro and in E. coli cells. MD simulations were performed to investigate how DNA polymerase affected replicative bypass and mutations when D-nucleosides replaced with L-nucleosides. This study will provide a basis for the ability to assess the cytotoxic and mutagenic properties of the L-nucleoside drugs.
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Affiliation(s)
- Yuhe Kan
- grid.410726.60000 0004 1797 8419School of Chemical Sciences, University of Chinese Academy of Sciences, Beijing, 100049 People’s Republic of China ,grid.411643.50000 0004 1761 0411School of Life Sciences, Inner Mongolia University, Hohhot, 010021 Inner Mongolia People’s Republic of China ,Qilu Pharmaceutical (Inner Mongolia) CO., LTD., Hohhot, 010080 Inner Mongolia People’s Republic of China
| | - Zhaoyang Jin
- grid.410726.60000 0004 1797 8419School of Chemical Sciences, University of Chinese Academy of Sciences, Beijing, 100049 People’s Republic of China
| | - Yongqi Ke
- grid.410726.60000 0004 1797 8419School of Chemical Sciences, University of Chinese Academy of Sciences, Beijing, 100049 People’s Republic of China
| | - Dao Lin
- grid.410726.60000 0004 1797 8419School of Chemical Sciences, University of Chinese Academy of Sciences, Beijing, 100049 People’s Republic of China
| | - Liang Yan
- grid.410726.60000 0004 1797 8419School of Chemical Sciences, University of Chinese Academy of Sciences, Beijing, 100049 People’s Republic of China
| | - Li Wu
- grid.410726.60000 0004 1797 8419School of Chemical Sciences, University of Chinese Academy of Sciences, Beijing, 100049 People’s Republic of China ,grid.11135.370000 0001 2256 9319State Key Laboratory of Natural and Biomimetic Drugs, School of Pharmaceutical Sciences, Peking University, Beijing, 100191 People’s Republic of China
| | - Yujian He
- grid.410726.60000 0004 1797 8419School of Chemical Sciences, University of Chinese Academy of Sciences, Beijing, 100049 People’s Republic of China ,grid.11135.370000 0001 2256 9319State Key Laboratory of Natural and Biomimetic Drugs, School of Pharmaceutical Sciences, Peking University, Beijing, 100191 People’s Republic of China ,grid.410726.60000 0004 1797 8419School of Future Technology, University of Chinese Academy of Sciences, Beijing, 100049 People’s Republic of China
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2
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Hervey JRD, Freund N, Houlihan G, Dhaliwal G, Holliger P, Taylor AI. Efficient synthesis and replication of diverse sequence libraries composed of biostable nucleic acid analogues. RSC Chem Biol 2022; 3:1209-1215. [PMID: 36320888 PMCID: PMC9533476 DOI: 10.1039/d2cb00035k] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2022] [Accepted: 04/15/2022] [Indexed: 11/10/2022] Open
Abstract
Functional nucleic acids can be evolved in vitro using cycles of selection and amplification, starting from diverse-sequence libraries, which are typically restricted to natural or partially-modified polymer chemistries. Here, we describe the efficient DNA-templated synthesis and reverse transcription of libraries entirely composed of serum nuclease resistant alternative nucleic acid chemistries validated in nucleic acid therapeutics; locked nucleic acid (LNA), 2'-O-methyl-RNA (2'OMe-RNA), or mixtures of the two. We evaluate yield and diversity of synthesised libraries and measure the aggregate error rate of a selection cycle. We find that in addition to pure 2'-O-methyl-RNA and LNA, several 2'OMe-RNA/LNA blends seem suitable and promising for discovery of biostable functional nucleic acids for biomedical applications.
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Affiliation(s)
- John R D Hervey
- Cambridge Institute of Therapeutic Immunology & Infectious Disease (CITIID), University of Cambridge Cambridge CB2 0AW UK
| | - Niklas Freund
- Medical Research Council Laboratory of Molecular Biology Cambridge CB2 0QH UK
| | - Gillian Houlihan
- Medical Research Council Laboratory of Molecular Biology Cambridge CB2 0QH UK
| | - Gurpreet Dhaliwal
- Cambridge Institute of Therapeutic Immunology & Infectious Disease (CITIID), University of Cambridge Cambridge CB2 0AW UK
| | - Philipp Holliger
- Medical Research Council Laboratory of Molecular Biology Cambridge CB2 0QH UK
| | - Alexander I Taylor
- Cambridge Institute of Therapeutic Immunology & Infectious Disease (CITIID), University of Cambridge Cambridge CB2 0AW UK
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3
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Shanmugasundaram M, Senthilvelan A, Kore AR. An Efficient Gram-Scale Chemical Synthesis of Purine Locked Nucleic Acid Nucleoside-5'-O-Triphosphates. Curr Protoc 2022; 2:e436. [PMID: 35723503 DOI: 10.1002/cpz1.436] [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] [Indexed: 06/15/2023]
Abstract
This article presents a simple, reliable, straight-forward, general, and efficient chemical method for the gram-scale synthesis of purine locked nucleic acid (LNA) nucleotides, such as LNA guanosine-5'-O-triphosphate (LNA-GTP) and LNA adenosine-5'-O-triphosphate (LNA-ATP), starting from the corresponding nucleoside. The reaction pathway employs an improved protection-free "one-pot, three-step" Ludwig synthetic strategy. The first step involves monophosphorylation of nucleoside with phosphorus oxychloride followed by reaction with tributylammonium pyrophosphate and subsequent hydrolysis of the resulting cyclic intermediate to furnish the corresponding LNA nucleotide in good yields. It is noteworthy that the reaction affords high-purity (>99.5%) LNA nucleotide after diethylaminoethyl Sepharose column purification. © 2022 Wiley Periodicals LLC. Basic Protocol: Synthesis of LNA nucleoside-5'-O-triphosphates.
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Affiliation(s)
| | | | - Anilkumar R Kore
- Life Sciences Solutions Group, Thermo Fisher Scientific, Austin, Texas
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4
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Chan KY, Kinghorn AB, Hollenstein M, Tanner JA. Chemical modifications for a next generation of nucleic acid aptamers. Chembiochem 2022; 23:e202200006. [PMID: 35416400 DOI: 10.1002/cbic.202200006] [Citation(s) in RCA: 18] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2022] [Revised: 04/11/2022] [Indexed: 11/08/2022]
Abstract
In the past three decades, in vitro systematic evolution of ligands by exponential enrichment (SELEX) has yielded many aptamers for translational applications in both research and clinical settings. Despite their promise as an alternative to antibodies, the low success rate of SELEX (~ 30%) has been a major bottleneck that hampers the further development of aptamers. One hurdle is the lack of chemical diversity in nucleic acids. To address this, the aptamer chemical repertoire has been extended by introducing exotic chemical groups, which provide novel binding functionalities. This review will focus on how modified aptamers can be selected and evolved, with illustration of some successful examples. In particular, unique chemistries are exemplified. Various strategies of incorporating modified building blocks into the standard SELEX protocol are highlighted, with a comparison of the differences between pre-SELEX and post-SELEX modifications. Nucleic acid aptamers with extended functionality evolved from non-natural chemistries will open up new vistas for function and application of nucleic acids.
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Affiliation(s)
- Kwing Yeung Chan
- The University of Hong Kong, School of Biomedical Sciences, HONG KONG
| | | | | | - Julian Alexander Tanner
- The University of Hong Kong, School of Biomedical Sciences, 3/F Laboratory Block, 21 Sassoon Road, 000000, Pokfulam, HONG KONG
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5
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Shanmugasundaram M, Senthilvelan A, Kore AR. An improved protection-free one-pot chemical synthesis of purine locked nucleic acid nucleoside-5'-triphosphates. NUCLEOSIDES, NUCLEOTIDES & NUCLEIC ACIDS 2021; 41:36-44. [PMID: 34696692 DOI: 10.1080/15257770.2021.1994992] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/07/2021] [Revised: 10/13/2021] [Accepted: 10/14/2021] [Indexed: 10/20/2022]
Abstract
A simple, reliable, straightforward, and efficient method for the gram-scale chemical synthesis of purine locked nucleic acid (LNA) nucleotides such as LNA-guanosine-5'-triphosphate (LNA-GTP) and LNA-adenosine-5'-triphosphate (LNA-ATP) starting from the corresponding nucleoside is described. The overall reaction utilizes an improved "one-pot, three-step" Ludwig synthetic strategy that involves the monophosphorylation of LNA nucleoside, followed by the reaction with tributylammonium pyrophosphate and subsequent hydrolysis of the resulting cyclic intermediate using water to furnish the corresponding purine LNA nucleotide in good yield with high purity (>99.5%).
