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Chowdhury S, Wang J, Nuccio SP, Mao H, Di Antonio M. Short LNA-modified oligonucleotide probes as efficient disruptors of DNA G-quadruplexes. Nucleic Acids Res 2022; 50:7247-7259. [PMID: 35801856 PMCID: PMC9303293 DOI: 10.1093/nar/gkac569] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2022] [Revised: 06/09/2022] [Accepted: 06/18/2022] [Indexed: 12/20/2022] Open
Abstract
G-quadruplexes (G4s) are well known non-canonical DNA secondary structures that can form in human cells. Most of the tools available to investigate G4-biology rely on small molecule ligands that stabilise these structures. However, the development of probes that disrupt G4s is equally important to study their biology. In this study, we investigated the disruption of G4s using Locked Nucleic Acids (LNA) as invader probes. We demonstrated that strategic positioning of LNA-modifications within short oligonucleotides (10 nts.) can significantly accelerate the rate of G4-disruption. Single-molecule experiments revealed that short LNA-probes can promote disruption of G4s with mechanical stability sufficient to stall polymerases. We corroborated this using a single-step extension assay, revealing that short LNA-probes can relieve replication dependent polymerase-stalling at G4 sites. We further demonstrated the potential of such LNA-based probes to study G4-biology in cells. By using a dual-luciferase assay, we found that short LNA probes can enhance the expression of c-KIT to levels similar to those observed when the c-KIT promoter is mutated to prevent the formation of the c-KIT1 G4. Collectively, our data suggest a potential use of rationally designed LNA-modified oligonucleotides as an accessible chemical-biology tool for disrupting individual G4s and interrogating their biological functions in cells.
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Affiliation(s)
- Souroprobho Chowdhury
- Imperial College London, Chemistry Department, Molecular Sciences Research Hub, 82 Wood Lane, London W12 0BZ, UK.,Institute of Chemical Biology, Molecular Sciences Research Hub, 82 Wood Lane, London W12 0BZ, UK
| | - Jiayi Wang
- Department of Chemistry and Biochemistry, Kent State University, Kent, OH 44242, USA
| | - Sabrina Pia Nuccio
- Imperial College London, Chemistry Department, Molecular Sciences Research Hub, 82 Wood Lane, London W12 0BZ, UK.,Institute of Chemical Biology, Molecular Sciences Research Hub, 82 Wood Lane, London W12 0BZ, UK.,The Francis Crick Institute, 1 Midland Road, London NW1 1AT, UK
| | - Hanbin Mao
- Department of Chemistry and Biochemistry, Kent State University, Kent, OH 44242, USA
| | - Marco Di Antonio
- Imperial College London, Chemistry Department, Molecular Sciences Research Hub, 82 Wood Lane, London W12 0BZ, UK.,Institute of Chemical Biology, Molecular Sciences Research Hub, 82 Wood Lane, London W12 0BZ, UK.,The Francis Crick Institute, 1 Midland Road, London NW1 1AT, UK
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2
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Liano D, Monti L, Chowdhury S, Raguseo F, Di Antonio M. Long-range DNA interactions: inter-molecular G-quadruplexes and their potential biological relevance. Chem Commun (Camb) 2022; 58:12753-12762. [PMID: 36281554 PMCID: PMC9671097 DOI: 10.1039/d2cc04872h] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/04/2022]
Abstract
Guanine-rich DNA sequences are known to fold into secondary structures called G-quadruplexes (G4s), which can form from either individual DNA strands (intra-molecular) or multiple DNA strands (inter-molecular, iG4s). Intra-molecular G4s have been the object of extensive biological investigation due to their enrichment in gene-promoters and telomers. On the other hand, iG4s have never been considered in biological contexts, as the interaction between distal sequences of DNA to form an iG4 in cells was always deemed as highly unlikely. In this feature article, we challenge this dogma by presenting our recent discovery of the first human protein (CSB) displaying astonishing picomolar affinity and binding selectivity for iG4s. These findings suggest potential for iG4 structures to form in cells and highlight the need of further studies to unravel the fundamental biological roles of these inter-molecular DNA structures. Furthermore, we discuss how the potential for formation of iG4s in neuronal cells, triggered by repeat expansions in the C9orf72 gene, can lead to the formation of nucleic-acids based pathological aggregates in neurodegenerative diseases like ALS and FTD. Finally, based on our recent work on short LNA-modified probes, we provide a prespective on how the rational design of G4-selective chemical tools can be leveraged to further elucidate the biological relevance of iG4 structures in the context of ageing-related diseases. Intermolecular G-quadruplex structures can form within distal region of genomic DNA, contributing to chromatin looping. Herein, we discuss recent evidence supporting formation of iG4s in living cells and their potential biological function.![]()
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Affiliation(s)
- Denise Liano
- Imperial College London, Chemistry Department, Molecular Sciences Research Hub, 82 Wood Lane, W12 0BZ, London, UK
| | - Ludovica Monti
- Imperial College London, Chemistry Department, Molecular Sciences Research Hub, 82 Wood Lane, W12 0BZ, London, UK
- The Francis Crick Institute, 1 Midland Road, NW1 1AT, London, UK
| | - Souroprobho Chowdhury
- Imperial College London, Chemistry Department, Molecular Sciences Research Hub, 82 Wood Lane, W12 0BZ, London, UK
- The Institute of Chemical Biology, Molecular Science Research Hub, 82 Wood Lane, W12 0BZ, London, UK
| | - Federica Raguseo
- Imperial College London, Chemistry Department, Molecular Sciences Research Hub, 82 Wood Lane, W12 0BZ, London, UK
- The Institute of Chemical Biology, Molecular Science Research Hub, 82 Wood Lane, W12 0BZ, London, UK
| | - Marco Di Antonio
- Imperial College London, Chemistry Department, Molecular Sciences Research Hub, 82 Wood Lane, W12 0BZ, London, UK
- The Francis Crick Institute, 1 Midland Road, NW1 1AT, London, UK
- The Institute of Chemical Biology, Molecular Science Research Hub, 82 Wood Lane, W12 0BZ, London, UK
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3
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De Fazio AF, Misatziou D, Baker YR, Muskens OL, Brown T, Kanaras AG. Chemically modified nucleic acids and DNA intercalators as tools for nanoparticle assembly. Chem Soc Rev 2021; 50:13410-13440. [PMID: 34792047 PMCID: PMC8628606 DOI: 10.1039/d1cs00632k] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2021] [Indexed: 12/26/2022]
