1
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Dhara D, Mulard LA, Hollenstein M. Natural, modified and conjugated carbohydrates in nucleic acids. Chem Soc Rev 2025; 54:2948-2983. [PMID: 39936337 DOI: 10.1039/d4cs00799a] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/13/2025]
Abstract
Storage of genetic information in DNA occurs through a unique ordering of canonical base pairs. However, this would not be possible in the absence of the sugar-phosphate backbone which is essential for duplex formation. While over a hundred nucleobase modifications have been identified (mainly in RNA), Nature is rather conservative when it comes to alterations at the level of the (deoxy)ribose sugar moiety. This trend is not reflected in synthetic analogues of nucleic acids where modifications of the sugar entity is commonplace to improve the properties of DNA and RNA. In this review article, we describe the main incentives behind sugar modifications in nucleic acids and we highlight recent progress in this field with a particular emphasis on therapeutic applications, the development of xeno-nucleic acids (XNAs), and on interrogating nucleic acid etiology. We also describe recent strategies to conjugate carbohydrates and oligosaccharides to oligonucleotides since this represents a particularly powerful strategy to improve the therapeutic index of oligonucleotide drugs. The advent of glycoRNAs combined with progress in nucleic acid and carbohydrate chemistry, protein engineering, and delivery methods will undoubtedly yield more potent sugar-modified nucleic acids for therapeutic, biotechnological, and synthetic biology applications.
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Affiliation(s)
- Debashis Dhara
- Department of Structural Biology and Chemistry, Laboratory for Bioorganic Chemistry of Nucleic Acids, Institut Pasteur, Université Paris Cité, CNRS UMR 352328, rue du Docteur Roux, 75724 Paris Cedex 15, France.
- Department of Structural Biology and Chemistry, Laboratory for Chemistry of Biomolecules, Institut Pasteur, Université Paris Cité, CNRS UMR 3523, 28, rue du Docteur Roux, 75724 Paris Cedex 15, France
| | - Laurence A Mulard
- Department of Structural Biology and Chemistry, Laboratory for Chemistry of Biomolecules, Institut Pasteur, Université Paris Cité, CNRS UMR 3523, 28, rue du Docteur Roux, 75724 Paris Cedex 15, France
| | - Marcel Hollenstein
- Department of Structural Biology and Chemistry, Laboratory for Bioorganic Chemistry of Nucleic Acids, Institut Pasteur, Université Paris Cité, CNRS UMR 352328, rue du Docteur Roux, 75724 Paris Cedex 15, France.
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2
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Gutfreund C, Betz K, Abramov M, Coosemans F, Holliger P, Herdewijn P, Marx A. Structural insights into a DNA polymerase reading the xeno nucleic acid HNA. Nucleic Acids Res 2025; 53:gkae1156. [PMID: 39673482 PMCID: PMC11724289 DOI: 10.1093/nar/gkae1156] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2024] [Revised: 10/31/2024] [Accepted: 12/01/2024] [Indexed: 12/16/2024] Open
Abstract
Xeno nucleic acids (XNAs) are unnatural analogues of the natural nucleic acids in which the canonical ribose or deoxyribose rings are replaced with alternative sugars, congener structures or even open-ring configurations. The expanding repertoire of XNAs holds significant promise for diverse applications in molecular biology as well as diagnostics and therapeutics. Key advantages of XNAs over natural nucleic acids include their enhanced biostability, superior target affinity and (in some cases) catalytic activity. Natural systems generally lack the mechanisms to transcribe, reverse transcribe or replicate XNAs. This limitation has been overcome through the directed evolution of nucleic acid-modifying enzymes, especially polymerases (pols) and reverse transcriptases (RTs). Despite these advances, the mechanisms by which synthetic RT enzymes read these artificial genetic polymers remain largely unexplored, primarily due to a scarcity of structural information. This study unveils first structural insights into an evolved thermostable DNA pol interacting with the XNA 1,5-anhydrohexitol nucleic acid (HNA), revealing unprecedented HNA nucleotide conformations within a ternary complex with the enzyme. These findings not only deepen our understanding of HNA to DNA reverse transcription but also set the stage for future advancements of this and similar enzymes through deliberate design.
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Affiliation(s)
- Cédric Gutfreund
- Department of Chemistry, University of Konstanz, Universitätsstraße 10, 78457 Konstanz, Germany
| | - Karin Betz
- Department of Chemistry, University of Konstanz, Universitätsstraße 10, 78457 Konstanz, Germany
| | - Mikhail Abramov
- Department of Chemistry, University of Konstanz, Universitätsstraße 10, 78457 Konstanz, Germany
- Department of Medicinal Chemistry, KU Leuven, Herestraat 49 BOX 1030, 3000 Leuven, Belgium
| | - Frédérick Coosemans
- Department of Medicinal Chemistry, KU Leuven, Herestraat 49 BOX 1030, 3000 Leuven, Belgium
| | - Phillipp Holliger
- MRC Laboratory of Molecular Biology, Francis Crick Avenue, Cambridge Biomedical Campus, Cambridge CB2 0QH, UK
| | - Piet Herdewijn
- Department of Medicinal Chemistry, KU Leuven, Herestraat 49 BOX 1030, 3000 Leuven, Belgium
| | - Andreas Marx
- Department of Chemistry, University of Konstanz, Universitätsstraße 10, 78457 Konstanz, Germany
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3
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Rihon J, Mattelaer CA, Montalvão RW, Froeyen M, Pinheiro VB, Lescrinier E. Structural insights into the morpholino nucleic acid/RNA duplex using the new XNA builder Ducque in a molecular modeling pipeline. Nucleic Acids Res 2024; 52:2836-2847. [PMID: 38412249 PMCID: PMC11014352 DOI: 10.1093/nar/gkae135] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2023] [Accepted: 02/19/2024] [Indexed: 02/29/2024] Open
Abstract
The field of synthetic nucleic acids with novel backbone structures [xenobiotic nucleic acids (XNAs)] has flourished due to the increased importance of XNA antisense oligonucleotides and aptamers in medicine, as well as the development of XNA processing enzymes and new XNA genetic materials. Molecular modeling on XNA structures can accelerate rational design in the field of XNAs as it contributes in understanding and predicting how changes in the sugar-phosphate backbone impact on the complementation properties of the nucleic acids. To support the development of novel XNA polymers, we present a first-in-class open-source program (Ducque) to build duplexes of nucleic acid analogs with customizable chemistry. A detailed procedure is described to extend the Ducque library with new user-defined XNA fragments using quantum mechanics (QM) and to generate QM-based force field parameters for molecular dynamics simulations within standard packages such as AMBER. The tool was used within a molecular modeling workflow to accurately reproduce a selection of experimental structures for nucleic acid duplexes with ribose-based as well as non-ribose-based nucleosides. Additionally, it was challenged to build duplexes of morpholino nucleic acids bound to complementary RNA sequences.
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Affiliation(s)
- Jérôme Rihon
- Laboratory of Medicinal Chemistry, Rega Institute for Medical Research, Herestraat 49, Box 1030, B-3000 Leuven, Belgium
| | - Charles-Alexandre Mattelaer
- Laboratory of Medicinal Chemistry, Rega Institute for Medical Research, Herestraat 49, Box 1030, B-3000 Leuven, Belgium
- Quantum Chemistry and Physical Chemistry, Celestijnenlaan 200f, Box 2404, B-3001, Leuven, Belgium
| | - Rinaldo Wander Montalvão
- Laboratory of Medicinal Chemistry, Rega Institute for Medical Research, Herestraat 49, Box 1030, B-3000 Leuven, Belgium
- Gain Therapeutics sucursal en España, Barcelona Science Park, Baldiri Reixac 4-10, 08028 Barcelona, Spain
| | - Mathy Froeyen
- Laboratory of Medicinal Chemistry, Rega Institute for Medical Research, Herestraat 49, Box 1030, B-3000 Leuven, Belgium
| | - Vitor Bernardes Pinheiro
- Laboratory of Medicinal Chemistry, Rega Institute for Medical Research, Herestraat 49, Box 1030, B-3000 Leuven, Belgium
| | - Eveline Lescrinier
- Laboratory of Medicinal Chemistry, Rega Institute for Medical Research, Herestraat 49, Box 1030, B-3000 Leuven, Belgium
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4
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Ghezzo M, Grigoletto L, Rigo R, Herdewijn P, Groaz E, Sissi C. Modulation of the tetrameric I-motif folding of C-rich Tetrahymena telomeric sequences by hexitol nucleic acid (HNA) modifications. Biochimie 2023; 214:112-122. [PMID: 37558081 DOI: 10.1016/j.biochi.2023.08.003] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2023] [Revised: 08/01/2023] [Accepted: 08/06/2023] [Indexed: 08/11/2023]
Abstract
I-motifs are non-canonical DNA structures consisting of two parallel strands held together by hemiprotonated cytosine-cytosine+ base pairs, which intercalate to form a ordered column of stacked base pairs. This unique structure covers potential relevance in various fields, including gene regulation and biotechnological applications. A unique structural feature of I-motifs (iM), is the presence of sugar-sugar interactions through their extremely narrow minor grooves. Consistently, oligonucleotides containing pentose derivatives such as ribose, 2'-deoxyribose, arabinose, and 2'-deoxy-2'-fluoroarabinose highlighted a very different attitude to fold into iM. On the other hand, there is significant attention focused on exploring sugar-modifications that can increase nucleic acids resistance to nuclease degradation, a crucial requirement for therapeutic applications. An interesting example, not addressed in the iM field yet, is represented by hexitol nucleic acid (HNA), a metabolically stable six-membered ring analogue compatible with A-like double helix formation. Herein, we selected two DNA C-rich Tetrahymena telomeric sequences whose tetrameric iMs were already resolved by NMR and we investigated the iM folding of related HNA and RNA oligonucleotides by circular dichroism, differential scanning calorimetry and NMR. The comparison of their behaviours vs the DNA counterparts provided interesting insights into the influence of the sugar on iM folding. In particular, ribose and hexitol prevented iM formation. However, by clustering the hexitol-containing residues at the 3'-end, it was possible to modulate the distribution of the different topological species described for the DNA iMs. These data open new avenues for the exploitation of sugar modifications for I-motif characterization and applications.