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Affiliation(s)
| | | | - Anilkumar R Kore
- Life Sciences Solutions Group, Thermo Fisher Scientific, Austin, Texas, USA
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6
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Ochoa S, Milam VT. Modified Nucleic Acids: Expanding the Capabilities of Functional Oligonucleotides. Molecules 2020; 25:E4659. [PMID: 33066073 PMCID: PMC7587394 DOI: 10.3390/molecules25204659] [Citation(s) in RCA: 59] [Impact Index Per Article: 14.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2020] [Revised: 10/07/2020] [Accepted: 10/08/2020] [Indexed: 12/20/2022] Open
Abstract
In the last three decades, oligonucleotides have been extensively investigated as probes, molecular ligands and even catalysts within therapeutic and diagnostic applications. The narrow chemical repertoire of natural nucleic acids, however, imposes restrictions on the functional scope of oligonucleotides. Initial efforts to overcome this deficiency in chemical diversity included conservative modifications to the sugar-phosphate backbone or the pendant base groups and resulted in enhanced in vivo performance. More importantly, later work involving other modifications led to the realization of new functional characteristics beyond initial intended therapeutic and diagnostic prospects. These results have inspired the exploration of increasingly exotic chemistries highly divergent from the canonical nucleic acid chemical structure that possess unnatural physiochemical properties. In this review, the authors highlight recent developments in modified oligonucleotides and the thrust towards designing novel nucleic acid-based ligands and catalysts with specifically engineered functions inaccessible to natural oligonucleotides.
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Affiliation(s)
- Steven Ochoa
- School of Materials Science and Engineering, Georgia Institute of Technology, Atlanta, GA 30332, USA;
| | - Valeria T. Milam
- School of Materials Science and Engineering, Georgia Institute of Technology, Atlanta, GA 30332, USA;
- Petit Institute for Bioengineering and Bioscience, Georgia Institute of Technology, Atlanta, GA 30332, USA
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7
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Odeh F, Nsairat H, Alshaer W, Ismail MA, Esawi E, Qaqish B, Bawab AA, Ismail SI. Aptamers Chemistry: Chemical Modifications and Conjugation Strategies. Molecules 2019; 25:E3. [PMID: 31861277 PMCID: PMC6982925 DOI: 10.3390/molecules25010003] [Citation(s) in RCA: 186] [Impact Index Per Article: 37.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2019] [Revised: 12/14/2019] [Accepted: 12/17/2019] [Indexed: 12/21/2022] Open
Abstract
Soon after they were first described in 1990, aptamers were largely recognized as a new class of biological ligands that can rival antibodies in various analytical, diagnostic, and therapeutic applications. Aptamers are short single-stranded RNA or DNA oligonucleotides capable of folding into complex 3D structures, enabling them to bind to a large variety of targets ranging from small ions to an entire organism. Their high binding specificity and affinity make them comparable to antibodies, but they are superior regarding a longer shelf life, simple production and chemical modification, in addition to low toxicity and immunogenicity. In the past three decades, aptamers have been used in a plethora of therapeutics and drug delivery systems that involve innovative delivery mechanisms and carrying various types of drug cargos. However, the successful translation of aptamer research from bench to bedside has been challenged by several limitations that slow down the realization of promising aptamer applications as therapeutics at the clinical level. The main limitations include the susceptibility to degradation by nucleases, fast renal clearance, low thermal stability, and the limited functional group diversity. The solution to overcome such limitations lies in the chemistry of aptamers. The current review will focus on the recent arts of aptamer chemistry that have been evolved to refine the pharmacological properties of aptamers. Moreover, this review will analyze the advantages and disadvantages of such chemical modifications and how they impact the pharmacological properties of aptamers. Finally, this review will summarize the conjugation strategies of aptamers to nanocarriers for developing targeted drug delivery systems.
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Affiliation(s)
- Fadwa Odeh
- Faculty of Science, The University of Jordan, Amman 11942, Jordan; (F.O.); (H.N.); (A.A.B.)
- Hamdi Mango Center for Scientific Research, The University of Jordan, Amman 11942, Jordan
| | - Hamdi Nsairat
- Faculty of Science, The University of Jordan, Amman 11942, Jordan; (F.O.); (H.N.); (A.A.B.)
| | - Walhan Alshaer
- Cell Therapy Center, The University of Jordan, Amman 11942, Jordan
| | - Mohammad A. Ismail
- Faculty of Medicine, The University of Jordan, Amman 11942, Jordan; (M.A.I.); (E.E.); (B.Q.); (S.I.I.)
| | - Ezaldeen Esawi
- Faculty of Medicine, The University of Jordan, Amman 11942, Jordan; (M.A.I.); (E.E.); (B.Q.); (S.I.I.)
| | - Baraa Qaqish
- Faculty of Medicine, The University of Jordan, Amman 11942, Jordan; (M.A.I.); (E.E.); (B.Q.); (S.I.I.)
| | - Abeer Al Bawab
- Faculty of Science, The University of Jordan, Amman 11942, Jordan; (F.O.); (H.N.); (A.A.B.)
- Hamdi Mango Center for Scientific Research, The University of Jordan, Amman 11942, Jordan
| | - Said I. Ismail
- Faculty of Medicine, The University of Jordan, Amman 11942, Jordan; (M.A.I.); (E.E.); (B.Q.); (S.I.I.)
- Qatar Genome Project, Qatar Foundation, Doha 5825, Qatar
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8
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Garafutdinov RR, Sakhabutdinova AR, Kupryushkin MS, Pyshnyi DV. Prevention of DNA multimerization using phosphoryl guanidine primers during isothermal amplification with Bst exo- DNA polymerase. Biochimie 2019; 168:259-267. [PMID: 31765671 DOI: 10.1016/j.biochi.2019.11.013] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2019] [Accepted: 11/20/2019] [Indexed: 12/29/2022]
Abstract
Over the last two decades, isothermal amplification of nucleic acids has gained more attention due to a number of advantages over the widely used polymerase chain reaction. For isothermal amplification, DNA polymerases with strand-displacement activity are needed, and Bst exo- polymerase is one of the most commonly used. Unfortunately, Bst exo- causes nonspecific DNA amplification (so-called multimerization) under isothermal conditions that results in undesirable products (multimers) consisting of tandem nucleotide repeats. Multimerization occurs only for short ssDNA or primer dimers, and the efficiency of multimerization depends significantly on the reaction conditions, but slightly depends on the sequence of DNA templates. In this study we report the prevention of DNA multimerization using a new type of modified oligonucleotide primers with internucleosidic phosphates containing 1,3-dimethyl-2-imino-imidazolidine moieties (phosphoryl guanidine (PG) groups). Primers with one, two or three PG groups located at the 3'- or 5'-ends or in the middle of the primers were designed. It turned out, such bulky groups interfere with the moving of Bst exo- polymerase along DNA chains. However, one modified phosphate does not notably affect the efficiency of polymerization, and the elongation is completely inhibited only when three contiguous modifications occur. Multimerization of the linear ssDNA templates is blocked by three modifications in the middle of both primers whereas specific amplification of the circular ssDNA by rolling circle amplification is not inhibited. Thus, incorporation of three PG groups is sufficient to prevent multimerization and allows to create improved primers for reliable isothermal amplification with Bst exo- DNA polymerase.
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Affiliation(s)
- Ravil R Garafutdinov
- Institute of Biochemistry and Genetics, Ufa Federal Research Centre, Russian Academy of Sciences, 450054, Prosp. Oktyabrya, 71, Ufa, Bashkortostan, Russia.
| | - Assol R Sakhabutdinova
- Institute of Biochemistry and Genetics, Ufa Federal Research Centre, Russian Academy of Sciences, 450054, Prosp. Oktyabrya, 71, Ufa, Bashkortostan, Russia.
| | - Maxim S Kupryushkin
- Institute of Chemical Biology and Fundamental Medicine, Siberian Branch of the Russian Academy of Sciences, 630090, Lavrentiev Avenue 8, Novosibirsk, Russia.
| | - Dmitrii V Pyshnyi
- Institute of Chemical Biology and Fundamental Medicine, Siberian Branch of the Russian Academy of Sciences, Novosibirsk State University, 630090, Lavrentiev Avenue 8, Novosibirsk, Russia.
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9
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Le BT, Hughes Q, Rakesh S, Baker R, Jørgensen PT, Wengel J, Veedu RN. Unlocked nucleic acid modified primer-based enzymatic polymerization assay: towards allele-specific genotype detection of human platelet antigens. RSC Adv 2018; 8:32770-32774. [PMID: 35547719 PMCID: PMC9086379 DOI: 10.1039/c8ra06050a] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2018] [Accepted: 08/24/2018] [Indexed: 12/12/2022] Open
Abstract
Accurate detection of single nucleotide polymorphisms (SNPs) is paramount for the appropriate therapeutic intervention of debilitating diseases associated with SNPs. However, in some cases current nucleic acid probes fail to detect allele-specific mutations, for example, human platelet antigens, HPA-15a (TCC) and HPA-15b (TAC) alleles associated with neonatal alloimmune thrombocytopenia. Towards this, it is necessary to develop a novel assay for detection of allele-specific mutations. In this study, we investigated the potential of unlocked nucleic acid (UNA)-modified primers in SNP detection utilising an enzymatic polymerisation-based approach. Our results of primer extension and asymmetric polymerase chain reaction by KOD XL DNA polymerase revealed that UNA-modified primers achieved excellent allele-specificity in discriminating the human platelet antigen DNA template, whereas the DNA control primers were not able to differentiate between the normal and mutant alleles, demonstrating the scope of this novel UNA-based enzymatic approach as a robust methodology for efficient detection of allele-specific mismatches. Although further evaluation is required for other disease conditions, we firmly believe that our findings offer a great promise for the diagnosis of neonatal alloimmune thrombocytopenia and other SNP-related diseases.