Abstract
The self-assembly of inorganic nanoparticles to larger structures is of great research interest as it allows the fabrication of novel materials with collective properties correlated to the nanoparticles' individual characteristics. Recently developed methods for controlling nanoparticle organisation have enabled the fabrication of a range of new materials. Amongst these, the assembly of nanoparticles using DNA has attracted significant attention due to the highly selective recognition between complementary DNA strands, DNA nanostructure versatility, and ease of DNA chemical modification. In this review we discuss the application of various chemical DNA modifications and molecular intercalators as tools for the manipulation of DNA-nanoparticle structures. In detail, we discuss how DNA modifications and small molecule intercalators have been employed in the chemical and photochemical DNA ligation in nanostructures; DNA rotaxanes and catenanes associated with reconfigurable nanoparticle assemblies; and DNA backbone modifications including locked nucleic acids, peptide nucleic acids and borane nucleic acids, which affect the stability of nanostructures in complex environments. We conclude by highlighting the importance of maximising the synergy between the communities of DNA chemistry and nanoparticle self-assembly with the aim to enrich the library of tools available for the manipulation of nanostructures.
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Affiliation(s)
- Angela F De Fazio
- School of Physics and Astronomy, Faculty of Engineering and Physical Sciences, University of Southampton, Southampton, SO17 1BJ, UK.
- Istituto Italiano di Tecnologia, Via Morego 30, 16163 Genova, Italy
| | - Doxi Misatziou
- School of Physics and Astronomy, Faculty of Engineering and Physical Sciences, University of Southampton, Southampton, SO17 1BJ, UK.
| | - Ysobel R Baker
- Department of Chemistry, University of Oxford, Chemistry Research Laboratory, 12 Mansfield Road, Oxford, OX1 3TA, UK
| | - Otto L Muskens
- School of Physics and Astronomy, Faculty of Engineering and Physical Sciences, University of Southampton, Southampton, SO17 1BJ, UK.
- Institute for Life Sciences, University of Southampton, Southampton, SO17 1BJ, UK
| | - Tom Brown
- Department of Chemistry, University of Oxford, Chemistry Research Laboratory, 12 Mansfield Road, Oxford, OX1 3TA, UK
| | - Antonios G Kanaras
- School of Physics and Astronomy, Faculty of Engineering and Physical Sciences, University of Southampton, Southampton, SO17 1BJ, UK.
- Institute for Life Sciences, University of Southampton, Southampton, SO17 1BJ, UK
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4
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Nishikawa M, Tan M, Liao W, Kusamori K. Nanostructured DNA for the delivery of therapeutic agents. Adv Drug Deliv Rev 2019; 147:29-36. [PMID: 31614168 DOI: 10.1016/j.addr.2019.09.004] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2018] [Revised: 09/25/2019] [Accepted: 09/25/2019] [Indexed: 01/16/2023]
Abstract
DNA and RNA, the nucleic acids found in every living organism, are quite crucial, because not only do they store the genetic information, but also they are used as signals through interaction with various molecules within the body. The nature of nucleic acids, especially DNA, to form double-helix makes it possible to design nucleic acid-based nanostructures with various shapes. Because the shapes as well as the physicochemical properties determine their interaction with proteins or cells, nanostructured DNAs will have different features in the interaction compared with single- or double-stranded DNA. Some of these unique features of nanostructured DNA make ways for efficient delivery of therapeutic agents to specific targets. In this review, we begin with the factors affecting the properties of nanostructured DNA, followed by summarizing the methods for the development of nanostructured DNA. Further, we discuss the characteristics of nanostructured DNA and their applications for the delivery of bioactive compounds.
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Affiliation(s)
- Makiya Nishikawa
- Faculty of Pharmaceutical Sciences, Tokyo University of Science, Japan.
| | - Mengmeng Tan
- Faculty of Pharmaceutical Sciences, Tokyo University of Science, Japan; Graduate School of Pharmaceutical Sciences, Kyoto University, Japan
| | - Wenqing Liao
- Faculty of Pharmaceutical Sciences, Tokyo University of Science, Japan; Graduate School of Pharmaceutical Sciences, Kyoto University, Japan
| | - Kosuke Kusamori
- Faculty of Pharmaceutical Sciences, Tokyo University of Science, Japan
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5
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Ickert S, Schwaar T, Springer A, Grabarics M, Riedel J, Beck S, Pagel K, Linscheid MW. Comparison of the fragmentation behavior of DNA and LNA single strands and duplexes. JOURNAL OF MASS SPECTROMETRY : JMS 2019; 54:402-411. [PMID: 30771235 DOI: 10.1002/jms.4344] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/11/2018] [Revised: 02/08/2019] [Accepted: 02/11/2019] [Indexed: 06/09/2023]
Abstract
DNA and locked nucleic acid (LNA) were characterized as single strands, as well as double stranded DNA-DNA duplexes and DNA-LNA hybrids using tandem mass spectrometry with collision-induced dissociation. Additionally, ion mobility spectrometry was carried out on selected species. Oligonucleotide duplexes of different sequences-bearing mismatch positions and abasic sites of complementary DNA 15-mers-were investigated to unravel general trends in their stability in the gas phase. Single-stranded LNA oligonucleotides were also investigated with respect to their gas phase behavior and fragmentation upon collision-induced dissociation. In contrast to the collision-induced dissociation of DNA, almost no base loss was observed for LNAs. Here, backbone cleavages were the dominant dissociation pathways. This finding was further underlined by the need for higher activation energies. Base losses from the LNA strand were also absent in fragmentation experiments of the investigated DNA-LNA hybrid duplexes. While DNA-DNA duplexes dissociated easily into single stranded fragments, the high stability of DNA-LNA hybrids resulted in predominant fragmentation of the DNA part rather than the LNA, while base losses were only observed from the DNA single strand of the hybrid.