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Affiliation(s)
- Michele Ghezzo
- Dept. of Pharmaceutical and Pharmacological Sciences, University of Padova, v. Marzolo 5 35131, Padova, Italy
| | - Luca Grigoletto
- Dept. of Pharmaceutical and Pharmacological Sciences, University of Padova, v. Marzolo 5 35131, Padova, Italy; KU Leuven, Rega Institute for Medical Research, Medicinal Chemistry, Herestraat 49-Box 1041, 3000, Leuven, Belgium
| | - Riccardo Rigo
- Dept. of Pharmaceutical and Pharmacological Sciences, University of Padova, v. Marzolo 5 35131, Padova, Italy
| | - Piet Herdewijn
- KU Leuven, Rega Institute for Medical Research, Medicinal Chemistry, Herestraat 49-Box 1041, 3000, Leuven, Belgium
| | - Elisabetta Groaz
- Dept. of Pharmaceutical and Pharmacological Sciences, University of Padova, v. Marzolo 5 35131, Padova, Italy; KU Leuven, Rega Institute for Medical Research, Medicinal Chemistry, Herestraat 49-Box 1041, 3000, Leuven, Belgium.
| | - Claudia Sissi
- Dept. of Pharmaceutical and Pharmacological Sciences, University of Padova, v. Marzolo 5 35131, Padova, Italy.
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5
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Schofield P, Taylor AI, Rihon J, Peña Martinez CD, Zinn S, Mattelaer CA, Jackson J, Dhaliwal G, Schepers G, Herdewijn P, Lescrinier E, Christ D, Holliger P. Characterization of an HNA aptamer suggests a non-canonical G-quadruplex motif. Nucleic Acids Res 2023; 51:7736-7748. [PMID: 37439359 PMCID: PMC10450178 DOI: 10.1093/nar/gkad592] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2021] [Revised: 06/09/2023] [Accepted: 07/05/2023] [Indexed: 07/14/2023] Open
Abstract
Nucleic acids not only form the basis of heredity, but are increasingly a source of novel nano-structures, -devices and drugs. This has spurred the development of chemically modified alternatives (xeno nucleic acids (XNAs)) comprising chemical configurations not found in nature to extend their chemical and functional scope. XNAs can be evolved into ligands (XNA aptamers) that bind their targets with high affinity and specificity. However, detailed investigations into structural and functional aspects of XNA aptamers have been limited. Here we describe a detailed structure-function analysis of LYS-S8-19, a 1',5'-anhydrohexitol nucleic acid (HNA) aptamer to hen egg-white lysozyme (HEL). Mapping of the aptamer interaction interface with its cognate HEL target antigen revealed interaction epitopes, affinities, kinetics and hot-spots of binding energy similar to protein ligands such as anti-HEL-nanobodies. Truncation analysis and molecular dynamics (MD) simulations suggest that the HNA aptamer core motif folds into a novel and not previously observed HNA tertiary structure, comprising non-canonical hT-hA-hT/hT-hT-hT triplet and hG4-quadruplex structures, consistent with its recognition by two different G4-specific antibodies.
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Affiliation(s)
- Peter Schofield
- Garvan Institute of Medical Research, Darlinghurst, Sydney, NSW 2010, Australia
- St Vincent's Clinical School, Faculty of Medicine, University of New South Wales, Kensington, Sydney, NSW 2010, Australia
| | - Alexander I Taylor
- MRC Laboratory of Molecular Biology, Cambridge CB2 2QH, UK
- Cambridge Institute of Therapeutic Immunology & Infectious Disease (CITIID), University of Cambridge, Cambridge CB2 0AW, UK
| | - Jérôme Rihon
- Rega Institute, Laboratory of Medicinal Chemistry, Katholieke Universiteit Leuven, Herestraat 49, B 3000, Leuven, Belgium
| | - Cristian D Peña Martinez
- Garvan Institute of Medical Research, Darlinghurst, Sydney, NSW 2010, Australia
- St Vincent's Clinical School, Faculty of Medicine, University of New South Wales, Kensington, Sydney, NSW 2010, Australia
| | - Sacha Zinn
- Garvan Institute of Medical Research, Darlinghurst, Sydney, NSW 2010, Australia
- St Vincent's Clinical School, Faculty of Medicine, University of New South Wales, Kensington, Sydney, NSW 2010, Australia
| | - Charles-Alexandre Mattelaer
- Rega Institute, Laboratory of Medicinal Chemistry, Katholieke Universiteit Leuven, Herestraat 49, B 3000, Leuven, Belgium
| | - Jennifer Jackson
- Garvan Institute of Medical Research, Darlinghurst, Sydney, NSW 2010, Australia
| | - Gurpreet Dhaliwal
- Cambridge Institute of Therapeutic Immunology & Infectious Disease (CITIID), University of Cambridge, Cambridge CB2 0AW, UK
| | - Guy Schepers
- Rega Institute, Laboratory of Medicinal Chemistry, Katholieke Universiteit Leuven, Herestraat 49, B 3000, Leuven, Belgium
| | - Piet Herdewijn
- Rega Institute, Laboratory of Medicinal Chemistry, Katholieke Universiteit Leuven, Herestraat 49, B 3000, Leuven, Belgium
| | - Eveline Lescrinier
- Rega Institute, Laboratory of Medicinal Chemistry, Katholieke Universiteit Leuven, Herestraat 49, B 3000, Leuven, Belgium
| | - Daniel Christ
- Garvan Institute of Medical Research, Darlinghurst, Sydney, NSW 2010, Australia
- St Vincent's Clinical School, Faculty of Medicine, University of New South Wales, Kensington, Sydney, NSW 2010, Australia
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6
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Gasse C, Srivastava P, Schepers G, Jose J, Hollenstein M, Marlière P, Herdewijn P. Controlled E. coli Aggregation Mediated by DNA and XNA Hybridization. Chembiochem 2023; 24:e202300191. [PMID: 37119472 DOI: 10.1002/cbic.202300191] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2023] [Revised: 04/26/2023] [Accepted: 04/27/2023] [Indexed: 05/01/2023]
Abstract
Chemical cell surface modification is a fast-growing field of research, due to its enormous potential in tissue engineering, cell-based immunotherapy, and regenerative medicine. However, engineering of bacterial tissues by chemical cell surface modification has been vastly underexplored and the identification of suitable molecular handles is in dire need. We present here, an orthogonal nucleic acid-protein conjugation strategy to promote artificial bacterial aggregation. This system gathers the high selectivity and stability of linkage to a protein Tag expressed at the cell surface and the modularity and reversibility of aggregation due to oligonucleotide hybridization. For the first time, XNA (xeno nucleic acids in the form of 1,5-anhydrohexitol nucleic acids) were immobilized via covalent, SNAP-tag-mediated interactions on cell surfaces to induce bacterial aggregation.