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Affiliation(s)
- Bao T Le
- Centre for Comparative Genomics, Murdoch University Perth Australia-6150
- Perron Institute for Neurological and Translational Science Perth Australia-6009
| | | | | | - Ross Baker
- Perth Blood Institute Nedlands Perth WA Australia
| | - Per T Jørgensen
- BioNEC, Department of Physics, Chemistry and Pharmacy, University of Southern Denmark Odense M 5231 Denmark
| | - Jesper Wengel
- BioNEC, Department of Physics, Chemistry and Pharmacy, University of Southern Denmark Odense M 5231 Denmark
| | - Rakesh N Veedu
- Centre for Comparative Genomics, Murdoch University Perth Australia-6150
- Perron Institute for Neurological and Translational Science Perth Australia-6009
- BioNEC, Department of Physics, Chemistry and Pharmacy, University of Southern Denmark Odense M 5231 Denmark
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10
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Xiao Y, Liu Q, Tang X, Yang Z, Wu L, He Y. Mirror-Image Thymidine Discriminates against Incorporation of Deoxyribonucleotide Triphosphate into DNA and Repairs Itself by DNA Polymerases. Bioconjug Chem 2017; 28:2125-2134. [PMID: 28686433 DOI: 10.1021/acs.bioconjchem.7b00301] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
DNA polymerases are known to recognize preferably d-nucleotides over l-nucleotides during DNA synthesis. Here, we report that several general DNA polymerases catalyze polymerization reactions of nucleotides directed by the DNA template containing an l-thymidine (l-T). The results display that the 5'-3' primer extension of natural nucleotides get to the end at chiral modification site with Taq and Phanta Max DNA polymerases, but the primer extension proceeds to the end of the template catalyzed by Deep Vent (exo-), Vent (exo-), and Therminator DNA polymerases. Furthermore, templating l-nucleoside displays a lag in the deoxyribonucleotide triphosphate (dNTP) incorporation rates relative to natural template by kinetics analysis, and polymerase chain reactions were inhibited with the DNA template containing two or three consecutive l-Ts. Most interestingly, no single base mutation or mismatch mixture corresponding to the location of l-T in the template was found, which is physiologically significant because they provide a theoretical basis on the involvement of DNA polymerase in the effective repair of l-T that may lead to cytotoxicity.
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Affiliation(s)
- Yating Xiao
- School of Chemistry and Chemical Engineering, University of Chinese Academy of Sciences , Beijing 100049, China
| | - Qingju Liu
- School of Chemistry and Chemical Engineering, University of Chinese Academy of Sciences , Beijing 100049, China
| | - Xinjing Tang
- State Key Laboratory of Natural and Biomimetic Drugs, School of Pharmaceutical Sciences, Peking University , Beijing 100191, China
| | - Zhenjun Yang
- State Key Laboratory of Natural and Biomimetic Drugs, School of Pharmaceutical Sciences, Peking University , Beijing 100191, China
| | - Li Wu
- School of Chemistry and Chemical Engineering, University of Chinese Academy of Sciences , Beijing 100049, China.,State Key Laboratory of Natural and Biomimetic Drugs, School of Pharmaceutical Sciences, Peking University , Beijing 100191, China
| | - Yujian He
- School of Chemistry and Chemical Engineering, University of Chinese Academy of Sciences , Beijing 100049, China.,State Key Laboratory of Natural and Biomimetic Drugs, School of Pharmaceutical Sciences, Peking University , Beijing 100191, China
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11
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Lipi F, Chen S, Chakravarthy M, Rakesh S, Veedu RN. In vitro evolution of chemically-modified nucleic acid aptamers: Pros and cons, and comprehensive selection strategies. RNA Biol 2016; 13:1232-1245. [PMID: 27715478 PMCID: PMC5207382 DOI: 10.1080/15476286.2016.1236173] [Citation(s) in RCA: 76] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2023] Open
Abstract
Nucleic acid aptamers are single-stranded DNA or RNA oligonucleotide sequences that bind to a specific target molecule with high affinity and specificity through their ability to adopt 3-dimensional structure in solution. Aptamers have huge potential as targeted therapeutics, diagnostics, delivery agents and as biosensors. However, aptamers composed of natural nucleotide monomers are quickly degraded in vivo and show poor pharmacodynamic properties. To overcome this, chemically-modified nucleic acid aptamers are developed by incorporating modified nucleotides after or during the selection process by Systematic Evolution of Ligands by EXponential enrichment (SELEX). This review will discuss the development of chemically-modified aptamers and provide the pros and cons, and new insights on in vitro aptamer selection strategies by using chemically-modified nucleic acid libraries.
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Affiliation(s)
- Farhana Lipi
- a Western Australian Neuroscience Research Institute , Perth , Australia
| | - Suxiang Chen
- a Western Australian Neuroscience Research Institute , Perth , Australia.,b Centre for Comparative Genomics, Murdoch University , Perth , Australia
| | - Madhuri Chakravarthy
- a Western Australian Neuroscience Research Institute , Perth , Australia.,b Centre for Comparative Genomics, Murdoch University , Perth , Australia
| | - Shilpa Rakesh
- a Western Australian Neuroscience Research Institute , Perth , Australia
| | - Rakesh N Veedu
- a Western Australian Neuroscience Research Institute , Perth , Australia.,b Centre for Comparative Genomics, Murdoch University , Perth , Australia
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12
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Tang S, Wei H, Hu T, Jiang J, Chang J, Guan Y, Zhao G. Suppression of rolling circle amplification by nucleotide analogs in circular template for three DNA polymerases. Biosci Biotechnol Biochem 2016; 80:1555-61. [PMID: 27151504 DOI: 10.1080/09168451.2016.1171699] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/21/2022]
Abstract
Among wide applications of nucleotide analogs, their roles in enzyme catalytic reactions are significant in both fundamental and medical researches. By introducing analogs into circular templates, we succeeded in determining effects of four analogs on RCA efficiency for three different DNA polymerases. Results showed an obvious suppression effect for 2'-OMeRNA modification, which might be due to the size of the C2'-modified moieties. 2'-F RNA, LNA and PS had little interference, suggesting good analog candidates for application in RCA. Different polymerases and nucleobases made a little difference according to analogs we used. These results are useful for understanding polymerase catalytic mechanism and analogs applications in RCA reaction.
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Affiliation(s)
- Suming Tang
- a Department of Biochemistry and Molecular Biology , China Medical University , Shenyang , China
| | - Hua Wei
- a Department of Biochemistry and Molecular Biology , China Medical University , Shenyang , China.,b Department of Aquaculture , Animal Science and Veterinary Medicine College, Shenyang Agricultural University , Shenyang , China
| | - Tianyu Hu
- a Department of Biochemistry and Molecular Biology , China Medical University , Shenyang , China
| | - Jiquan Jiang
- a Department of Biochemistry and Molecular Biology , China Medical University , Shenyang , China
| | - Jinglin Chang
- a Department of Biochemistry and Molecular Biology , China Medical University , Shenyang , China
| | - Yifu Guan
- a Department of Biochemistry and Molecular Biology , China Medical University , Shenyang , China
| | - Guojie Zhao
- a Department of Biochemistry and Molecular Biology , China Medical University , Shenyang , China
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13
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Elle IC, Karlsen KK, Terp MG, Larsen N, Nielsen R, Derbyshire N, Mandrup S, Ditzel HJ, Wengel J. Selection of LNA-containing DNA aptamers against recombinant human CD73. MOLECULAR BIOSYSTEMS 2016; 11:1260-70. [PMID: 25720604 DOI: 10.1039/c5mb00045a] [Citation(s) in RCA: 32] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Subscribe] [Scholar Register] [Indexed: 02/01/2023]
Abstract
LNA-containing DNA aptamers against CD73 (human ecto-5'-nucleotidase), a protein frequently overexpressed in solid tumours, were isolated by SELEX. A pre-defined stem-loop library, containing LNA in the forward primer region, was enriched with CD73 binding sequences through six rounds of SELEX with recombinant his-tagged CD73 immobilised on anti-his plates. Enriched pools isolated from rounds one, three and six were subjected to next-generation sequencing and analysed for enrichment using custom bioinformatics software. The software identified aptamer sequences via the primers and then performed several steps including sequence unification, clustering and alignment to identify enriched sequences. Three enriched sequences were synthesised for further analysis, two of which showed sequence similarities. These sequences exhibited binding to the recombinant CD73 with KD values of 10 nM and 3.5 nM when tested by surface plasmon resonance. Truncated variants of these aptamers and variants where the LNA nucleotides were substituted for the DNA equivalent also exhibited affinity for the recombinant CD73 in the low nanomolar range. In enzyme inhibition assays with recombinant CD73 the aptamer sequences were able to decrease the activity of the protein. However, the aptamers exhibited no binding to cellular CD73 by flow cytometry analysis likely since the epitope recognised by the aptamer was not available for binding on the cellular protein.
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Affiliation(s)
- Ida C Elle
- Nucleic Acid Center, Department of Physics, Chemistry and Pharmacy, University of Southern Denmark, Campusvej 55, 5230 Odense M, Denmark.