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Affiliation(s)
- Stefanie Ickert
- Department of Chemistry, Humboldt-Universitaet zu Berlin, Berlin, Germany
- Federal Institute for Materials Research and Testing, Berlin, Germany
| | - Timm Schwaar
- Federal Institute for Materials Research and Testing, Berlin, Germany
| | - Andreas Springer
- Department of Chemistry and Biochemistry, Freie Universitaet Berlin, Berlin, Germany
| | - Márkó Grabarics
- Department of Molecular Physics, Fritz Haber Institute of the Max Planck Society, Berlin, Germany
| | - Jens Riedel
- Federal Institute for Materials Research and Testing, Berlin, Germany
| | - Sebastian Beck
- Department of Chemistry, Humboldt-Universitaet zu Berlin, Berlin, Germany
| | - Kevin Pagel
- Department of Chemistry and Biochemistry, Freie Universitaet Berlin, Berlin, Germany
- Department of Molecular Physics, Fritz Haber Institute of the Max Planck Society, Berlin, Germany
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6
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The ability of locked nucleic acid oligonucleotides to pre-structure the double helix: A molecular simulation and binding study. PLoS One 2019; 14:e0211651. [PMID: 30753192 PMCID: PMC6372149 DOI: 10.1371/journal.pone.0211651] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2018] [Accepted: 01/17/2019] [Indexed: 02/07/2023] Open
Abstract
Locked nucleic acid (LNA) oligonucleotides bind DNA target sequences forming Watson-Crick and Hoogsteen base pairs, and are therefore of interest for medical applications. To be biologically active, such an oligonucleotide has to efficiently bind the target sequence. Here we used molecular dynamics simulations and electrophoresis mobility shift assays to elucidate the relation between helical structure and affinity for LNA-containing oligonucleotides. In particular, we have studied how LNA substitutions in the polypyrimidine strand of a duplex (thus forming a hetero duplex, i.e. a duplex with a DNA polypurine strand and an LNA/DNA polypyrimidine strand) enhance triplex formation. Based on seven polypyrimidine single strand oligonucleotides, having LNAs in different positions and quantities, we show that alternating LNA with one or more non-modified DNA nucleotides pre-organizes the hetero duplex toward a triple-helical-like conformation. This in turn promotes triplex formation, while consecutive LNAs distort the duplex structure disfavoring triplex formation. The results support the hypothesis that a pre-organization in the hetero duplex structure enhances the binding of triplex forming oligonucleotides. Our findings may serve as a criterion in the design of new tools for efficient oligonucleotide hybridization.
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7
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Nakagaki A, Hirano S, Urakawa A, Mitake M, Kishino T. Transgenic mice with a tandem duplication of the Necdin gene overexpress Necdin. Mamm Genome 2018; 29:680-689. [PMID: 30225647 DOI: 10.1007/s00335-018-9784-1] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2018] [Accepted: 09/12/2018] [Indexed: 01/13/2023]
Abstract
Necdin (Ndn) transgenic (Tg) mice were generated with a bacterial artificial chromosome (BAC) clone. Droplet digital PCR (ddPCR) and inverse PCR methods revealed that the transgene consisted of four fragments with a total length of 171 kb. Two of these fragments were tandem tail-to-tail duplicates of 77 kb and 37 kb that both contained a Ndn gene. The transgene was inserted in chromosome 15qD1. Ndn is a paternally expressed imprinted gene; however, the total expression level of Ndn in hemizygous Tg mice was approximately twofold higher than that in wild-type mice. ddPCR assays with locked nucleic acid (LNA) TaqMan probes revealed that transgenic Ndn expression was almost equal to endogenous Ndn expression, despite there being two copies of the Ndn gene in the transgene, indicating an interaction between the transcriptional regulation of endogenous Ndn and the transgene. ddPCR assays with LNA TaqMan probes were also applied for imprinting analysis to confirm exclusive paternal expression in tissues with low Ndn expression. This is the first report of a Tg mouse with a tandem duplication of a Ndn transgene and Ndn overexpression, which will be useful for the in vivo study of Ndn overexpression and for rescue experiments of the neonatal lethality seen in the Ndn knockout mouse.
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Affiliation(s)
- Ayumi Nakagaki
- Division of Functional Genomics, Center for Frontier Life Sciences, Nagasaki University, Sakamoto 1-12-4, Nagasaki, 852-8523, Japan
| | - Shiori Hirano
- Division of Functional Genomics, Center for Frontier Life Sciences, Nagasaki University, Sakamoto 1-12-4, Nagasaki, 852-8523, Japan
| | - Asuka Urakawa
- Division of Functional Genomics, Center for Frontier Life Sciences, Nagasaki University, Sakamoto 1-12-4, Nagasaki, 852-8523, Japan
| | - Maiko Mitake
- Division of Functional Genomics, Center for Frontier Life Sciences, Nagasaki University, Sakamoto 1-12-4, Nagasaki, 852-8523, Japan
| | - Tatsuya Kishino
- Division of Functional Genomics, Center for Frontier Life Sciences, Nagasaki University, Sakamoto 1-12-4, Nagasaki, 852-8523, Japan.