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Affiliation(s)
- Cécile Gasse
- Génomique Métabolique, Genoscope Institut François Jacob, CEA, CNRS Univ Evry, Université Paris-Saclay, 2 Rue Gaston Crémieux, 91057, Evry, France
| | - Puneet Srivastava
- Laboratory of Medicinal Chemistry, Rega Institute for Biomedical Research, KU Leuven, Herestraat 49, Box 1041, 3000, Leuven, Belgium
| | - Guy Schepers
- Laboratory of Medicinal Chemistry, Rega Institute for Biomedical Research, KU Leuven, Herestraat 49, Box 1041, 3000, Leuven, Belgium
| | - Joachim Jose
- Institute of Pharmaceutical and Medicinal Chemistry, University of Münster, Corrensstr. 48, D-48149, Münster, Germany
| | - Marcel Hollenstein
- Institut Pasteur, Université Paris Cité, Department of Structural Biology and Chemistry, Laboratory for Bioorganic Chemistry of Nucleic Acids, CNRS UMR3523, 28, rue du Docteur Roux, 75724, Paris Cedex 15, France
| | - Philippe Marlière
- The European Syndicate of Synthetic Scientists and Industrialists (TESSSI), 81 rue Réaumur, 75002, Paris, France
| | - Piet Herdewijn
- Laboratory of Medicinal Chemistry, Rega Institute for Biomedical Research, KU Leuven, Herestraat 49, Box 1041, 3000, Leuven, Belgium
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7
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Ivanov GS, Tribulovich VG, Pestov NB, David TI, Amoah AS, Korneenko TV, Barlev NA. Artificial genetic polymers against human pathologies. Biol Direct 2022; 17:39. [PMID: 36474260 PMCID: PMC9727881 DOI: 10.1186/s13062-022-00353-7] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2022] [Accepted: 11/29/2022] [Indexed: 12/12/2022] Open
Abstract
Originally discovered by Nielsen in 1991, peptide nucleic acids and other artificial genetic polymers have gained a lot of interest from the scientific community. Due to their unique biophysical features these artificial hybrid polymers are now being employed in various areas of theranostics (therapy and diagnostics). The current review provides an overview of their structure, principles of rational design, and biophysical features as well as highlights the areas of their successful implementation in biology and biomedicine. Finally, the review discusses the areas of improvement that would allow their use as a new class of therapeutics in the future.
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Affiliation(s)
- Gleb S Ivanov
- Institute of Cytology, Tikhoretsky Ave 4, Saint Petersburg, Russia, 194064
- St. Petersburg State Technological Institute (Technical University), Saint Petersburg, Russia, 190013
| | - Vyacheslav G Tribulovich
- St. Petersburg State Technological Institute (Technical University), Saint Petersburg, Russia, 190013
| | - Nikolay B Pestov
- Chumakov Federal Scientific Center for Research and Development of Immune-and-Biological Products, Moscow, Russia, 108819
- Phystech School of Biological and Medical Physics, Moscow Institute of Physics and Technology, Dolgoprudny, Moscow Region, Russia, 141701
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Moscow, Russia, 117997
- Institute of Biomedical Chemistry, Moscow, Russia, 119121б
| | - Temitope I David
- Phystech School of Biological and Medical Physics, Moscow Institute of Physics and Technology, Dolgoprudny, Moscow Region, Russia, 141701
| | - Abdul-Saleem Amoah
- Phystech School of Biological and Medical Physics, Moscow Institute of Physics and Technology, Dolgoprudny, Moscow Region, Russia, 141701
| | - Tatyana V Korneenko
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Moscow, Russia, 117997
| | - Nikolai A Barlev
- Institute of Cytology, Tikhoretsky Ave 4, Saint Petersburg, Russia, 194064.
- Institute of Biomedical Chemistry, Moscow, Russia, 119121б.
- School of Medicine, Nazarbayev University, 010000, Astana, Kazakhstan.
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8
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Rietmeyer L, Li De La Sierra-Gallay I, Schepers G, Dorchêne D, Iannazzo L, Patin D, Touzé T, van Tilbeurgh H, Herdewijn P, Ethève-Quelquejeu M, Fonvielle M. Amino-acyl tXNA as inhibitors or amino acid donors in peptide synthesis. Nucleic Acids Res 2022; 50:11415-11425. [PMID: 36350642 PMCID: PMC9723616 DOI: 10.1093/nar/gkac1023] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2022] [Revised: 10/17/2022] [Accepted: 10/21/2022] [Indexed: 11/10/2022] Open
Abstract
Xenobiotic nucleic acids (XNAs) offer tremendous potential for synthetic biology, biotechnology, and molecular medicine but their ability to mimic nucleic acids still needs to be explored. Here, to study the ability of XNA oligonucleotides to mimic tRNA, we synthesized three L-Ala-tXNAs analogs. These molecules were used in a non-ribosomal peptide synthesis involving a bacterial Fem transferase. We compared the ability of this enzyme to use amino-acyl tXNAs containing 1',5'-anhydrohexitol (HNA), 2'-fluoro ribose (2'F-RNA) and 2'-fluoro arabinose. L-Ala-tXNA containing HNA or 2'F-RNA were substrates of the Fem enzyme. The synthesis of peptidyl-XNA and the resolution of their structures in complex with the enzyme show the impact of the XNA on protein binding. For the first time we describe functional tXNA in an in vitro assay. These results invite to test tXNA also as substitute for tRNA in translation.
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Affiliation(s)
| | | | - Guy Schepers
- Laboratory of Medicinal Chemistry, Rega Institute for Biomedical Research, KU Leuven, Herestraat 49, Box 1041, 3000 Leuven, Belgium
| | - Delphine Dorchêne
- INSERM UMR-S 1138, Centre de Recherche des Cordeliers, Sorbonne Université, Université Paris Cité, F-75006 Paris, France
| | - Laura Iannazzo
- Université Paris Cité, CNRS UMR 8601, Laboratoire de Chimie et Biochimie Pharmacologiques et Toxicologiques, F-75006Paris, France
| | - Delphine Patin
- Institute for Integrative Biology of the Cell (I2BC), CEA, CNRS, Université Paris-Saclay 91198, Gif-sur-Yvette, France
| | - Thierry Touzé
- Institute for Integrative Biology of the Cell (I2BC), CEA, CNRS, Université Paris-Saclay 91198, Gif-sur-Yvette, France
| | - Herman van Tilbeurgh
- Institute for Integrative Biology of the Cell (I2BC), CEA, CNRS, Université Paris-Saclay 91198, Gif-sur-Yvette, France
| | - Piet Herdewijn
- Laboratory of Medicinal Chemistry, Rega Institute for Biomedical Research, KU Leuven, Herestraat 49, Box 1041, 3000 Leuven, Belgium
| | - Mélanie Ethève-Quelquejeu
- Université Paris Cité, CNRS UMR 8601, Laboratoire de Chimie et Biochimie Pharmacologiques et Toxicologiques, F-75006Paris, France
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9
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Göppel T, Rosenberger JH, Altaner B, Gerland U. Thermodynamic and Kinetic Sequence Selection in Enzyme-Free Polymer Self-Assembly Inside a Non-Equilibrium RNA Reactor. Life (Basel) 2022; 12:life12040567. [PMID: 35455058 PMCID: PMC9032526 DOI: 10.3390/life12040567] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2022] [Revised: 04/03/2022] [Accepted: 04/06/2022] [Indexed: 11/18/2022] Open
Abstract
The RNA world is one of the principal hypotheses to explain the emergence of living systems on the prebiotic Earth. It posits that RNA oligonucleotides acted as both carriers of information as well as catalytic molecules, promoting their own replication. However, it does not explain the origin of the catalytic RNA molecules. How could the transition from a pre-RNA to an RNA world occur? A starting point to answer this question is to analyze the dynamics in sequence space on the lowest level, where mononucleotide and short oligonucleotides come together and collectively evolve into larger molecules. To this end, we study the sequence-dependent self-assembly of polymers from a random initial pool of short building blocks via templated ligation. Templated ligation requires two strands that are hybridized adjacently on a third strand. The thermodynamic stability of such a configuration crucially depends on the sequence context and, therefore, significantly influences the ligation probability. However, the sequence context also has a kinetic effect, since non-complementary nucleotide pairs in the vicinity of the ligation site stall the ligation reaction. These sequence-dependent thermodynamic and kinetic effects are explicitly included in our stochastic model. Using this model, we investigate the system-level dynamics inside a non-equilibrium ‘RNA reactor’ enabling a fast chemical activation of the termini of interacting oligomers. Moreover, the RNA reactor subjects the oligomer pool to periodic temperature changes inducing the reshuffling of the system. The binding stability of strands typically grows with the number of complementary nucleotides forming the hybridization site. While shorter strands unbind spontaneously during the cold phase, larger complexes only disassemble during the temperature peaks. Inside the RNA reactor, strand growth is balanced by cleavage via hydrolysis, such that the oligomer pool eventually reaches a non-equilibrium stationary state characterized by its length and sequence distribution. How do motif-dependent energy and stalling parameters affect the sequence composition of the pool of long strands? As a critical factor for self-enhancing sequence selection, we identify kinetic stalling due to non-complementary base pairs at the ligation site. Kinetic stalling enables cascades of self-amplification that result in a strong reduction of occupied states in sequence space. Moreover, we discuss the significance of the symmetry breaking for the transition from a pre-RNA to an RNA world.