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14
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Aaldering LJ, Tayeb H, Krishnan S, Fletcher S, Wilton SD, Veedu RN. Smart functional nucleic acid chimeras: enabling tissue specific RNA targeting therapy. RNA Biol 2016; 12:412-25. [PMID: 25849197 PMCID: PMC4615226 DOI: 10.1080/15476286.2015.1017234] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022] Open
Abstract
A major obstacle for effective utilization of therapeutic oligonucleotides such as siRNA, antisense, antimiRs etc. is to deliver them specifically to the target tissues. Toward this goal, nucleic acid aptamers are re-emerging as a prominent class of biomolecules capable of delivering target specific therapy and therapeutic monitoring by various molecular imaging modalities. This class of short oligonucleotide ligands with high affinity and specificity are selected from a large nucleic acid pool against a molecular target of choice. Poor cellular uptake of therapeutic oligonucleotides impedes gene-targeting efficacy in vitro and in vivo. In contrast, aptamer-oligonucleotide chimeras have shown the capacity to deliver siRNA, antimiRs, small molecule drugs etc. toward various targets and showed very promising results in various studies on different diseases models. However, to further improve the bio-stability of such chimeric conjugates, it is important to introduce chemically-modified nucleic acid analogs. In this review, we highlight the applications of nucleic acid aptamers for target specific delivery of therapeutic oligonucleotides.
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Affiliation(s)
- Lukas J Aaldering
- a Nucleic Acid Center; Department of Physics, Chemistry and Pharmacy ; University of Southern Denmark ; Odense , Denmark
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15
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Hoshino H, Kasahara Y, Fujita H, Kuwahara M, Morihiro K, Tsunoda SI, Obika S. Consecutive incorporation of functionalized nucleotides with amphiphilic side chains by novel KOD polymerase mutant. Bioorg Med Chem Lett 2015; 26:530-533. [PMID: 26627581 DOI: 10.1016/j.bmcl.2015.11.079] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2015] [Revised: 11/19/2015] [Accepted: 11/21/2015] [Indexed: 11/29/2022]
Abstract
Recently, 7-substituted 7-deazapurine nucleoside triphosphates and 5-substituted pyrimidine nucleoside triphosphates (dN(am)TPs) were synthesized to extend enzymatically using commercially available polymerase. However, extension was limited when we attempted to incorporate the substrates consecutively. To address this, we have produced a mutant polymerase that can efficiently accept the modified nucleotide with amphiphilic groups as substrates. Here we show that the KOD polymerase mutant, KOD exo(-)/A485L, had the ability to incorporate dN(am)TP continuously over 50nt, indicating that the mutant is sufficient for generating functional nucleic acid molecules.
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Affiliation(s)
- Hidekazu Hoshino
- Graduate School of Pharmaceutical Sciences, Osaka University, 1-6 Yamadaoka, Suita, Osaka 565-0871, Japan; National Institutes of Biomedical Innovation, Health and Nutrition (NIBIOHN), 7-6-8 Saito-Asagi, Ibaraki, Osaka 567-0085, Japan
| | - Yuuya Kasahara
- Graduate School of Pharmaceutical Sciences, Osaka University, 1-6 Yamadaoka, Suita, Osaka 565-0871, Japan; National Institutes of Biomedical Innovation, Health and Nutrition (NIBIOHN), 7-6-8 Saito-Asagi, Ibaraki, Osaka 567-0085, Japan
| | - Hiroto Fujita
- Graduate School of Science and Technology, Gunma University, 1-5-1 Tenjin-cho, Kiryu, Gunma 376-8515, Japan
| | - Masayasu Kuwahara
- Graduate School of Science and Technology, Gunma University, 1-5-1 Tenjin-cho, Kiryu, Gunma 376-8515, Japan.
| | - Kunihiko Morihiro
- Graduate School of Pharmaceutical Sciences, Osaka University, 1-6 Yamadaoka, Suita, Osaka 565-0871, Japan; National Institutes of Biomedical Innovation, Health and Nutrition (NIBIOHN), 7-6-8 Saito-Asagi, Ibaraki, Osaka 567-0085, Japan
| | - Shin-Ichi Tsunoda
- National Institutes of Biomedical Innovation, Health and Nutrition (NIBIOHN), 7-6-8 Saito-Asagi, Ibaraki, Osaka 567-0085, Japan
| | - Satoshi Obika
- Graduate School of Pharmaceutical Sciences, Osaka University, 1-6 Yamadaoka, Suita, Osaka 565-0871, Japan; National Institutes of Biomedical Innovation, Health and Nutrition (NIBIOHN), 7-6-8 Saito-Asagi, Ibaraki, Osaka 567-0085, Japan.
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16
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Kokil GR, Veedu RN, Ramm GA, Prins JB, Parekh HS. Type 2 diabetes mellitus: limitations of conventional therapies and intervention with nucleic acid-based therapeutics. Chem Rev 2015; 115:4719-43. [PMID: 25918949 DOI: 10.1021/cr5002832] [Citation(s) in RCA: 53] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Affiliation(s)
- Ganesh R Kokil
- †School of Pharmacy, Pharmacy Australia Centre of Excellence, The University of Queensland, Brisbane, QLD 4102, Australia
| | - Rakesh N Veedu
- §Center for Comparative Genomics, Murdoch University, 90 South Street, Murdoch, WA 6150, Australia.,∥Western Australian Neuroscience Research Institute, Perth, WA 6150, Australia.,‡School of Chemistry and Molecular Biosciences, The University of Queensland, Brisbane QLD 4072 Australia
| | - Grant A Ramm
- ⊥The Hepatic Fibrosis Group, QIMR Berghofer Medical Research Institute, Brisbane, QLD 4006, Australia.,#Faculty of Medicine and Biomedical Sciences, The University of Queensland, Brisbane, QLD 4006, Australia
| | - Johannes B Prins
- ∇Mater Research Institute, The University of Queensland, Brisbane, QLD 4101, Australia
| | - Harendra S Parekh
- †School of Pharmacy, Pharmacy Australia Centre of Excellence, The University of Queensland, Brisbane, QLD 4102, Australia
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17
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Fujita H, Nakajima K, Kasahara Y, Ozaki H, Kuwahara M. Polymerase-mediated high-density incorporation of amphiphilic functionalities into DNA: enhancement of nuclease resistance and stability in human serum. Bioorg Med Chem Lett 2014; 25:333-6. [PMID: 25475204 DOI: 10.1016/j.bmcl.2014.11.037] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2014] [Revised: 11/11/2014] [Accepted: 11/13/2014] [Indexed: 12/20/2022]
Abstract
Modified oligodeoxyribonucleotides (mdODNs) bearing multiple copies of an amphiphilic functional group were enzymatically synthesized by simultaneous incorporation of base-modified 5'-triphosphate analogs of 2'-deoxyguanosine (dG(am)TP), 2'-deoxyuridine (dU(am)TP), 2'-deoxyadenosine (dA(am)TP), and 2'-deoxycytosine (dC(am)TP). The amphiphilic functionality, that is, (E)-38,53-dioxo-2,5,8,11,14,17,20,23,26,29,32,35-dodecaoxa-39,52-diazapentapentacont-54-en-55-yl group, consists of the water soluble dodeca(ethylene glycol) chain and the hydrophobic dodecyl chain. An enzymatically synthesized ODN, composed of a 20-mer 5'-terminal segment containing 2'-O,4'-C-methylene-bridged/linked bicyclic ribonucleotide (B/L nucleotide) and a 12-mer 3'-terminal segment containing the nucleobase-modified analogs, exhibits very high resistance against phosphodiesterase I and is stable in human serum for a longer period when compared with ODN, where the 12-mer 3'-terminal segment contains unmodified nucleotides.
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Affiliation(s)
- Hiroto Fujita
- Graduate School of Science and Technology, Gunma University, 1-5-1 Tenjin-cho, Kiryu, Gunma 376-8515, Japan
| | - Kohsuke Nakajima
- Graduate School of Science and Technology, Gunma University, 1-5-1 Tenjin-cho, Kiryu, Gunma 376-8515, Japan
| | - Yuuya Kasahara
- Graduate School of Science and Technology, Gunma University, 1-5-1 Tenjin-cho, Kiryu, Gunma 376-8515, Japan; National Institute of Biomedical Innovation (NIBIO), 7-6-8 Asagi, Saito, Ibaraki, Osaka 567-0085, Japan
| | - Hiroaki Ozaki
- Graduate School of Science and Technology, Gunma University, 1-5-1 Tenjin-cho, Kiryu, Gunma 376-8515, Japan
| | - Masayasu Kuwahara
- Graduate School of Science and Technology, Gunma University, 1-5-1 Tenjin-cho, Kiryu, Gunma 376-8515, Japan.