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8
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Bohr HG, Shim I, Stein C, Ørum H, Hansen HF, Koch T. Electronic Structures of LNA Phosphorothioate Oligonucleotides. MOLECULAR THERAPY. NUCLEIC ACIDS 2017; 8:428-441. [PMID: 28918042 PMCID: PMC5537454 DOI: 10.1016/j.omtn.2017.05.011] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 11/21/2016] [Revised: 05/29/2017] [Accepted: 05/29/2017] [Indexed: 01/08/2023]
Abstract
Important oligonucleotides in anti-sense research have been investigated in silico and experimentally. This involves quantum mechanical (QM) calculations and chromatography experiments on locked nucleic acid (LNA) phosphorothioate (PS) oligonucleotides. iso-potential electrostatic surfaces are essential in this study and have been calculated from the wave functions derived from the QM calculations that provide binding information and other properties of these molecules. The QM calculations give details of the electronic structures in terms of e.g., energy and bonding, which make them distinguish or differentiate between the individual PS diastereoisomers determined by the position of sulfur atoms. Rules are derived from the electronic calculations of these molecules and include the effects of the phosphorothioate chirality and formation of electrostatic potential surfaces. Physical and electrochemical descriptors of the PS oligonucleotides are compared to the experiments in which chiral states on these molecules can be distinguished. The calculations demonstrate that electronic structure, electrostatic potential, and topology are highly sensitive to single PS configuration changes and can give a lead to understanding the activity of the molecules.
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Affiliation(s)
- Henrik G Bohr
- Department of Chemistry, B-206-DTU, The Technical University of Denmark, 2800 Lyngby, Denmark.
| | - Irene Shim
- Department of Chemistry, B-206-DTU, The Technical University of Denmark, 2800 Lyngby, Denmark
| | - Cy Stein
- Department of Medical Oncology and Experimental Therapeutics and Molecular and Cellular Biology, City of Hope Medical Center, 1500 E. Duarte Rd., Duarte, CA 91010, USA
| | - Henrik Ørum
- Anemonevej 4, Hareskov, 3500 Værløse, Denmark
| | - Henrik F Hansen
- Roche Innovation Center Copenhagen, Fremtidsvej 3, 2970, Denmark
| | - Troels Koch
- Roche Innovation Center Copenhagen, Fremtidsvej 3, 2970, Denmark
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9
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Eze NA, Sullivan RS, Milam VT. Analysis of in Situ LNA and DNA Hybridization Events on Microspheres. Biomacromolecules 2017; 18:1086-1096. [PMID: 28233983 DOI: 10.1021/acs.biomac.6b01373] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/15/2023]
Abstract
The hybridization activity of single-stranded DNA and locked nucleic acid (LNA) sequences on microspheres is quantified in situ using flow cytometry. In contrast to conventional sample preparation for flow cytometry that involves several wash steps for posthybridization analysis, the current work entails directly monitoring hybridization events as they occur between oligonucleotide-functionalized microspheres and fluorescently tagged 9 or 15 base-long targets. We find that the extent of hybridization between single-stranded, immobilized probes and soluble targets generally increases with target sequence length or with the incorporation of LNA nucleotides in one or both oligonucleotide strands involved in duplex formation. The rate constants for duplex formation, on the other hand, remain nearly identical for all but one probe-target sequence combination. The exception to this trend involves the LNA probe and shortest perfectly matched DNA target, which exhibit a rate constant that is an order of magnitude lower than any other probe-target pair, including a mismatched duplex case. Separate studies entailing brief heat treatments to suspensions generally do not consistently yield appreciable differences in associated target densities to probe-functionalized microspheres.
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Affiliation(s)
- Ngozi A Eze
- School of Materials Science and Engineering, ‡Wallace H. Coulter Department of Biomedical Engineering, §Parker H. Petit Institute for Bioengineering and Bioscience, Georgia Institute of Technology , 771 Ferst Drive NW, Atlanta, Georgia 30332-0245, United States
| | - Richard S Sullivan
- School of Materials Science and Engineering, ‡Wallace H. Coulter Department of Biomedical Engineering, §Parker H. Petit Institute for Bioengineering and Bioscience, Georgia Institute of Technology , 771 Ferst Drive NW, Atlanta, Georgia 30332-0245, United States
| | - Valeria T Milam
- School of Materials Science and Engineering, ‡Wallace H. Coulter Department of Biomedical Engineering, §Parker H. Petit Institute for Bioengineering and Bioscience, Georgia Institute of Technology , 771 Ferst Drive NW, Atlanta, Georgia 30332-0245, United States
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10
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Xu Y, Villa A, Nilsson L. The free energy of locking a ring: Changing a deoxyribonucleoside to a locked nucleic acid. J Comput Chem 2017; 38:1147-1157. [PMID: 28101966 PMCID: PMC5434909 DOI: 10.1002/jcc.24692] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2016] [Revised: 11/01/2016] [Accepted: 11/08/2016] [Indexed: 01/09/2023]
Abstract
Locked nucleic acid (LNA), a modified nucleoside which contains a bridging group across the ribose ring, improves the stability of DNA/RNA duplexes significantly, and therefore is of interest in biotechnology and gene therapy applications. In this study, we investigate the free energy change between LNA and DNA nucleosides. The transformation requires the breaking of the bridging group across the ribose ring, a problematic transformation in free energy calculations. To address this, we have developed a 3-step (easy to implement) and a 1-step protocol (more efficient, but more complicated to setup), for single and dual topologies in classical molecular dynamics simulations, using the Bennett Acceptance Ratio method to calculate the free energy. We validate the approach on the solvation free energy difference for the nucleosides thymidine, cytosine, and 5-methyl-cytosine. © 2017 The Authors. Journal of Computational Chemistry Published by Wiley Periodicals, Inc.