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10
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Largy E, König A, Ghosh A, Ghosh D, Benabou S, Rosu F, Gabelica V. Mass Spectrometry of Nucleic Acid Noncovalent Complexes. Chem Rev 2021; 122:7720-7839. [PMID: 34587741 DOI: 10.1021/acs.chemrev.1c00386] [Citation(s) in RCA: 43] [Impact Index Per Article: 10.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Nucleic acids have been among the first targets for antitumor drugs and antibiotics. With the unveiling of new biological roles in regulation of gene expression, specific DNA and RNA structures have become very attractive targets, especially when the corresponding proteins are undruggable. Biophysical assays to assess target structure as well as ligand binding stoichiometry, affinity, specificity, and binding modes are part of the drug development process. Mass spectrometry offers unique advantages as a biophysical method owing to its ability to distinguish each stoichiometry present in a mixture. In addition, advanced mass spectrometry approaches (reactive probing, fragmentation techniques, ion mobility spectrometry, ion spectroscopy) provide more detailed information on the complexes. Here, we review the fundamentals of mass spectrometry and all its particularities when studying noncovalent nucleic acid structures, and then review what has been learned thanks to mass spectrometry on nucleic acid structures, self-assemblies (e.g., duplexes or G-quadruplexes), and their complexes with ligands.
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Affiliation(s)
- Eric Largy
- Univ. Bordeaux, CNRS, INSERM, ARNA, UMR 5320, U1212, IECB, F-33600 Pessac, France
| | - Alexander König
- Univ. Bordeaux, CNRS, INSERM, ARNA, UMR 5320, U1212, IECB, F-33600 Pessac, France
| | - Anirban Ghosh
- Univ. Bordeaux, CNRS, INSERM, ARNA, UMR 5320, U1212, IECB, F-33600 Pessac, France
| | - Debasmita Ghosh
- Univ. Bordeaux, CNRS, INSERM, ARNA, UMR 5320, U1212, IECB, F-33600 Pessac, France
| | - Sanae Benabou
- Univ. Bordeaux, CNRS, INSERM, ARNA, UMR 5320, U1212, IECB, F-33600 Pessac, France
| | - Frédéric Rosu
- Univ. Bordeaux, CNRS, INSERM, IECB, UMS 3033, F-33600 Pessac, France
| | - Valérie Gabelica
- Univ. Bordeaux, CNRS, INSERM, ARNA, UMR 5320, U1212, IECB, F-33600 Pessac, France
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11
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Mattelaer CA, Mattelaer HP, Rihon J, Froeyen M, Lescrinier E. Efficient and Accurate Potential Energy Surfaces of Puckering in Sugar-Modified Nucleosides. J Chem Theory Comput 2021; 17:3814-3823. [PMID: 34000809 DOI: 10.1021/acs.jctc.1c00270] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]
Abstract
Puckering of the sugar unit in nucleosides and nucleotides is an important structural aspect that directly influences the helical structure of nucleic acids. The preference for specific puckering modes in nucleic acids can be analyzed via in silico conformational analysis, but the large amount of conformations and the accuracy of the analysis leads to an extensive amount of computational time. In this paper, we show that the combination of geometry optimizations with the HF-3c method with single point energies at the RI-MP2 level results in accurate results for the puckering potential energy surface (PES) of DNA and RNA nucleosides while significantly reducing the necessary computational time. Applying this method to a series of known xeno nucleic acids (XNAs) allowed us to rapidly explore the puckering PES of each of the respective nucleosides and to explore the puckering PES of six-membered modified XNA (HNA and β-homo-DNA) for the first time.
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Affiliation(s)
- Charles-Alexandre Mattelaer
- KU Leuven, Rega Institute for Medical Research, Medicinal Chemistry, Herestraat 49 - Box 1041, 3000 Leuven, Belgium
| | - Henri-Philippe Mattelaer
- Campus Drie Eiken, Laboratory of Medicinal Chemistry, UAntwerp, Universiteitsplein 1, B-2610 Wilrijk, Belgium
| | - Jérôme Rihon
- KU Leuven, Rega Institute for Medical Research, Medicinal Chemistry, Herestraat 49 - Box 1041, 3000 Leuven, Belgium
| | - Matheus Froeyen
- KU Leuven, Rega Institute for Medical Research, Medicinal Chemistry, Herestraat 49 - Box 1041, 3000 Leuven, Belgium
| | - Eveline Lescrinier
- KU Leuven, Rega Institute for Medical Research, Medicinal Chemistry, Herestraat 49 - Box 1041, 3000 Leuven, Belgium
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12
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Structural Studies of HNA Substrate Specificity in Mutants of an Archaeal DNA Polymerase Obtained by Directed Evolution. Biomolecules 2020; 10:biom10121647. [PMID: 33302546 PMCID: PMC7763228 DOI: 10.3390/biom10121647] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2020] [Revised: 11/30/2020] [Accepted: 12/02/2020] [Indexed: 02/05/2023] Open
Abstract
Archaeal DNA polymerases from the B-family (polB) have found essential applications in biotechnology. In addition, some of their variants can accept a wide range of modified nucleotides or xenobiotic nucleotides, such as 1,5-anhydrohexitol nucleic acid (HNA), which has the unique ability to selectively cross-pair with DNA and RNA. This capacity is essential to allow the transmission of information between different chemistries of nucleic acid molecules. Variants of the archaeal polymerase from Thermococcus gorgonarius, TgoT, that can either generate HNA from DNA (TgoT_6G12) or DNA from HNA (TgoT_RT521) have been previously identified. To understand how DNA and HNA are recognized and selected by these two laboratory-evolved polymerases, we report six X-ray structures of these variants, as well as an in silico model of a ternary complex with HNA. Structural comparisons of the apo form of TgoT_6G12 together with its binary and ternary complexes with a DNA duplex highlight an ensemble of interactions and conformational changes required to promote DNA or HNA synthesis. MD simulations of the ternary complex suggest that the HNA-DNA hybrid duplex remains stable in the A-DNA helical form and help explain the presence of mutations in regions that would normally not be in contact with the DNA if it were not in the A-helical form. One complex with two incorporated HNA nucleotides is surprisingly found in a one nucleotide-backtracked form, which is new for a DNA polymerase. This information can be used for engineering a new generation of more efficient HNA polymerase variants.
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13
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Istrate A, Johannsen S, Istrate A, Sigel RKO, Leumann CJ. NMR solution structure of tricyclo-DNA containing duplexes: insight into enhanced thermal stability and nuclease resistance. Nucleic Acids Res 2019; 47:4872-4882. [PMID: 30916334 PMCID: PMC6511864 DOI: 10.1093/nar/gkz197] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2018] [Revised: 03/12/2019] [Accepted: 03/13/2019] [Indexed: 01/14/2023] Open
Abstract
Tc-DNA is a conformationally constrained oligonucleotide analogue which shows significant increase in thermal stability when hybridized with RNA, DNA or tc-DNA. Remarkably, recent studies revealed that tc-DNA antisense oligonucleotides (AO) hold great promise for the treatment of Duchenne muscular dystrophy and spinal muscular atrophy. To date, no high-resolution structural data is available for fully modified tc-DNA duplexes and little is known about the origins of their enhanced thermal stability. Here, we report the structures of a fully modified tc-DNA oligonucleotide paired with either complementary RNA, DNA or tc-DNA. All three investigated duplexes maintain a right-handed helical structure with Watson-Crick base pairing and overall geometry intermediate between A- and B-type, but closer to A-type structures. All sugars of the tc-DNA and RNA residues adopt a North conformation whereas the DNA deoxyribose are found in a South-East-North conformation equilibrium. The conformation of the tc-DNA strand in the three determined structures is nearly identical and despite the different nature and local geometry of the complementary strand, the overall structures of the examined duplexes are very similar suggesting that the tc-DNA strand dominates the duplex structure.
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Affiliation(s)
- Andrei Istrate
- Department of Chemistry and Biochemistry, University of Bern, Freiestrasse 3, Bern CH-3012, Switzerland
| | - Silke Johannsen
- Department of Chemistry, Winterthurerstrasse 190, University of Zürich, Zürich CH-8057, Switzerland
| | - Alena Istrate
- Department of Chemistry and Biochemistry, University of Bern, Freiestrasse 3, Bern CH-3012, Switzerland
| | - Roland K O Sigel
- Department of Chemistry, Winterthurerstrasse 190, University of Zürich, Zürich CH-8057, Switzerland
| | - Christian J Leumann
- Department of Chemistry and Biochemistry, University of Bern, Freiestrasse 3, Bern CH-3012, Switzerland
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14
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Vanmeert M, Razzokov J, Mirza MU, Weeks SD, Schepers G, Bogaerts A, Rozenski J, Froeyen M, Herdewijn P, Pinheiro VB, Lescrinier E. Rational design of an XNA ligase through docking of unbound nucleic acids to toroidal proteins. Nucleic Acids Res 2019; 47:7130-7142. [PMID: 31334814 PMCID: PMC6649754 DOI: 10.1093/nar/gkz551] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2019] [Revised: 05/24/2019] [Accepted: 06/12/2019] [Indexed: 02/06/2023] Open
Abstract
Xenobiotic nucleic acids (XNA) are nucleic acid analogues not present in nature that can be used for the storage of genetic information. In vivo XNA applications could be developed into novel biocontainment strategies, but are currently limited by the challenge of developing XNA processing enzymes such as polymerases, ligases and nucleases. Here, we present a structure-guided modelling-based strategy for the rational design of those enzymes essential for the development of XNA molecular biology. Docking of protein domains to unbound double-stranded nucleic acids is used to generate a first approximation of the extensive interaction of nucleic acid processing enzymes with their substrate. Molecular dynamics is used to optimise that prediction allowing, for the first time, the accurate prediction of how proteins that form toroidal complexes with nucleic acids interact with their substrate. Using the Chlorella virus DNA ligase as a proof of principle, we recapitulate the ligase's substrate specificity and successfully predict how to convert it into an XNA-templated XNA ligase.