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Poongavanam V, Madala PK, Højland T, Veedu RN. Computational investigation of locked nucleic acid (LNA) nucleotides in the active sites of DNA polymerases by molecular docking simulations. PLoS One 2014; 9:e102126. [PMID: 25036012 PMCID: PMC4103837 DOI: 10.1371/journal.pone.0102126] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2013] [Accepted: 06/16/2014] [Indexed: 01/07/2023] Open
Abstract
Aptamers constitute a potential class of therapeutic molecules typically selected from a large pool of oligonucleotides against a specific target. With a scope of developing unique shorter aptamers with very high biostability and affinity, locked nucleic acid (LNA) nucleotides have been investigated as a substrate for various polymerases. Various reports showed that some thermophilic B-family DNA polymerases, particularly KOD and Phusion DNA polymerases, accepted LNA-nucleoside 5'-triphosphates as substrates. In this study, we investigated the docking of LNA nucleotides in the active sites of RB69 and KOD DNA polymerases by molecular docking simulations. The study revealed that the incoming LNA-TTP is bound in the active site of the RB69 and KOD DNA polymerases in a manner similar to that seen in the case of dTTP, and with LNA structure, there is no other option than the locked C3'-endo conformation which in fact helps better orienting within the active site.
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Affiliation(s)
- Vasanthanathan Poongavanam
- Nucleic Acid Center and Department of Physics, Chemistry and Pharmacy, University of Southern Denmark, Odense M, Denmark
| | - Praveen K. Madala
- Institute of Molecular Bioscience, The University of Queensland, Brisbane, Queensland, Australia
| | - Torben Højland
- Nucleic Acid Center and Department of Physics, Chemistry and Pharmacy, University of Southern Denmark, Odense M, Denmark
| | - Rakesh N. Veedu
- Nucleic Acid Center and Department of Physics, Chemistry and Pharmacy, University of Southern Denmark, Odense M, Denmark
- School of Chemistry and Molecular Biosciences, The University of Queensland, Brisbane, Queensland, Australia
- * E-mail:
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19
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Pinheiro VB, Holliger P. Towards XNA nanotechnology: new materials from synthetic genetic polymers. Trends Biotechnol 2014; 32:321-8. [PMID: 24745974 PMCID: PMC4039137 DOI: 10.1016/j.tibtech.2014.03.010] [Citation(s) in RCA: 76] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2013] [Revised: 03/17/2014] [Accepted: 03/18/2014] [Indexed: 12/21/2022]
Abstract
Nucleic acids display remarkable properties beyond information storage and propagation. The well-understood base pairing rules have enabled nucleic acids to be assembled into nanostructures of ever increasing complexity. Although nanostructures can be constructed using other building blocks, including peptides and lipids, it is the capacity to evolve that sets nucleic acids apart from all other nanoscale building materials. Nonetheless, the poor chemical and biological stability of DNA and RNA constrain their applications. Recent advances in nucleic acid chemistry and polymerase engineering enable the synthesis, replication, and evolution of a range of synthetic genetic polymers (XNAs) with improved chemical and biological stability. We discuss the impact of this technology on the generation of XNA ligands, enzymes, and nanostructures with tailor-made chemistry.
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Affiliation(s)
- Vitor B Pinheiro
- MRC Laboratory of Molecular Biology, Francis Crick Avenue, Cambridge, CB2 0QH, UK
| | - Philipp Holliger
- MRC Laboratory of Molecular Biology, Francis Crick Avenue, Cambridge, CB2 0QH, UK.
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20
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Kong HY, Byun J. Nucleic Acid aptamers: new methods for selection, stabilization, and application in biomedical science. Biomol Ther (Seoul) 2014; 21:423-34. [PMID: 24404332 PMCID: PMC3879913 DOI: 10.4062/biomolther.2013.085] [Citation(s) in RCA: 129] [Impact Index Per Article: 12.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2013] [Revised: 11/05/2013] [Accepted: 11/05/2013] [Indexed: 12/19/2022] Open
Abstract
The adoption of oligonucleotide aptamer is well on the rise, serving an ever increasing demand for versatility in biomedical field. Through the SELEX (Systematic Evolution of Ligands by EXponential enrichment), aptamer that can bind to specific target with high affinity and specificity can be obtained. Aptamers are single-stranded nucleic acid molecules that can fold into complex threedimensional structures, forming binding pockets and clefts for the specific recognition and tight binding of any given molecular target. Recently, aptamers have attracted much attention because they not only have all of the advantages of antibodies, but also have unique merits such as thermal stability, ease of synthesis, reversibility, and little immunogenicity. The advent of novel technologies is revolutionizing aptamer applications. Aptamers can be easily modified by various chemical reactions to introduce functional groups and/or nucleotide extensions. They can also be conjugated to therapeutic molecules such as drugs, drug containing carriers, toxins, or photosensitizers. Here, we discuss new SELEX strategies and stabilization methods as well as applications in drug delivery and molecular imaging.
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Affiliation(s)
- Hoon Young Kong
- Department of Molecular Biology, Institute of Nanosensor and Biotechnology, Dankook University, Yongin 448-701, Republic of Korea
| | - Jonghoe Byun
- Department of Molecular Biology, Institute of Nanosensor and Biotechnology, Dankook University, Yongin 448-701, Republic of Korea
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21
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Kuwahara M, Obika S. In vitro selection of BNA (LNA) aptamers. ARTIFICIAL DNA, PNA & XNA 2014; 4:39-48. [PMID: 24044051 DOI: 10.4161/adna.25786] [Citation(s) in RCA: 46] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Received: 05/31/2013] [Accepted: 07/17/2013] [Indexed: 01/03/2023]
Abstract
Recently, we achieved the first in vitro selection of 2'-O,4'-C-methylene bridged/locked nucleic acid (2',4'-BNA/LNA) aptamers. High-affinity thrombin-binding aptamers (TBAs) were obtained from DNA-based libraries containing 2'-O,4'-C-methylene-bridged/linked bicyclic ribonucleotides (B/L nucleotides) in the 5'-primer region, using the method of capillary electrophoresis systematic evolution of ligands by exponential enrichment (CE-SELEX). Furthermore, a similar selection protocol could provide TBAs that contain B/L nucleotides in both primer and random regions. We review technical challenges involved in the generation of various BNA libraries using analogs of B/L nucleoside-5'-triphosphate and polymerase variants and also discuss applications of these libraries to the selection of BNA (LNA) aptamers, as well as future prospects for their therapeutic and diagnostic uses.
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Affiliation(s)
- Masayasu Kuwahara
- Graduate School of Science and Technology; Gunma University; Gunma, Japan
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22
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Li B, Dong S, Wu J, Zhang J, Chen G, Dong Q, Zhu X, Wang X. Preparation of 5'-O-(1-Thiotriphosphate)-modified oligonucleotides using polymerase-endonuclease amplification reaction (PEAR). PLoS One 2013; 8:e67558. [PMID: 23861771 PMCID: PMC3701678 DOI: 10.1371/journal.pone.0067558] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2013] [Accepted: 05/21/2013] [Indexed: 12/12/2022] Open
Abstract
Antisense oligonucleotides (ASODNs) have been widely used as an important tool for regulating gene expression, and developed into therapeutics. Natural ODNs are susceptible to nuclease degradation, nucleic acid analogues, however, have less side effects, stronger stability and more potent activities. Large-scale de novo synthesis of a certain oligonucleotide has been very difficult and costly. In a previous preliminary study, we developed the polymerase-endonuclease amplification reaction (PEAR) for amplification and large-scale preparation of natural antisense ODNs. Here we extended the method in preparation of a widely used modified oligonucleotide with 5′-O-(1-Thiotriphosphate) modifications. Using electrospray ionization liquid chromatography mass spectrometry (ESI/LC/MS) detection, the purity of the PEAR product was measured as high as 100.0%. Using PEAR a large amount of a specific oligonucleotide can be produced starting from a small amount of synthetic seeds. It is suggested that PEAR can be a useful tool for large-scale production of modified oligonucleotides.
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Affiliation(s)
- Biao Li
- Department of Biotechnology, Ocean University of China, Qingdao, Shandong, People's Republic of China
| | - Shihua Dong
- Department of Biotechnology, Ocean University of China, Qingdao, Shandong, People's Republic of China
| | - Jiajun Wu
- Department of Biotechnology, Ocean University of China, Qingdao, Shandong, People's Republic of China
| | - Jianye Zhang
- Department of Biotechnology, Ocean University of China, Qingdao, Shandong, People's Republic of China
| | - Gang Chen
- Department of Biotechnology, Ocean University of China, Qingdao, Shandong, People's Republic of China
| | - Quanjiang Dong
- Qingdao Municipal Hospital, Qingdao, Shandong, People's Republic of China
| | - Xinhong Zhu
- Qingdao Municipal Hospital, Qingdao, Shandong, People's Republic of China
| | - Xiaolong Wang
- Department of Biotechnology, Ocean University of China, Qingdao, Shandong, People's Republic of China
- * E-mail:
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23
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Bergen K, Betz K, Welte W, Diederichs K, Marx A. Structures of KOD and 9°N DNA polymerases complexed with primer template duplex. Chembiochem 2013; 14:1058-62. [PMID: 23733496 DOI: 10.1002/cbic.201300175] [Citation(s) in RCA: 44] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2013] [Indexed: 12/29/2022]
Abstract
Replicate it: Structures of KOD and 9°N DNA polymerases, two enzymes that are widely used to replicate DNA with highly modified nucleotides, were solved at high resolution in complex with primer/template duplex. The data elucidate substrate interaction of the two enzymes and pave the way for further optimisation of the enzymes and substrates.