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Affiliation(s)
- You Xu
- Department of Biosciences and Nutrition, Karolinska Institutet, Huddinge, SE-141 83, Sweden
| | - Alessandra Villa
- Department of Biosciences and Nutrition, Karolinska Institutet, Huddinge, SE-141 83, Sweden
| | - Lennart Nilsson
- Department of Biosciences and Nutrition, Karolinska Institutet, Huddinge, SE-141 83, Sweden
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11
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Ghosh S, Chakrabarti R. Spontaneous Unzipping of Xylonucleic Acid Assisted by a Single-Walled Carbon Nanotube: A Computational Study. J Phys Chem B 2016; 120:3642-52. [DOI: 10.1021/acs.jpcb.6b02035] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Affiliation(s)
- Soumadwip Ghosh
- Department of Chemistry, Indian Institute of Technology Bombay, Powai, Mumbai 40076, India
| | - Rajarshi Chakrabarti
- Department of Chemistry, Indian Institute of Technology Bombay, Powai, Mumbai 40076, India
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12
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Darnell DK, Antin PB. LNA-based in situ hybridization detection of mRNAs in embryos. Methods Mol Biol 2015; 1211:69-76. [PMID: 25218377 DOI: 10.1007/978-1-4939-1459-3_6] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/24/2022]
Abstract
In situ hybridization (ISH) in embryos allows the visualization of specific RNAs as a readout of gene expression during normal development or after experimental manipulations. ISH using short DNA probes containing locked nucleic acid nucleotides (LNAs) holds the additional advantage of allowing the detection of specific RNA splice variants or of closely related family members that differ in only short regions, creating new diagnostic and detection opportunities. Here we describe methods for using short (14-24 nt) DNA probes containing LNA nucleotides to detect moderately to highly expressed RNAs in whole chick embryos during the first 5 days of embryonic development. The protocol is easily adaptable for use with embryos of other vertebrate species.
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Affiliation(s)
- Diana K Darnell
- Molecular Cardiovascular Research Program, Department of Cellular and Molecular Medicine, University of Arizona, Tucson, AZ, 85724, USA
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13
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Kierzek R, Turner DH, Kierzek E. Microarrays for identifying binding sites and probing structure of RNAs. Nucleic Acids Res 2014; 43:1-12. [PMID: 25505162 PMCID: PMC4288193 DOI: 10.1093/nar/gku1303] [Citation(s) in RCA: 75] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
Oligonucleotide microarrays are widely used in various biological studies. In this review, application of oligonucleotide microarrays for identifying binding sites and probing structure of RNAs is described. Deep sequencing allows fast determination of DNA and RNA sequence. High-throughput methods for determination of secondary structures of RNAs have also been developed. Those methods, however, do not reveal binding sites for oligonucleotides. In contrast, microarrays directly determine binding sites while also providing structural insights. Microarray mapping can be used over a wide range of experimental conditions, including temperature, pH, various cations at different concentrations and the presence of other molecules. Moreover, it is possible to make universal microarrays suitable for investigations of many different RNAs, and readout of results is rapid. Thus, microarrays are used to provide insight into oligonucleotide sequences potentially able to interfere with biological function. Better understanding of structure-function relationships of RNA can be facilitated by using microarrays to find RNA regions capable to bind oligonucleotides. That information is extremely important to design optimal sequences for antisense oligonucleotides and siRNA because both bind to single-stranded regions of target RNAs.
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Affiliation(s)
- Ryszard Kierzek
- Institute of Bioorganic Chemistry Polish Academy of Sciences, 61-704 Poznan, Noskowskiego 12/14, Poland
| | - Douglas H Turner
- Department of Chemistry, University of Rochester, Rochester, NY 14627, USA
| | - Elzbieta Kierzek
- Institute of Bioorganic Chemistry Polish Academy of Sciences, 61-704 Poznan, Noskowskiego 12/14, Poland
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14
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Suresh G, Priyakumar UD. Structures, dynamics, and stabilities of fully modified locked nucleic acid (β-D-LNA and α-L-LNA) duplexes in comparison to pure DNA and RNA duplexes. J Phys Chem B 2013; 117:5556-64. [PMID: 23617391 DOI: 10.1021/jp4016068] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
Abstract
Locked nucleic acid (LNA) is a chemical modification which introduces a -O-CH2- linkage in the furanose sugar of nucleic acids and blocks its conformation in a particular state. Two types of modifications, namely, 2'-O,4'-C-methylene-β-D-ribofuranose (β-D-LNA) and 2'-O,4'-C-methylene-α-L-ribofuranose (α-L-LNA), have been shown to yield RNA and DNA duplex-like structures, respectively. LNA modifications lead to increased melting temperatures of DNA and RNA duplexes, and have been suggested as potential therapeutic agents in antisense therapy. In this study, molecular dynamics (MD) simulations were performed on fully modified LNA duplexes and pure DNA and RNA duplexes sharing a similar sequence to investigate their structure, stabilities, and solvation properties. Both LNA duplexes undergo unwinding of the helical structure compared to the pure DNA and RNA duplexes. Though the α-LNA substituent has been proposed to mimic deoxyribose sugar in its conformational properties, the fully modified duplex was found to exhibit unique structural and dynamic properties with respect to the other three nucleic acid structures. Free energy calculations accurately capture the enhanced stabilization of the LNA duplex structures compared to DNA and RNA molecules as observed in experiments. π-stacking interaction between bases from complementary strands is shown to be one of the contributors to enhanced stabilization upon LNA substitution. A combination of two factors, namely, nature of the -O-CH2- linkage in the LNAs vs their absence in the pure duplexes and similar conformations of the sugar rings in DNA and α-LNA vs the other two, is suggested to contribute to the stark differences among the four duplexes studied here in terms of their structural, dynamic, and energetic properties.