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Affiliation(s)
- Michiel Vanmeert
- Medicinal Chemistry, Rega Institute for Medical Research, KU Leuven, Herestraat 49, box 1041, 3000 Leuven, Belgium
| | - Jamoliddin Razzokov
- Research group PLASMANT, Department of Chemistry, University of Antwerp, Universiteitsplein 1, B-2610 Antwerp, Belgium
| | - Muhammad Usman Mirza
- Medicinal Chemistry, Rega Institute for Medical Research, KU Leuven, Herestraat 49, box 1041, 3000 Leuven, Belgium
- Centre for Research in Molecular Medicine (CRiMM), University of Lahore, Pakistan
| | - Stephen D Weeks
- Biocrystallography, KU Leuven, Herestraat 49, box 822, 3000 Leuven, Belgium
| | - Guy Schepers
- Medicinal Chemistry, Rega Institute for Medical Research, KU Leuven, Herestraat 49, box 1041, 3000 Leuven, Belgium
| | - Annemie Bogaerts
- Research group PLASMANT, Department of Chemistry, University of Antwerp, Universiteitsplein 1, B-2610 Antwerp, Belgium
| | - Jef Rozenski
- Medicinal Chemistry, Rega Institute for Medical Research, KU Leuven, Herestraat 49, box 1041, 3000 Leuven, Belgium
| | - Mathy Froeyen
- Medicinal Chemistry, Rega Institute for Medical Research, KU Leuven, Herestraat 49, box 1041, 3000 Leuven, Belgium
| | - Piet Herdewijn
- Medicinal Chemistry, Rega Institute for Medical Research, KU Leuven, Herestraat 49, box 1041, 3000 Leuven, Belgium
| | - Vitor B Pinheiro
- Medicinal Chemistry, Rega Institute for Medical Research, KU Leuven, Herestraat 49, box 1041, 3000 Leuven, Belgium
- University College London, Department of Structural and Molecular Biology, Gower Street, London, WC1E 6BT, UK
| | - Eveline Lescrinier
- Medicinal Chemistry, Rega Institute for Medical Research, KU Leuven, Herestraat 49, box 1041, 3000 Leuven, Belgium
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15
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Li X, Dumbre SG, Lescrinier E, Groaz E, Herdewijn P. Synthesis and Conformation of Pentopyranoside Nucleoside Phosphonates. J Org Chem 2019; 84:6589-6603. [PMID: 31046278 DOI: 10.1021/acs.joc.8b03178] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
In contrast to natural nucleosides, where the nucleobase is positioned at the anomeric center, we report the synthesis of pentopyranoside nucleosides with a phosphonate functionality at the 1'-anomeric oxygen. Starting from l-arabinose, key functionalized l- glycero- and l- erythro-pentopyranose carbohydrate synthons were prepared and further elaborated into the final six-membered ring nucleosides via nucleobase incorporation and phosphonomethylation reactions. NMR analysis demonstrated that these nucleoside phosphonates exist in solution as conformers predominantly adopting a chair structure in which the base moiety is equatorially positioned. Such conformation prevents unfavorable 1,3-diaxial steric and electronic interactions. Notably, the stereochemical outcome of the Vorbrüggen glycosylation step utilized en route to the thymine analogue clearly suggests the absence of anchimeric assistance, as opposed to what is usually observed during nucleoside synthesis using protected furanose precursors. The finding that the diphosphates of the compounds developed in this study are recognized by DNA polymerases is important in view of the future selection of artificial genetic systems and dedicated polymerases as well as applications in therapy.
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Affiliation(s)
- Xiaochen Li
- KU Leuven, Rega Institute for Medical Research , Medicinal Chemistry , Herestraat 49, Box 1041 , 3000 Leuven , Belgium
| | - Shrinivas G Dumbre
- KU Leuven, Rega Institute for Medical Research , Medicinal Chemistry , Herestraat 49, Box 1041 , 3000 Leuven , Belgium
| | - Eveline Lescrinier
- KU Leuven, Rega Institute for Medical Research , Medicinal Chemistry , Herestraat 49, Box 1041 , 3000 Leuven , Belgium
| | - Elisabetta Groaz
- KU Leuven, Rega Institute for Medical Research , Medicinal Chemistry , Herestraat 49, Box 1041 , 3000 Leuven , Belgium
| | - Piet Herdewijn
- KU Leuven, Rega Institute for Medical Research , Medicinal Chemistry , Herestraat 49, Box 1041 , 3000 Leuven , Belgium
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Abstract
The emergence of functional cooperation between the three main classes of biomolecules - nucleic acids, peptides and lipids - defines life at the molecular level. However, how such mutually interdependent molecular systems emerged from prebiotic chemistry remains a mystery. A key hypothesis, formulated by Crick, Orgel and Woese over 40 year ago, posits that early life must have been simpler. Specifically, it proposed that an early primordial biology lacked proteins and DNA but instead relied on RNA as the key biopolymer responsible not just for genetic information storage and propagation, but also for catalysis, i.e. metabolism. Indeed, there is compelling evidence for such an 'RNA world', notably in the structure of the ribosome as a likely molecular fossil from that time. Nevertheless, one might justifiably ask whether RNA alone would be up to the task. From a purely chemical perspective, RNA is a molecule of rather uniform composition with all four bases comprising organic heterocycles of similar size and comparable polarity and pK a values. Thus, RNA molecules cover a much narrower range of steric, electronic and physicochemical properties than, e.g. the 20 amino acid side-chains of proteins. Herein we will examine the functional potential of RNA (and other nucleic acids) with respect to self-replication, catalysis and assembly into simple protocellular entities.
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17
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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: 1.8] [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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18
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Anosova I, Kowal EA, Dunn MR, Chaput JC, Van Horn WD, Egli M. The structural diversity of artificial genetic polymers. Nucleic Acids Res 2015; 44:1007-21. [PMID: 26673703 PMCID: PMC4756832 DOI: 10.1093/nar/gkv1472] [Citation(s) in RCA: 120] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2015] [Accepted: 11/30/2015] [Indexed: 11/13/2022] Open
Abstract
Synthetic genetics is a subdiscipline of synthetic biology that aims to develop artificial genetic polymers (also referred to as xeno-nucleic acids or XNAs) that can replicate in vitro and eventually in model cellular organisms. This field of science combines organic chemistry with polymerase engineering to create alternative forms of DNA that can store genetic information and evolve in response to external stimuli. Practitioners of synthetic genetics postulate that XNA could be used to safeguard synthetic biology organisms by storing genetic information in orthogonal chromosomes. XNA polymers are also under active investigation as a source of nuclease resistant affinity reagents (aptamers) and catalysts (xenozymes) with practical applications in disease diagnosis and treatment. In this review, we provide a structural perspective on known antiparallel duplex structures in which at least one strand of the Watson-Crick duplex is composed entirely of XNA. Currently, only a handful of XNA structures have been archived in the Protein Data Bank as compared to the more than 100 000 structures that are now available. Given the growing interest in xenobiology projects, we chose to compare the structural features of XNA polymers and discuss their potential to access new regions of nucleic acid fold space.
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Affiliation(s)
- Irina Anosova
- The Biodesign Institute, Virginia G. Piper Center for Personalized Diagnostics, School of Molecular Sciences, Magnetic Resonance Research Center, Arizona State University, Tempe, AZ 85287-5001, USA
| | - Ewa A Kowal
- Department of Biochemistry, Center for Structural Biology, and Vanderbilt Ingram Cancer Center, Vanderbilt University, School of Medicine, Nashville, TN 37232-0146, USA
| | - Matthew R Dunn
- Department of Pharmaceutical Sciences, University of California-Irvine, Irvine, CA 92697, USA
| | - John C Chaput
- Department of Pharmaceutical Sciences, University of California-Irvine, Irvine, CA 92697, USA
| | - Wade D Van Horn
- The Biodesign Institute, Virginia G. Piper Center for Personalized Diagnostics, School of Molecular Sciences, Magnetic Resonance Research Center, Arizona State University, Tempe, AZ 85287-5001, USA
| | - Martin Egli
- Department of Biochemistry, Center for Structural Biology, and Vanderbilt Ingram Cancer Center, Vanderbilt University, School of Medicine, Nashville, TN 37232-0146, USA
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19
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Das S, Samanta PK, Pati SK. Watson–Crick base pairing, electronic and photophysical properties of triazole modified adenine analogues: a computational study. NEW J CHEM 2015. [DOI: 10.1039/c5nj01566a] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/13/2023]
Abstract
Triazole adenine nucleobase analogues show fluorescence in the UV-Vis region and form Watson–Crick base pairing with thymine nucleobases.