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Affiliation(s)
- Konrad Bergen
- Department of Chemistry, Konstanz Research School Chemical Biology, University of Konstanz, Universitätsstrasse 10, 78457 Konstanz, Germany
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24
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Affiliation(s)
- Kasper K Karlsen
- Nucleic Acid Center, Department of Physics, Chemistry, and Pharmacy, University of Southern Denmark, Odense M, Denmark
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Kasahara Y, Irisawa Y, Ozaki H, Obika S, Kuwahara M. 2',4'-BNA/LNA aptamers: CE-SELEX using a DNA-based library of full-length 2'-O,4'-C-methylene-bridged/linked bicyclic ribonucleotides. Bioorg Med Chem Lett 2013; 23:1288-92. [PMID: 23374873 DOI: 10.1016/j.bmcl.2012.12.093] [Citation(s) in RCA: 41] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2012] [Revised: 12/25/2012] [Accepted: 12/28/2012] [Indexed: 01/24/2023]
Abstract
DNA-based aptamers that contain 2'-O,4'-C-methylene-bridged/linked bicyclic ribonucleotides (B/L nucleotides) over the entire length were successfully obtained using a capillary electrophoresis systematic evolution of ligands by exponential enrichment (CE-SELEX) method. A modified DNA library was prepared with an enzyme mix of KOD Dash and KOD mutant DNA polymerases. Forty 2'-O,4'-C-methylene bridged/locked nucleic acid (2',4'-BNA/LNA) aptamers were isolated from an enriched pool and classified into six groups according to their sequence. 2',4'-BNA/LNA aptamers of groups V and VI bound human thrombin with K(d) values in the range of several 10 nanomolar levels.
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Affiliation(s)
- Yuuya Kasahara
- Graduate School of Engineering, Gunma University, 1-5-1 Tenjin-cho, Kiryu, Gunma 376-8515, Japan
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26
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Nawale GN, Gore KR, Höbartner C, Pradeepkumar PI. Incorporation of 4'-C-aminomethyl-2'-O-methylthymidine into DNA by thermophilic DNA polymerases. Chem Commun (Camb) 2013; 48:9619-21. [PMID: 22908130 DOI: 10.1039/c2cc35222b] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/17/2023]
Abstract
The dual modified nucleotide 4'-C-aminomethyl-2'-O-methylthymidine 5'-triphosphate was synthesized and enzymatically incorporated into DNA by the thermophilic DNA polymerases Pfu and Therminator III. The dual ribose modification imparted increased exonuclease resistance to DNA compared to the well-known 2'-O-methyl modification.
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Affiliation(s)
- Ganesh N Nawale
- Department of Chemistry, Indian Institute of Technology Bombay, Powai, Mumbai 400076, India
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27
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Lundin KE, Højland T, Hansen BR, Persson R, Bramsen JB, Kjems J, Koch T, Wengel J, Smith CIE. Biological activity and biotechnological aspects of locked nucleic acids. ADVANCES IN GENETICS 2013; 82:47-107. [PMID: 23721720 DOI: 10.1016/b978-0-12-407676-1.00002-0] [Citation(s) in RCA: 73] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Abstract
Locked nucleic acid (LNA) is one of the most promising new nucleic acid analogues that has been produced under the past two decades. In this chapter, we have tried to cover many of the different areas, where this molecule has been used to improve the function of synthetic oligonucleotides (ONs). The use of LNA in antisense ONs, including gapmers, splice-switching ONs, and siLNA, as well as antigene ONs, is reviewed. Pharmacokinetics as well as pharmacodynamics of LNA ONs and a description of selected compounds in, or close to, clinical testing are described. In addition, new LNA modifications and the adaptation of enzymes for LNA incorporation are reviewed. Such enzymes may become important for the development of stabilized LNA-containing aptamers.
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Affiliation(s)
- Karin E Lundin
- Clinical Research Center, Department of Laboratory Medicine, Karolinska Institutet, Novum, Huddinge, Stockholm, Sweden.
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28
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Amplification and re-generation of LNA-modified libraries. Molecules 2012; 17:13087-97. [PMID: 23128088 PMCID: PMC6268865 DOI: 10.3390/molecules171113087] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2012] [Revised: 10/31/2012] [Accepted: 11/01/2012] [Indexed: 12/14/2022] Open
Abstract
Locked nucleic acids (LNA) confer high thermal stability and nuclease resistance to oligonucleotides. The discovery of polymerases that accept LNA triphosphates has led us to propose a scheme for the amplification and re-generation of LNA-containing oligonucleotide libraries. Such libraries could be used for in vitro selection of e.g., native LNA aptamers. We maintained an oligonucleotide library encoding 40 randomized positions with LNA ATP, GTP, CTP, and TTP for 7 rounds of ‘mock’ in vitro selection in the absence of a target and analyzed the sequence composition after rounds 1, 4 and 7. We observed a decrease in LNA-A content from 20.5% in round 1 to 6.6% in round 7. This decrease was accompanied by a substantial bias against successive LNA-As (poly-LNA adenosine tracts) and a relative over-representation of single LNA-As. Maintaining a library with LNA TTP yielded similar results. Together, these results suggest that dispersed LNA monomers are tolerated in our in vitro selection protocol, and that LNA-modified libraries can be sustained for up to at least seven selection rounds, albeit at reduced levels. This enables the discovery of native LNA aptamers and similar oligonucleotide structures.
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29
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Kasahara Y, Kuwahara M. Artificial specific binders directly recovered from chemically modified nucleic acid libraries. J Nucleic Acids 2012; 2012:156482. [PMID: 23094139 PMCID: PMC3472525 DOI: 10.1155/2012/156482] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2012] [Accepted: 08/19/2012] [Indexed: 11/18/2022] Open
Abstract
Specific binders comprised of nucleic acids, that is, RNA/DNA aptamers, are attractive functional biopolymers owing to their potential broad application in medicine, food hygiene, environmental analysis, and biological research. Despite the large number of reports on selection of natural DNA/RNA aptamers, there are not many examples of direct screening of chemically modified nucleic acid aptamers. This is because of (i) the inferior efficiency and accuracy of polymerase reactions involving transcription/reverse-transcription of modified nucleotides compared with those of natural nucleotides, (ii) technical difficulties and additional time and effort required when using modified nucleic acid libraries, and (iii) ambiguous efficacies of chemical modifications in binding properties until recently; in contrast, the effects of chemical modifications on biostability are well studied using various nucleotide analogs. Although reports on the direct screening of a modified nucleic acid library remain in the minority, chemical modifications would be essential when further functional expansion of nucleic acid aptamers, in particular for medical and biological uses, is considered. This paper focuses on enzymatic production of chemically modified nucleic acids and their application to random screenings. In addition, recent advances and possible future research are also described.
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Affiliation(s)
- Yuuya Kasahara
- Graduate School of Engineering, Gunma University, 1-5-1 Tenjin-cho, Kiryu 376-8515, Japan
| | - Masayasu Kuwahara
- Graduate School of Engineering, Gunma University, 1-5-1 Tenjin-cho, Kiryu 376-8515, Japan
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30
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Crouzier L, Dubois C, Edwards SL, Lauridsen LH, Wengel J, Veedu RN. Efficient reverse transcription using locked nucleic acid nucleotides towards the evolution of nuclease resistant RNA aptamers. PLoS One 2012; 7:e35990. [PMID: 22558297 PMCID: PMC3338489 DOI: 10.1371/journal.pone.0035990] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2012] [Accepted: 03/26/2012] [Indexed: 01/04/2023] Open
Abstract
BACKGROUND Modified nucleotides are increasingly being utilized in the de novo selection of aptamers for enhancing their drug-like character and abolishing the need for time consuming trial-and-error based post-selection modifications. Locked nucleic acid (LNA) is one of the most prominent and successful nucleic acid analogues because of its remarkable properties, and widely explored as building blocks in therapeutic oligonucleotides. Evolution of LNA-modified RNA aptamers requires an efficient reverse transcription method for PCR enrichment of the selected RNA aptamer candidates. Establishing this key step is a pre-requisite for performing LNA-modified RNA aptamer selection. METHODOLOGY In this study three different reverse transcriptases were investigated towards the enzymatic recognition of LNA nucleotides. Both incorporation as well as reading capabilities of the LNA nucleotides was investigated to fully understand the limitations of the enzymatic recognition. CONCLUSIONS We found that SuperScript® III Reverse Transcriptase is an efficient enzyme for the recognition of LNA nucleotides, making it a prime candidate to be used in de novo selection of LNA containing RNA aptamers.