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Affiliation(s)
- Gorle Suresh
- Center for Computational Natural Sciences and Bioinformatics, International Institute of Information Technology, Hyderabad, India
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Thazhathveetil AK, Vura-Weis J, Trifonov A, Wasielewski MR, Lewis FD. Dynamics and efficiency of hole transport in LNA:DNA hybrid diblock oligomers. J Am Chem Soc 2012; 134:16434-40. [PMID: 22958189 DOI: 10.1021/ja307989t] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023]
Abstract
We report here the effect of replacing one or both of the purine or pyrimidine blocks of a diblock stilbene donor-acceptor capped hairpin with locked nucleic acid (LNA) bases on the dynamics and efficiency of hole transport. The structures of the DNA and LNA:DNA hybrids are tentatively assigned to B- or A-type structures on the basis of their circular dichroism spectra. Replacing the bases in either the A-block or the G-block of the diblock DNA hairpin with LNA bases results in a modest decrease in the base-to-base hopping rate constant and quantum yield for charge separation. Somewhat larger decreases are observed when all of the purine or pyrimidine bases are replaced by LNA bases.
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Affiliation(s)
- Arun K Thazhathveetil
- Department of Chemistry and Argonne-Northwestern Solar Energy Research Center, Northwestern University, Evanston, Illinois 60208, USA
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16
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Priya NG, Pandey N, Rajagopal R. LNA probes substantially improve the detection of bacterial endosymbionts in whole mount of insects by fluorescent in-situ hybridization. BMC Microbiol 2012; 12:81. [PMID: 22624773 PMCID: PMC3536699 DOI: 10.1186/1471-2180-12-81] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2011] [Accepted: 05/02/2012] [Indexed: 12/03/2022] Open
Abstract
Background Detection of unculturable bacteria and their localization in the host, by fluorescent in-situ hybridization (FISH), is a powerful technique in the study of host-bacteria interaction. FISH probes are designed to target the 16 s rRNA region of the bacteria to be detected. LNA probes have recently been used in FISH studies and proven to be more efficient. To date no report has employed LNA probes for FISH detection of bacterial endosymbiont in the whole mount tissues. Further, though speculated, bacteriocytes have not been reported from males of Bemisia tabaci. Results In this study, we compared the efficiency in detecting bacteria by fluorescent DNA oligonucleotides versus modified probes containing Locked Nucleic Acid (LNA) substitution in their structure. We used the insect Bemisia tabaci as the experimental material since it carried simultaneous infection by two bacteria: one a primary endosymbiont, Portiera (and present in more numbers) while the other a secondary endosymbiont Arsenophonus (and present in less numbers). Thus a variation in the abundance of bacteria was expected. While detecting both the bacteria, we found a significant increase in the signal whenever LNA probes were used. However, the difference was more pronounced in detecting the secondary endosymbiont, wherein DNA probes gave weak signals when compared to LNA probes. Also, signal to noise ratio for LNA probes was higher than DNA probes. We found that LNA considerably improved sensitivity of FISH, as compared to the commonly used DNA oligonucleotide probe. Conclusion By employing LNA probes we could detect endosymbiotic bacteria in males, which have never been reported previously. We were able to detect bacteriocytes containing Portiera and Arsenophonus in the males of B. tabaci. Thus, employing LNA probes at optimized conditions will help to significantly improve detection of bacteria at the lowest concentration and may give a comprehensible depiction about their specific distribution within samples.
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Affiliation(s)
- Natarajan Gayatri Priya
- Gut Biology Lab, Department of Zoology, University of Delhi, Room No 117, Delhi 110007, India
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17
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Ramaswamy A, Froeyen M, Herdewijn P, Ceulemans A. Helical structure of xylose-DNA. J Am Chem Soc 2010; 132:587-95. [PMID: 20017539 DOI: 10.1021/ja9065877] [Citation(s) in RCA: 37] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Synthetic biology and systems chemistry demonstrate a growing interest in modified nucleotides to achieve an enzymatically stable artificial nucleic acid. A potential candidate system is xylose-DNA, in which the 2'-deoxy-beta-D-ribo-furanose is substituted by 2'-deoxy-beta-D-xylo-furanose. We present here the helical structure and conformational analysis of xylose-DNA on the basis of 35 ns MD simulations of a 29-base-pair DNA duplex. Starting from a right-handed xylose-DNA helix, we observe a remarkable conformational transition from right- to left-handed helix. The left-handed xylose-DNA is highly dynamic, involving screwing and unscrewing motion of the helix. The sugar pucker induced helical changes influence the backbone to adopt the backbone angles for xylose-DNA while retaining the Watson-Crick base pairing and stacking interactions. The results demonstrate the chiral orthogonality of the ribose and xylose based episomes. As far as stability and compactness of information storage is concerned, the ribose based natural DNA is unsurpassed.