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Affiliation(s)
- Shubhajit Das
- New Chemistry Unit
- Jawaharlal Nehru Centre for Advanced Scientific Research
- Bangalore 560064
- India
| | - Pralok K Samanta
- Theoretical Sciences Unit
- Jawaharlal Nehru Centre for Advanced Scientific Research
- Bangalore 560064
- India
| | - Swapan K Pati
- New Chemistry Unit
- Jawaharlal Nehru Centre for Advanced Scientific Research
- Bangalore 560064
- India
- Theoretical Sciences Unit
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20
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Abstract
The emergence of catalysis in early genetic polymers like RNA is considered a key transition in the origin of life1, predating the appearance of protein enzymes. DNA also demonstrates the capacity to fold into three-dimensional structures and form catalysts in vitro2. However, to what degree these natural biopolymers comprise functionally privileged chemical scaffolds3 for folding or the evolution of catalysis is not known. The ability of synthetic genetic polymers (XNAs) with alternative backbone chemistries not found in nature to fold into defined structures and bind ligands4 raises the possibility that these too might be capable of forming catalysts (XNAzymes). Here we report the discovery of such XNAzymes, elaborated in four different chemistries (ANA (arabino nucleic acids)5, FANA (2′-fluoroarabino nucleic acids)6, HNA (hexitol nucleic acids) and CeNA (cyclohexene nucleic acids)7 directly from random XNA oligomer pools, exhibiting in trans RNA endonuclease and ligase activities. We also describe an XNA-XNA ligase metalloenzyme in the FANA framework, establishing catalysis in an entirely synthetic system and enabling the synthesis of FANA oligomers and an active RNA endonuclease FANAzyme from its constituent parts. These results extend catalysis beyond biopolymers and establish technologies for the discovery of catalysts in a wide range of polymer scaffolds not found in nature8. Evolution of catalysis independent of any natural polymer has implications for the definition of chemical boundary conditions for the emergence of life on earth and elsewhere in the universe9.
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21
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Halder A, Datta A, Bhattacharyya D, Mitra A. Why does substitution of thymine by 6-ethynylpyridone increase the thermostability of DNA double helices? J Phys Chem B 2014; 118:6586-96. [PMID: 24857638 DOI: 10.1021/jp412416p] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Abstract
Efficiency of 6-ethynylpyridone (E), a potential thymine (T) analogue, which forms high-fidelity base pairs with adenine (A) and gives rise to stabler DNA duplexes, with stability comparable to those containing canonical cytosine(C):guanine(G) base pairs, has been reported recently. Estimates of the interaction energies, involving geometry optimization at the DFT level (including middle range dispersion interactions) followed by single point energy calculation at MP2 level, in excellent correlation with the experimentally observed trends, show that E binds more strongly and more discriminately with A than T does. Detailed analysis reveals that the increase in base-base interaction arises out of conjugation of acetylenic π electrons with the ring π system of E, which results in not only an extra stabilizing C-H···π interaction in the EA pair, but also a strengthening of the conventional hydrogen bonds. However, the computed base-base interaction energy for the EA pair was found to be much less than that of the canonical CG pair, implying that the difference in the TA versus EA base pairing interaction alone cannot explain the large experimentally observed increase in the thermostability of DNA duplexes, where a TA pair is replaced with an EA pair. Our computations show that the conjugation of acetylenic π electrons with the ring π system also possibly plays a role in increasing the stacking potential of the EA pair, which in turn can explain its marked influence in the enhancement of duplex stability.
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Affiliation(s)
- Antarip Halder
- Center for Computational Natural Sciences and Bioinformatics, International Institute of Information Technology Hyderabad , Gachibowli, Hyderabad, 500032, AP, India
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22
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Seth PP, Swayze EE. Unnatural Nucleoside Analogs for Antisense Therapy. METHODS AND PRINCIPLES IN MEDICINAL CHEMISTRY 2014. [DOI: 10.1002/9783527676545.ch12] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
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C3'-endo-puckered pyrrolidine containing PNA has favorable geometry for RNA binding: novel ethano locked PNA (ethano-PNA). Bioorg Med Chem 2013; 21:4092-101. [PMID: 23743441 DOI: 10.1016/j.bmc.2013.05.015] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2013] [Revised: 05/08/2013] [Accepted: 05/09/2013] [Indexed: 11/22/2022]
Abstract
A novel peptide nucleic acid (PNA) analogue is designed with a constraint in the aminoethyl segment of the aegPNA backbone so that the dihedral angle β is restricted within 60-80°, compatible to form PNA:RNA duplexes. The designed monomer is further functionalized with positively charged amino-/guanidino-groups. The appropriately protected monomers were synthesized and incorporated into aegPNA oligomers at predetermined positions and their binding abilities with cDNA and RNA were investigated. A single incorporation of the modified PNA monomer into a 12-mer PNA sequence resulted in stronger binding with complementary RNA over cDNA. No significant changes in the CD signatures of the derived duplexes of modified PNA with complementary RNA were observed.
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24
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Abstract
For over 20 years, laboratories around the world have been applying the principles of Darwinian evolution to isolate DNA and RNA molecules with specific ligand-binding or catalytic activities. This area of synthetic biology, commonly referred to as in vitro genetics, is made possible by the availability of natural polymerases that can replicate genetic information in the laboratory. Moving beyond natural nucleic acids requires organic chemistry to synthesize unnatural analogues and polymerase engineering to create enzymes that recognize artificial substrates. Progress in both of these areas has led to the emerging field of synthetic genetics, which explores the structural and functional properties of synthetic genetic polymers by in vitro evolution. This review examines recent advances in the Darwinian evolution of artificial genetic polymers and their potential downstream applications in exobiology, molecular medicine, and synthetic biology.
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Affiliation(s)
- John C Chaput
- Center for Evolutionary Medicine and Informatics in the Biodesign Institute, and Department of Chemistry and Biochemistry, Arizona State University, Tempe, AZ 85287-5301, USA.
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25
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Šponer J, Mládek A, Šponer JE, Svozil D, Zgarbová M, Banáš P, Jurečka P, Otyepka M. The DNA and RNA sugar-phosphate backbone emerges as the key player. An overview of quantum-chemical, structural biology and simulation studies. Phys Chem Chem Phys 2012; 14:15257-77. [PMID: 23072945 DOI: 10.1039/c2cp41987d] [Citation(s) in RCA: 68] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Abstract
Knowledge of geometrical and physico-chemical properties of the sugar-phosphate backbone substantially contributes to the comprehension of the structural dynamics, function and evolution of nucleic acids. We provide a side by side overview of structural biology/bioinformatics, quantum chemical and molecular mechanical/simulation studies of the nucleic acids backbone. We highlight main features, advantages and limitations of these techniques, with a special emphasis given to their synergy. The present status of the research is then illustrated by selected examples which include classification of DNA and RNA backbone families, benchmark structure-energy quantum chemical calculations, parameterization of the dihedral space of simulation force fields, incorporation of arsenate into DNA, sugar-phosphate backbone self-cleavage in small RNA enzymes, and intricate geometries of the backbone in recurrent RNA building blocks. Although not apparent from the current literature showing limited overlaps between the QM, simulation and bioinformatics studies of the nucleic acids backbone, there in fact should be a major cooperative interaction between these three approaches in studies of the sugar-phosphate backbone.
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Affiliation(s)
- Jiří Šponer
- Institute of Biophysics, Academy Sciences of the Czech Republic, Královopolská 135, 612 65 Brno, Czech Republic.