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Affiliation(s)
- Lucile Crouzier
- School of Chemistry and Molecular Biosciences, The University of Queensland, St Lucia, Brisbane, Queensland, Australia
- Institute Polytechnique LaSalle Beauvais, Beauvais, France
| | - Camille Dubois
- School of Chemistry and Molecular Biosciences, The University of Queensland, St Lucia, Brisbane, Queensland, Australia
- Institute Polytechnique LaSalle Beauvais, Beauvais, France
| | - Stacey L. Edwards
- School of Chemistry and Molecular Biosciences, The University of Queensland, St Lucia, Brisbane, Queensland, Australia
| | - Lasse H. Lauridsen
- School of Chemistry and Molecular Biosciences, The University of Queensland, St Lucia, Brisbane, Queensland, Australia
- The Novo Nordisk Foundation Center for Biosustainability, Scion DTU, Hørsholm, Denmark
| | - Jesper Wengel
- Nucleic Acid Center, Department of Physics and Chemistry, University of Southern Denmark, Odense, Denmark
| | - Rakesh N. Veedu
- School of Chemistry and Molecular Biosciences, The University of Queensland, St Lucia, Brisbane, Queensland, Australia
- * E-mail:
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31
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Enzymatic polymerisation involving 2'-amino-LNA nucleotides. Bioorg Med Chem Lett 2012; 22:3522-6. [PMID: 22503454 DOI: 10.1016/j.bmcl.2012.03.073] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2012] [Revised: 03/19/2012] [Accepted: 03/21/2012] [Indexed: 11/21/2022]
Abstract
The triphosphate of the thymine derivative of 2'-amino-LNA (2'-amino-LNA-TTP) was synthesised and found to be a good substrate for Phusion® HF DNA polymerase, allowing enzymatic synthesis of modified DNA encoded by an unmodified template. To complement this, 2'-amino-LNA-T phosphoramidites were incorporated into DNA oligonucleotides which were used as templates for enzymatic synthesis of unmodified DNA using either KOD, KOD XL or Phusion polymerases. 2'-Amino-LNA-T in the template and 2'-amino-LNA-TTP as a substrate both decreased reaction rate and yield compared to unmodified DNA, especially for sequences with multiple 2'-amino-LNA-T nucleotides.
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32
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Højland T, Veedu RN, Vester B, Wengel J. Enzymatic synthesis of DNA strands containing α-L-LNA (α-L-configured locked nucleic acid) thymine nucleotides. ARTIFICIAL DNA, PNA & XNA 2012; 3:14-21. [PMID: 22679529 PMCID: PMC3368812 DOI: 10.4161/adna.19272] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 06/01/2023]
Abstract
We describe the first enzymatic incorporation of an α-L-LNA nucleotide into an oligonucleotide. It was found that the 5'-triphosphate of α-L-LNA is a substrate for the DNA polymerases KOD, 9°N(m), Phusion and HIV RT. Three dispersed α-L-LNA thymine nucleotides can be incorporated into DNA strands by all four polymerases, but they were unable to perform consecutive incorporations of α-L-LNA nucleotides. In addition it was found that primer extension can be achieved using templates containing one α-L-LNA nucleotide.
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Affiliation(s)
- Torben Højland
- Department of Physics, Chemistry and Pharmacy; Nucleic Acid Center; Department of Biochemistry and Molecular Biology; University of Southern Denmark; Odense, Denmark
| | - Rakesh N. Veedu
- Department of Physics, Chemistry and Pharmacy; Nucleic Acid Center; Department of Biochemistry and Molecular Biology; University of Southern Denmark; Odense, Denmark
- School of Chemistry and Molecular Biosciences; The University of Queensland; Brisbane, Australia
| | - Birte Vester
- Department of Physics, Chemistry and Pharmacy; Nucleic Acid Center; Department of Biochemistry and Molecular Biology; University of Southern Denmark; Odense, Denmark
| | - Jesper Wengel
- Department of Physics, Chemistry and Pharmacy; Nucleic Acid Center; Department of Biochemistry and Molecular Biology; University of Southern Denmark; Odense, Denmark
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33
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Lauridsen LH, Rothnagel JA, Veedu RN. Enzymatic recognition of 2'-modified ribonucleoside 5'-triphosphates: towards the evolution of versatile aptamers. Chembiochem 2011; 13:19-25. [PMID: 22162282 DOI: 10.1002/cbic.201100648] [Citation(s) in RCA: 48] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2011] [Indexed: 01/21/2023]
Abstract
The quest for effective, selective and nontoxic nucleic-acid-based drugs has led to designing modifications of naturally occurring nucleosides. A number of modified nucleic acids have been made in the past decades in the hope that they would prove useful in target-validation studies and therapeutic applications involving antisense, RNAi, aptamer, and ribozyme-based technologies. Since their invention in the early 1990s, aptamers have emerged as a very promising class of therapeutics, with one drug entering the market for the treatment of age-related macular degeneration. To combat the limitations of aptamers containing naturally occurring nucleotides, chemically modified nucleotides have to be used. In order to apply modified nucleotides in aptamer drug development, their enzyme-recognition capabilities must be understood. For this purpose, several modified nucleoside 5'-triphosphates were synthesized and investigated as substrates for various enzymes. Herein, we review studies on the enzyme-recognition of various 2'-sugar-modified NTPs that were carried out with a view to their effective utilization in SELEX processes to generate versatile aptamers.
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Affiliation(s)
- Lasse H Lauridsen
- School of Chemistry and Molecular Biosciences, The University of Queensland, Brisbane, Australia
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34
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Doessing H, Vester B. Locked and unlocked nucleosides in functional nucleic acids. Molecules 2011; 16:4511-26. [PMID: 21629180 PMCID: PMC6264650 DOI: 10.3390/molecules16064511] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2011] [Revised: 05/19/2011] [Accepted: 05/25/2011] [Indexed: 12/28/2022] Open
Abstract
Nucleic acids are able to adopt a plethora of structures, many of which are of interest in therapeutics, bio- or nanotechnology. However, structural and biochemical stability is a major concern which has been addressed by incorporating a range of modifications and nucleoside derivatives. This review summarizes the use of locked nucleic acid (LNA) and un-locked nucleic acid (UNA) monomers in functional nucleic acids such as aptamers, ribozymes, and DNAzymes.
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Affiliation(s)
| | - Birte Vester
- Nucleic Acid Center, Department of Biochemistry and Molecular Biology, University of Southern Denmark, Campusvej 55, Odense M 5230, Denmark; E-Mail: (H.D.)
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35
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Campbell MA, Wengel J. Locked vs. unlocked nucleic acids (LNA vs. UNA): contrasting structures work towards common therapeutic goals. Chem Soc Rev 2011; 40:5680-9. [PMID: 21556437 DOI: 10.1039/c1cs15048k] [Citation(s) in RCA: 176] [Impact Index Per Article: 13.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
Oligonucleotide chemistry has been developed greatly over the past three decades, with many advances in increasing nuclease resistance, enhancing duplex stability and assisting with cellular uptake. Locked nucleic acid (LNA) is a structurally rigid modification that increases the binding affinity of a modified-oligonucleotide. In contrast, unlocked nucleic acid (UNA) is a highly flexible modification, which can be used to modulate duplex characteristics. In this tutorial review, we will compare the synthetic routes to both of these modifications, contrast the structural features, examine the hybridization properties of LNA and UNA modified duplexes, and discuss how they have been applied within biotechnology and drug research. LNA has found widespread use in antisense oligonucleotide technology, where it can stabilize interactions with target RNA and protect from cellular nucleases. The newly emerging field of siRNAs has made use of LNA and, recently, also UNA. These modifications are able to increase double-stranded RNA stability in serum and decrease off-target effects seen with conventional siRNAs. LNA and UNA are also emerging as versatile modifications for aptamers. Their application to known aptamer structures has opened up the possibility of future selection of LNA-modified aptamers. Each of these oligonucleotide technologies has the potential to become a new type of therapy to treat a wide variety of diseases, and LNA and UNA will no doubt play a part in future developments of therapeutic and diagnostic oligonucleotides.
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Affiliation(s)
- Meghan A Campbell
- Nucleic Acid Center, Institute for Physics and Chemistry, University of Southern Denmark, Odense, Denmark
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36
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Abstract
Nucleic acid aptamers are in vitro-selected small, single-stranded DNA or RNA oligonucleotides that can specifically recognize their target on the basis of their unique 3-dimensional structures. Recent advances in the development of escort aptamers to deliver and enhance the efficacy of other therapeutic agents have drawn enthusiasm in exploiting cell-type-specific aptamers as drug delivery vehicles. This review mainly focuses on the recent developments of aptamer-mediated targeted delivery systems. We also place particular emphasis on aptamers evolved against cell membrane receptors and possibilities for translation to clinical applications.
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Affiliation(s)
- Jiehua Zhou
- Division of Molecular and Cellular Biology, Beckman Research Institute of City of Hope, Duarte, California, USA
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37
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Kuwahara M, Takano Y, Kasahara Y, Nara H, Ozaki H, Sawai H, Sugiyama A, Obika S. Study on suitability of KOD DNA polymerase for enzymatic production of artificial nucleic acids using base/sugar modified nucleoside triphosphates. Molecules 2010; 15:8229-40. [PMID: 21076389 PMCID: PMC6259326 DOI: 10.3390/molecules15118229] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2010] [Revised: 11/06/2010] [Accepted: 11/10/2010] [Indexed: 01/26/2023] Open
Abstract
Recently, KOD and its related DNA polymerases have been used for preparing various modified nucleic acids, including not only base-modified nucleic acids, but also sugar-modified ones, such as bridged/locked nucleic acid (BNA/LNA) which would be promising candidates for nucleic acid drugs. However, thus far, reasons for the effectiveness of KOD DNA polymerase for such purposes have not been clearly elucidated. Therefore, using mutated KOD DNA polymerases, we studied here their catalytic properties upon enzymatic incorporation of nucleotide analogues with base/sugar modifications. Experimental data indicate that their characteristic kinetic properties enabled incorporation of various modified nucleotides. Among those KOD mutants, one achieved efficient successive incorporation of bridged nucleotides with a 2′-ONHCH2CH2-4′ linkage. In this study, the characteristic kinetic properties of KOD DNA polymerase for modified nucleoside triphosphates were shown, and the effectiveness of genetic engineering in improvement of the enzyme for modified nucleotide polymerization has been demonstrated.