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Affiliation(s)
- Amutha Ramaswamy
- INPAC institute for Nanoscale Physics and Chemistry and Quantum Chemistry Group of K. U. Leuven, Celestijnenlaan 200F, B-3001 Leuven, Belgium
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18
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Kierzek E. Binding of short oligonucleotides to RNA: studies of the binding of common RNA structural motifs to isoenergetic microarrays. Biochemistry 2009; 48:11344-56. [PMID: 19835418 DOI: 10.1021/bi901264v] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Binding of short oligonucleotides to RNA is important for many biological processes. On the basis of RNAi phenomena, antisense, and ribozyme approaches, it is useful in the inhibition of biological functions. To be considered as potential therapeutics, oligonucleotides must bind strongly and selectively to a complementary fragment of target RNA. Microarray technologies also involve the binding of oligonucleotide probes to DNA or RNA. Herein, the hybridization of common structural motifs of RNA, i.e., hairpins, internal loops, bulges, 3'- and 5'-dangling ends, and pseudoknots to isoenergetic microarray probes is presented. The analysis demonstrates that microarray probes bind to bulges, internal loops, and dangling ends as expected. Probes may also bind to terminal helixes, however, possibly due to the rearrangement of base pairs. These results suggest that isoenergetic microarray mapping can provide data to facilitate and improve RNA secondary structure prediction. However, optimal results require combination with chemical and/or enzymatic mapping.
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Affiliation(s)
- Elzbieta Kierzek
- Institute of Bioorganic Chemistry, Polish Academy of Sciences, 60-704 Poznan, Noskowskiego 12/14, Poland.
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19
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Carlucci M, Kierzek E, Marciniak A, Turner DH, Kierzek R. Chemical synthesis of LNA-2-thiouridine and its influence on stability and selectivity of oligonucleotide binding to RNA. Biochemistry 2009; 48:10882-93. [PMID: 19835380 PMCID: PMC2839159 DOI: 10.1021/bi901506f] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Hybridization to RNA is important for many applications, including antisense therapeutics, RNA interference, and microarray screening. Similar thermodynamic stabilities of A-U and G-U base pairs result in difficulties in selective binding to RNA. Moreover, A-U pairs are weaker than G-C pairs so that binding is sometimes weak when many A-U pairs are present. It is known, however, that replacement of uridine with 2-thiouridine significantly improves binding and selectivity. To test for additional improvement of binding and of the specificity for binding A over G, LNA-2-thiouridine was synthesized for the first time and incorporated into many LNA-2'-O-methyl-RNA/RNA duplexes. UV melting was used to measure the thermodynamic effect of replacing 2'-O-methyluridine with 2'-O-methyl-2-thiouridine or LNA-2-thiouridine. The 2-thiouridine usually enhances binding and selectivity. Selectivity is optimized when a single 2-thiouridine is placed at an internal position in a duplex.
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Affiliation(s)
- Marta Carlucci
- Institute of Bioorganic Chemistry, Polish Academy of Sciences, 61-704 Poznan, Noskowskiego 12/14, Poland
| | - Elzbieta Kierzek
- Institute of Bioorganic Chemistry, Polish Academy of Sciences, 61-704 Poznan, Noskowskiego 12/14, Poland
| | - Anna Marciniak
- Institute of Bioorganic Chemistry, Polish Academy of Sciences, 61-704 Poznan, Noskowskiego 12/14, Poland
| | - Douglas H. Turner
- Department of Chemistry, University of Rochester, RC Box 270216, Rochester, NY 14627-0216, USA
- Center for Pediatric Biomedical Research, University of Rochester, School of Medicine and Dentistry, Rochester, NY 14642, USA
| | - Ryszard Kierzek
- Institute of Bioorganic Chemistry, Polish Academy of Sciences, 61-704 Poznan, Noskowskiego 12/14, Poland
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20
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Kierzek E, Pasternak A, Pasternak K, Gdaniec Z, Yildirim I, Turner DH, Kierzek R. Contributions of stacking, preorganization, and hydrogen bonding to the thermodynamic stability of duplexes between RNA and 2'-O-methyl RNA with locked nucleic acids. Biochemistry 2009; 48:4377-87. [PMID: 19348504 DOI: 10.1021/bi9002056] [Citation(s) in RCA: 42] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Locked nucleic acids (LNA) considerably enhance the thermodynamic stability of DNA and RNA duplexes. We report the thermodynamic stabilities of LNA-2'-O-methyl RNA/RNA duplexes designed to provide insight into the contributions of stacking and hydrogen bonding interactions to the enhanced stability. The results show that hydrogen bonding of LNA nucleotides is similar to that of 2'-O-methyl RNA nucleotides, whereas the 3'-stacking interactions are on average approximately 0.7 kcal/mol more favorable at 37 degrees C than for 2'-O-methyl or RNA nucleotides. Moreover, NMR spectra suggest helical preorganization of the single-stranded tetramer, C(L)A(M)A(L)U(M), probably due to restriction of some torsion angles. Thus, enhanced stacking interactions and helical preorganization of single-stranded oligonucleotides contribute to the extraordinary stabilization of duplexes by LNA nucleotides.
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Affiliation(s)
- Elzbieta Kierzek
- Institute of Bioorganic Chemistry, Polish Academy of Sciences, 60-714 Poznan, Noskowskiego 12/14, Poland.