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Seth PP, Yu J, Jazayeri A, Pallan PS, Allerson CR, Østergaard ME, Liu F, Herdewijn P, Egli M, Swayze EE. Synthesis and antisense properties of fluoro cyclohexenyl nucleic acid (F-CeNA), a nuclease stable mimic of 2'-fluoro RNA. J Org Chem 2012; 77:5074-85. [PMID: 22591005 DOI: 10.1021/jo300594b] [Citation(s) in RCA: 34] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
We report the design and synthesis of 2'-fluoro cyclohexenyl nucleic acid (F-CeNA) pyrimidine phosphoramidites and the synthesis and biophysical, structural, and biological evaluation of modified oligonucleotides. The synthesis of the nucleoside phosphoramidites was accomplished in multigram quantities starting from commercially available methyl-D-mannose pyranoside. Installation of the fluorine atom was accomplished using nonafluorobutanesulfonyl fluoride, and the cyclohexenyl ring system was assembled by means of a palladium-catalyzed Ferrier rearrangement. Installation of the nucleobase was carried out under Mitsunobu conditions followed by standard protecting group manipulations to provide the desired pyrimidine phosphoramidites. Biophysical evaluation indicated that F-CeNA shows behavior similar to that of a 2'-modified nucleotide, and duplexes with RNA showed slightly lower duplex thermostability as compared to that of the more rigid 3'-fluoro hexitol nucleic acid (FHNA). However, F-CeNA modified oligonucleotides were significantly more stable against digestion by snake venom phosphodiesterases (SVPD) as compared to unmodified DNA, 2'-fluoro RNA (FRNA), 2'-methoxyethyl RNA (MOE), and FHNA modified oligonucleotides. Examination of crystal structures of a modified DNA heptamer duplex d(GCG)-T*-d(GCG):d(CGCACGC) by X-ray crystallography indicated that the cyclohexenyl ring system exhibits both the (3)H(2) and (2)H(3) conformations, similar to the C3'-endo/C2'-endo conformation equilibrium seen in natural furanose nucleosides. In the (2)H(3) conformation, the equatorial fluorine engages in a relatively close contact with C8 (2.94 Å) of the 3'-adjacent dG nucleotide that may represent a pseudo hydrogen bond. In contrast, the cyclohexenyl ring of F-CeNA was found to exist exclusively in the (3)H(2) (C3'-endo like) conformation in the crystal structure of the modified A-form DNA decamer duplex [d(GCGTA)-T*-d(ACGC)](2.) In an animal experiment, a 16-mer F-CeNA gapmer ASO showed similar RNA affinity but significantly improved activity compared to that of a sequence matched MOE ASO, thus establishing F-CeNA as a useful modification for antisense applications.
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Affiliation(s)
- Punit P Seth
- Isis Pharmaceuticals, 2855 Gazelle Court, Carlsbad, California 92010, United States.
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27
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D'Alonzo D, Guaragna A, Palumbo G. Exploring the role of chirality in nucleic acid recognition. Chem Biodivers 2012; 8:373-413. [PMID: 21404424 DOI: 10.1002/cbdv.201000303] [Citation(s) in RCA: 38] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
The study of the base-pairing properties of nucleic acids with sugar moieties in the backbone belonging to the L-series (β-L-DNA, β-L-RNA, and their analogs) are reviewed. The major structural factors underlying the formation of stable heterochiral complexes obtained by incorporation of modified nucleotides into natural duplexes, or by hybridization between homochiral strands of opposite sense of chirality are highlighted. In addition, the perspective use of L-nucleic acids as candidates for various therapeutic applications, or as tools for both synthetic biology and etiology-oriented investigations on the structure and stereochemistry of natural nucleic acids is discussed.
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Affiliation(s)
- Daniele D'Alonzo
- Dipartimento di Chimica Organica e Biochimica, Università di Napoli Federico II, Complesso Universitario Monte Sant'Angelo, via Cinthia, 4, I-80126 Napoli.
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Maiti M, Nauwelaerts K, Lescrinier E, Herdewijn P. Structural and binding study of modified siRNAs with the Argonaute 2 PAZ domain by NMR spectroscopy. Chemistry 2011; 17:1519-28. [PMID: 21268154 DOI: 10.1002/chem.201000765] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2010] [Indexed: 11/05/2022]
Abstract
By using high-resolution NMR spectroscopy, the structures of a natural short interfering RNA (siRNA) and of several altritol nucleic acid (ANA)-modified siRNAs were determined. The interaction of modified siRNAs with the PAZ domain of the Argonaute 2 protein of Drosophila melanogaster was also studied. The structures show that the modified siRNA duplexes (ANA/RNA) adopt a geometry very similar to the naturally occurring A-type siRNA duplex. All ribose residues, except for the 3' overhang, show 3'-endo conformation. The six-membered altritol sugar in ANA occurs in a chair conformation with the nucleobase in an axial position. In all siRNA duplexes, two overhanging nucleotides at the 3' end enhance the stability of the first neighboring base pair by a stacking interaction. The first overhanging nucleotide has a rather fixed position, whereas the second overhanging nucleotide shows larger flexibility. NMR binding studies of the PAZ domain with ANA-modified siRNAs demonstrate that modifications in the double-stranded region of the antisense strand have some small effects on the binding affinity as compared with the unmodified siRNA. Modification of the 3' overhang with thymidine (dTdT) residues shows a sixfold increase in the binding affinity compared with the unmodified siRNA (relative binding affinity of 17% compared with dTdT-modified overhang), whereas modification of the 3' overhang with ANA largely decreases the binding affinity.
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Affiliation(s)
- Mohitosh Maiti
- Laboratory of Medicinal Chemistry, Rega Institute for Medical Research, Katholieke Universiteit Leuven, Minderbroedersstraat 10, 3000 Leuven, Belgium
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29
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Erande N, Gunjal AD, Fernandes M, Kumar VA. Probing the furanose conformation in the 2′–5′strand of isoDNA : RNA duplexes by freezing the nucleoside conformations. Chem Commun (Camb) 2011; 47:4007-9. [DOI: 10.1039/c0cc05402j] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/25/2023]
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30
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Lu H, Krueger AT, Gao J, Liu H, Kool ET. Toward a designed genetic system with biochemical function: polymerase synthesis of single and multiple size-expanded DNA base pairs. Org Biomol Chem 2010; 8:2704-10. [PMID: 20407680 DOI: 10.1039/c002766a] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
The development of alternative architectures for genetic information-encoding systems offers the possibility of new biotechnological tools as well as basic insights into the function of the natural system. In order to examine the potential of benzo-expanded DNA (xDNA) to encode and transfer biochemical information, we carried out a study of the processing of single xDNA pairs by DNA Polymerase I Klenow fragment (Kf, an A-family sterically rigid enzyme) and by the Sulfolobus solfataricus polymerase Dpo4 (a flexible Y-family polymerase). Steady-state kinetics were measured and compared for enzymatic synthesis of the four correct xDNA pairs and twelve mismatched pairs, by incorporation of dNTPs opposite single xDNA bases. Results showed that, like Kf, Dpo4 in most cases selected the correctly paired partner for each xDNA base, but with efficiency lowered by the enlarged pair size. We also evaluated kinetics for extension by these polymerases beyond xDNA pairs and mismatches, and for exonuclease editing by the Klenow exo+ polymerase. Interestingly, the two enzymes were markedly different: Dpo4 extended pairs with relatively high efficiencies (within 18-200-fold of natural DNA), whereas Kf essentially failed at extension. The favorable extension by Dpo4 was tested further by stepwise synthesis of up to four successive xDNA pairs on an xDNA template.
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Affiliation(s)
- Haige Lu
- Department of Chemistry, Stanford University, Stanford, CA 94305, USA
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31
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Abstract
Starting from pyranose nucleic acids, several series of modified nucleic acids with a six-membered carbohydrate moiety (mimic) have been synthesized and analyzed over a period of 20 years, and this work is summarized here. The process starts with structural and conformational considerations, followed by synthetic efforts and a structural analysis, and ends up with a biological confirmation of the concept, demonstrating that these modified nucleic acids represent very valuable tools in chemistry and biology.
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Affiliation(s)
- Piet Herdewijn
- Laboratory for Medicinal Chemistry, Rega Institute for Medical Research, Minderbroedersstraat 10, B-3000 Leuven.
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32
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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: 38] [Impact Index Per Article: 2.5] [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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33
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D'Alonzo D, Van Aerschot A, Guaragna A, Palumbo G, Schepers G, Capone S, Rozenski J, Herdewijn P. Synthesis and base pairing properties of 1',5'-anhydro-L-hexitol nucleic acids (L-HNA). Chemistry 2010; 15:10121-31. [PMID: 19739223 DOI: 10.1002/chem.200901847] [Citation(s) in RCA: 26] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Abstract
Oligonucleotides composed of 1',5'-anhydro-arabino-hexitol nucleosides belonging to the L series (L-HNA) were prepared and preliminarily studied as a novel potential base-pairing system. Synthesis of enantiopure L-hexitol nucleotide monomers equipped with a 2'-(N(6)-benzoyladenin-9-yl) or a 2'-(thymin-1-yl) moiety was carried out by a de novo approach based on a domino reaction as key step. The L oligonucleotide analogues were evaluated in duplex formation with natural complements as well as with unnatural sugar-modified oligonucleotides. In many cases stable homo- and heterochiral associations were found. Besides T(m) measurements, detection of heterochiral complexes was unambiguously confirmed by LC-MS studies. Interestingly, circular dichroism measurements of the most stable duplexes suggested that L-HNA form left-handed helices with both D and L oligonucleotides.