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Affiliation(s)
- Masayasu Kuwahara
- Graduate School of Engineering, Gunma University, 1-5-1 Tenjin-cho, Kiryu, Gunma 376-8515, Japan.
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38
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Veedu RN, Burri HV, Kumar P, Sharma PK, Hrdlicka PJ, Vester B, Wengel J. Polymerase-directed synthesis of C5-ethynyl locked nucleic acids. Bioorg Med Chem Lett 2010; 20:6565-8. [PMID: 20932755 DOI: 10.1016/j.bmcl.2010.09.044] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2010] [Revised: 09/06/2010] [Accepted: 09/08/2010] [Indexed: 11/17/2022]
Abstract
Modified nucleic acids have considerable potential in nanobiotechnology for the development of nanomedicines and new materials. Locked nucleic acid (LNA) is one of the most prominent nucleic acid analogues reported so far and we herein for the first time report the enzymatic incorporation of LNA-U and C5-ethynyl LNA-U nucleotides into oligonucleotides. Phusion High Fidelity and KOD DNA polymerases efficiently incorporated LNA-U and C5-ethynyl LNA-U nucleotides into a DNA strand and T7 RNA polymerase successfully accepted the LNA-U nucleoside 5'-triphosphate as substrate for RNA transcripts.
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Affiliation(s)
- Rakesh N Veedu
- Nucleic Acid Center, Department of Physics & Chemistry, University of Southern Denmark, Campusvej 55, Odense M 5230, Denmark.
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39
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Kuwahara M, Sugimoto N. Molecular evolution of functional nucleic acids with chemical modifications. Molecules 2010; 15:5423-44. [PMID: 20714306 PMCID: PMC6257756 DOI: 10.3390/molecules15085423] [Citation(s) in RCA: 104] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2010] [Revised: 07/14/2010] [Accepted: 08/06/2010] [Indexed: 01/10/2023] Open
Abstract
Nucleic acids are attractive materials for creating functional molecules that have applications as catalysts, specific binders, and molecular switches. Nucleic acids having such functions can be obtained by random screening, typically using in vitro selection methods. These methods have helped explore the potential abilities of nucleic acids and steadily contributed to their evolution, i.e., creation of RNA/DNA enzymes, aptamers, and aptazymes. Chemical modification would be a key means to further increase their performance, e.g., expansion of function diversity, enhancement of activity, and improvement of biostability for biological use. Indeed, in the past two decades, random screening involving chemical modification, post-SELEX chemical modification, and rational design methods have been advanced, and combining and integrating these methods may produce a new class of functional nucleic acids. This review focuses on the effectiveness of chemical modifications on the evolution of nucleic acids as functional molecules and the outlook for related technologies.
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Affiliation(s)
- Masayasu Kuwahara
- Chemistry Laboratory of Artificial Biomolecules (CLAB), Graduate School of Engineering, Gunma University, 1-5-1 Tenjin-cho, Kiryu, Gunma 376-8515, Japan
| | - Naoki Sugimoto
- Frontier Institute for Biomolecular Engineering Research (FIBER) and Faculty of Frontiers of Innovative Research in Science and Technology (FIRST), Konan University, 7-1-20 Minatojima-Minamimachi, Chuo-Ku, Kobe 650-0047, Japan; E-Mail: (N.S.)
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40
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Marton S, Reyes-Darias JA, Sánchez-Luque FJ, Romero-López C, Berzal-Herranz A. In vitro and ex vivo selection procedures for identifying potentially therapeutic DNA and RNA molecules. Molecules 2010; 15:4610-38. [PMID: 20657381 PMCID: PMC6257598 DOI: 10.3390/molecules15074610] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2010] [Revised: 06/17/2010] [Accepted: 06/24/2010] [Indexed: 02/05/2023] Open
Abstract
It was only relatively recently discovered that nucleic acids participate in a variety of biological functions, besides the storage and transmission of genetic information. Quite apart from the nucleotide sequence, it is now clear that the structure of a nucleic acid plays an essential role in its functionality, enabling catalysis and specific binding reactions. In vitro selection and evolution strategies have been extremely useful in the analysis of functional RNA and DNA molecules, helping to expand our knowledge of their functional repertoire and to identify and optimize DNA and RNA molecules with potential therapeutic and diagnostic applications. The great progress made in this field has prompted the development of ex vivo methods for selecting functional nucleic acids in the cellular environment. This review summarizes the most important and most recent applications of in vitro and ex vivo selection strategies aimed at exploring the therapeutic potential of nucleic acids.
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Affiliation(s)
- Soledad Marton
- Instituto de Parasitología y Biomedicina López-Neyra, CSIC, P.T. Ciencias de la Salud, Av. del Conocimiento s/n, Armilla, 18100 Granada, Spain.
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41
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Veedu RN, Wengel J. Locked nucleic acids: promising nucleic acid analogs for therapeutic applications. Chem Biodivers 2010; 7:536-42. [PMID: 20232325 DOI: 10.1002/cbdv.200900343] [Citation(s) in RCA: 193] [Impact Index Per Article: 13.8] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
Abstract
Locked Nucleic Acid (LNA) is a unique nucleic-acid modification possessing very high binding affinity and excellent specificity toward complementary RNA or DNA oligonucleotides. The remarkable properties exhibited by LNA oligonucleotides have been employed in different nucleic acid-based therapeutic strategies both in vitro and in vivo. Herein, we highlight the applications of LNA nucleotides for controlling gene expression.
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Affiliation(s)
- Rakesh N Veedu
- Nucleic Acid Center, Department of Physics and Chemistry, University of Southern Denmark, Campusvej 55, DK-5230 Odense M.
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42
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Wang X, Gou D, Xu SY. Polymerase-endonuclease amplification reaction (PEAR) for large-scale enzymatic production of antisense oligonucleotides. PLoS One 2010; 5:e8430. [PMID: 20062528 PMCID: PMC2797076 DOI: 10.1371/journal.pone.0008430] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2009] [Accepted: 11/30/2009] [Indexed: 11/24/2022] Open
Abstract
Antisense oligonucleotides targeting microRNAs or their mRNA targets prove to be powerful tools for molecular biology research and may eventually emerge as new therapeutic agents. Synthetic oligonucleotides are often contaminated with highly homologous failure sequences. Synthesis of a certain oligonucleotide is difficult to scale up because it requires expensive equipment, hazardous chemicals and a tedious purification process. Here we report a novel thermocyclic reaction, polymerase-endonuclease amplification reaction (PEAR), for the amplification of oligonucleotides. A target oligonucleotide and a tandem repeated antisense probe are subjected to repeated cycles of denaturing, annealing, elongation and cleaving, in which thermostable DNA polymerase elongation and strand slipping generate duplex tandem repeats, and thermostable endonuclease (PspGI) cleavage releases monomeric duplex oligonucleotides. Each round of PEAR achieves over 100-fold amplification. The product can be used in one more round of PEAR directly, and the process can be further repeated. In addition to avoiding dangerous materials and improved product purity, this reaction is easy to scale up and amenable to full automation. PEAR has the potential to be a useful tool for large-scale production of antisense oligonucleotide drugs.
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Affiliation(s)
- Xiaolong Wang
- Department of Biotechnology, Ocean University of China, Qingdao, Shandong, People's Republic of China.
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43
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Veedu RN, Vester B, Wengel J. Polymerase directed incorporation studies of LNA-G nucleoside 5′-triphosphate and primer extension involving all four LNA nucleotides. NEW J CHEM 2010. [DOI: 10.1039/b9nj00628a] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
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44
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Veedu RN, Wengel J. Locked nucleic acid nucleoside triphosphates and polymerases: on the way towards evolution of LNA aptamers. MOLECULAR BIOSYSTEMS 2009; 5:787-92. [PMID: 19603111 DOI: 10.1039/b905513b] [Citation(s) in RCA: 41] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/03/2023]
Abstract
Among numerous nucleic acid analogs reported in the past decades, locked nucleic acid (LNA) has received substantial attention and has become a significant tool within chemical biology disciplines like molecular biology research, diagnostics and therapeutic development. However, despite their obvious structurally unique properties, LNA-based aptamers for diagnostic and therapeutic applications remain largely unexplored. Future evolution of LNA oligonucleotide aptamers will depend on scientific breakthroughs relating to enzymatic polymerization using LNA nucleoside triphosphates as substrates. Herein, we highlight recent developments in this direction using various polymerases.
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Affiliation(s)
- Rakesh N Veedu
- Department of Physics and Chemistry, Nucleic Acid Center, University of Southern Denmark, Campusvej 55, Odense M, Denmark
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