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21
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Fathalla M, Lawrence CM, Zhang N, Sessler JL, Jayawickramarajah J. Base-pairing mediated non-covalent polymers. Chem Soc Rev 2009; 38:1608-20. [PMID: 19587956 DOI: 10.1039/b806484a] [Citation(s) in RCA: 98] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
The naturally occurring nucleic acid bases (nucleobases) adenine, thymine (uracil), guanine, and cytosine are widely appreciated for their ability to stabilize canonical Watson-Crick base-pairing motifs, as well as a number of other well-characterized arrangements, such as Hoogsteen and wobble heterodimers, and a variety of homodimers. In this tutorial review, the use of these kinds of interactions to form synthetic polymeric and oligomeric ensembles is summarized. Particular emphasis will be placed on synthetic analogues of guanine that stabilize the formation of well-defined higher order aggregates, as well as de novo polymeric systems whose properties are modulated by the presence of nucleobase derivatives incorporated within or attached to the chain-defining backbone. In both cases, nucleobase-nucleobase interactions serve to underlie the chemistry, establish the structural morphology, and enable the development of bioinspired, environmentally responsive materials.
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Affiliation(s)
- Maher Fathalla
- Department of Chemistry, Tulane University, 2015 Percival Stern Hall, Louisiana 70118, USA
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22
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Ivanova A, Shushkov P, Rösch N. Systematic Study of the Influence of Base-Step Parameters on the Electronic Coupling between Base-Pair Dimers: Comparison of A-DNA and B-DNA Forms. J Phys Chem A 2008; 112:7106-14. [DOI: 10.1021/jp8031513] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Anela Ivanova
- Department Chemie, Theoretische Chemie, Technische Universität München, 85747 Garching, Germany
| | - Philip Shushkov
- Department Chemie, Theoretische Chemie, Technische Universität München, 85747 Garching, Germany
| | - Notker Rösch
- Department Chemie, Theoretische Chemie, Technische Universität München, 85747 Garching, Germany
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Doi Y, Chiba J, Morikawa T, Inouye M. Artificial DNA Made Exclusively of Nonnatural C-Nucleosides with Four Types of Nonnatural Bases. J Am Chem Soc 2008; 130:8762-8. [DOI: 10.1021/ja801058h] [Citation(s) in RCA: 61] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/02/2023]
Affiliation(s)
- Yasuhiro Doi
- Graduate School of Pharmaceutical Sciences, University of Toyama, Sugitani 2630, Toyama 930-0194, Japan
| | - Junya Chiba
- Graduate School of Pharmaceutical Sciences, University of Toyama, Sugitani 2630, Toyama 930-0194, Japan
| | - Tomoyuki Morikawa
- Graduate School of Pharmaceutical Sciences, University of Toyama, Sugitani 2630, Toyama 930-0194, Japan
| | - Masahiko Inouye
- Graduate School of Pharmaceutical Sciences, University of Toyama, Sugitani 2630, Toyama 930-0194, Japan
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24
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He W, Franzini RM, Achim C. Metal-Containing Nucleic Acid Structures Based on Synergetic Hydrogen and Coordination Bonding. PROGRESS IN INORGANIC CHEMISTRY 2008. [DOI: 10.1002/9780470144428.ch8] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
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25
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Darnell DK, Kaur S, Stanislaw S, Konieczka JH, Konieczka JK, Yatskievych TA, Antin PB. MicroRNA expression during chick embryo development. Dev Dyn 2007; 235:3156-65. [PMID: 17013880 DOI: 10.1002/dvdy.20956] [Citation(s) in RCA: 198] [Impact Index Per Article: 11.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022] Open
Abstract
MicroRNAs (miRNAs) are small, abundant, noncoding RNAs that modulate protein abundance by interfering with target mRNA translation or stability. miRNAs are detected in organisms from all domains and may regulate 30% of transcripts in vertebrates. Understanding miRNA function requires a detailed determination of expression, yet this has not been reported in an amniote species. High-throughput whole mount in situ hybridization was performed on chicken embryos to map expression of 135 miRNA genes including five miRNAs that had not been previously reported in chicken. Eighty-four miRNAs were detected before day 5 of embryogenesis, and 75 miRNAs showed differential expression. Whereas few miRNAs were expressed during formation of the primary germ layers, the number of miRNAs detected increased rapidly during organogenesis. Patterns highlighted cell-type, organ or structure-specific expression, localization within germ layers and their derivatives, and expression in multiple cell and tissue types and within sub-regions of structures and tissues. A novel group of miRNAs was highly expressed in most tissues but much reduced in one or a few organs, including the heart. This study presents the first comprehensive overview of miRNA expression in an amniote organism and provides an important foundation for investigations of miRNA gene regulation and function.
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Affiliation(s)
- Diana K Darnell
- Department of Cell Biology and Anatomy, University of Arizona, Tucson, Arizona, USA
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26
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Affiliation(s)
- Henrik Orum
- CSO Santaris Pharma A/S,, Hørsholm, Denmark.
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27
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Bogucka M, Naus P, Pathmasiri W, Barman J, Chattopadhyaya J. Facile preparation of the oxetane-nucleosides. Org Biomol Chem 2005; 3:4362-72. [PMID: 16327897 DOI: 10.1039/b511406c] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023]
Abstract
Efficient and practical large scale synthesis of suitably protected 1',2'-oxetane locked purine and pyrimidine nucleosides for incorporation in oligo-DNA or -RNA by solid-phase synthesis is reported. A high regio and stereoselectivity with preferential formation of the beta-anomer in the glycosylation reaction, using the Vorbrüggen procedure, was achieved by a convergent synthetic procedure with orthogonal protection strategy using either 1,2-di-O-acetyl-3,4-O-isopropylidene-6-O-(4-toluoyl)-d-psicofuranose or 2-O-acetyl-6-O-benzyl-1,3,4-tri-O-(4-toluoyl)-d-psicofuranose as the glycosyl donor.
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Affiliation(s)
- Małgorzata Bogucka
- Department of Bioorganic Chemistry, Box 581, Biomedical Center, University of Uppsala, S-75123 Uppsala, Sweden
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