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Affiliation(s)
- Daniele D'Alonzo
- Dipartimento di Chimica Organica e Biochimica, Università Federico II, Napoli, via Cinthia 4, 80126 Napoli, Italy
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34
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Appella DH. Non-natural nucleic acids for synthetic biology. Curr Opin Chem Biol 2009; 13:687-96. [PMID: 19879178 PMCID: PMC3152792 DOI: 10.1016/j.cbpa.2009.09.030] [Citation(s) in RCA: 52] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2009] [Revised: 09/24/2009] [Accepted: 09/29/2009] [Indexed: 11/29/2022]
Abstract
Genetic manipulation is an important facet of synthetic biology but can be complicated by undesired nuclease degradation. Incorporating non-natural nucleic acids into a gene could convey resistance to nucleases and promote expression. The compatibility of non-natural nucleosides with polymerases is reviewed with a focus on results from the past two years. Details are provided about how the different systems could be useful in synthetic biology.
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Affiliation(s)
- Daniel H Appella
- National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Department of Health and Human Services, Bethesda, MD 20892, USA.
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35
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Delaney JC, Gao J, Liu H, Shrivastav N, Essigmann JM, Kool ET. Efficient replication bypass of size-expanded DNA base pairs in bacterial cells. Angew Chem Int Ed Engl 2009; 48:4524-7. [PMID: 19444841 DOI: 10.1002/anie.200805683] [Citation(s) in RCA: 47] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
Abstract
Supersize me! Size-expanded DNA bases (xDNA) are able to encode natural DNA sequences in replication. In vitro experiments with a DNA polymerase show nucleotide incorporation opposite the xDNA bases with correct pairing. In vivo experiments using E. coli show that two xDNA bases (xA and xC, see picture) encode the correct replication partners.
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Affiliation(s)
- James C Delaney
- Department of Chemistry, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
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36
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Renders M, Abramov M, Froeyen M, Herdewijn P. Polymerase-catalysed incorporation of glucose nucleotides into a DNA duplex. Chemistry 2009; 15:5463-70. [PMID: 19308979 DOI: 10.1002/chem.200801951] [Citation(s) in RCA: 15] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
Abstract
The enzymatic recognition of six-membered ring nucleoside triphosphates--in particular the 6'-triphosphates of (beta-D-glucopyranosyl)thymine, (2',3'-dideoxy-beta-D-glucopyranosyl)thymine, (3',4'-dideoxy-beta-D-glucopyranosyl)thymine and (2',3'-dideoxy-beta-D-glucopyranosyl)adenine--was investigated. Despite the facts that the pyranose nucleic acids obtained by polymerisation of these monomers do not hybridise in solution with DNA and that the geometry of a DNA strand in a natural duplex differs from that of a pyranose nucleic acid, elongation of the DNA duplex with all four nucleotide analogues by Vent (exo(-)) polymerase was observed. Modelling experiments showed that hydrogen bonds are formed when 2',3'-dideoxy-beta-homo-T building blocks or beta-D-gluco-T building blocks are incorporated opposite adenosine residues in the template but not when they are incorporated opposite thymine residues in the template. The model shows a near perfect alignment of a secondary hydroxy group at the end of the primer and the alpha-phosphate group of the incoming triphosphate. The results of these experiments provide new information on the role of the active site of the enzyme in the polymerisation reaction.
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Affiliation(s)
- Marleen Renders
- Laboratory of Medicinal Chemistry, Rega Institute for Medical Research, Katholieke Universiteit Leuven, Minderbroedersstraat 10, 3000 Leuven, Belgium
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37
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Delaney J, Gao J, Liu H, Shrivastav N, Essigmann J, Kool E. Efficient Replication Bypass of Size-Expanded DNA Base Pairs in Bacterial Cells. Angew Chem Int Ed Engl 2009. [DOI: 10.1002/ange.200805683] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
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38
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D’Alonzo D, Guaragna A, Van Aerschot A, Herdewijn P, Palumbo G. De novo approach to l-anhydrohexitol nucleosides as building blocks for the synthesis of l-hexitol nucleic acids (l-HNA). Tetrahedron Lett 2008. [DOI: 10.1016/j.tetlet.2008.07.159] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/21/2022]
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39
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Lagoja IM, Marchand A, Van Aerschot A, Herdewijn P. Synthesis of 1,5-anhydrohexitol building blocks for oligonucleotide synthesis. ACTA ACUST UNITED AC 2008; Chapter 1:Unit 1.9. [PMID: 18428902 DOI: 10.1002/0471142700.nc0109s14] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Abstract
This unit describes in detail, the optimized preparations of 1,5-anhydrohexitol and the 1,5-anhydrohexitol building blocks for oligonucleotide synthesis (hG, hA, hC, hT).
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40
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Nauwelaerts K, Fisher M, Froeyen M, Lescrinier E, Aerschot AV, Xu D, DeLong R, Kang H, Juliano RL, Herdewijn P. Structural characterization and biological evaluation of small interfering RNAs containing cyclohexenyl nucleosides. J Am Chem Soc 2007; 129:9340-8. [PMID: 17616127 DOI: 10.1021/ja067047q] [Citation(s) in RCA: 37] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
CeNA is an oligonucleotide where the (deoxy)ribose sugars have been replaced by cyclohexenyl moieties. We have determined the NMR structure of a CeNA:RNA duplex and have modeled this duplex in the crystal structure of a PIWI protein. An N puckering of the ribose nucleosides, a 2H3 conformation of the cyclohexenyl nucleosides, and an A-like helix conformation of the backbone, which deviates from the standard A-type helix by a larger twist and a smaller slide, are observed. The model of the CeNA:RNA duplex bound to the PIWI protein does not show major differences in the interaction of the guide CeNA with the protein when compared with dsRNA, suggesting that CeNA modified oligonucleotides might be useful as siRNAs. Incorporation of one or two CeNA units in the sense or antisense strands of dsRNA led to similar or enhanced activity compared to unmodified siRNAs. This was tested by targeting inhibition of expression of the MDR1 gene with accompanying changes in P-glycoprotein expression, drug transport, and drug resistance.
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Affiliation(s)
- Koen Nauwelaerts
- Laboratory of Medicinal Chemistry, Rega Institute for Medical Research, Minderbroedersstraat 10, Leuven, Belgium
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41
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Corradini R, Sforza S, Tedeschi T, Marchelli R. Chirality as a tool in nucleic acid recognition: principles and relevance in biotechnology and in medicinal chemistry. Chirality 2007; 19:269-94. [PMID: 17345563 DOI: 10.1002/chir.20372] [Citation(s) in RCA: 109] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/31/2023]
Abstract
The understanding of the interaction of chiral species with DNA or RNA is very important for the development of new tools in biology and of new drugs. Several cases in which chirality is a crucial point in determining the DNA binding mode are reviewed and discussed, with the aim of illustrating how chirality can be considered as a tool for improving the understanding of mechanisms and the effectiveness of nucleic acid recognition. The review is divided into two parts: the former describes examples of chiral species interacting with DNA: intercalators, metal complexes, and groove binders; the latter part is dedicated to chirality in DNA analogs, with discussion of phosphate stereochemistry and chirality of ribose substitutes, in particular of peptide nucleic acids (PNAs) for which a number of works have been published recently dealing with the effect of chirality in DNA recognition. The discussion is intended to show how enantiomeric recognition originates at the molecular level, by exploiting the enormous progresses recently achieved in the field of structural characterization of complexes formed by nucleic acid with their ligands by crystallographic and spectroscopic methods. Examples of application of the DNA binding molecules described and the role of chirality in DNA recognition relevant for biotechnology or medicinal chemistry are reported.
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Affiliation(s)
- Roberto Corradini
- Dipartimento di Chimica Organica e Industriale, Università di Parma, I-4310 Parma, Italy.
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42
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Nauwelaerts K, Lescrinier E, Herdewijn P. Structure of the alpha-homo-DNA:RNA duplex and the function of twist and slide to catalogue nucleic acid duplexes. Chemistry 2007; 13:90-8. [PMID: 16991180 DOI: 10.1002/chem.200600363] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
High-resolution NMR studies of an alpha-homo-DNA:RNA duplex reveal the formation of a right-handed parallel-oriented helix. It differs significantly from a standard A- or B-type helix by a small twist value (26.2 degrees ), which leads to a helical pitch of 13.7 base pairs per helical turn, a negative inclination (-1.78 Angstrom) and a large x displacement (5.90 Angstrom). The rise (3.4 Angstrom) is similar to that found in B-DNA. The solution of this new helix structure has stimulated us to develop a mathematical and geometrical model based on slide and twist parameters to describe nucleic acid duplexes. All existing duplexes can be positioned within this landscape, which can be used to understand the helicalization process.
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Affiliation(s)
- Koen Nauwelaerts
- Laboratory of Medicinal Chemistry, Rega Institute for Medical Research, Minderbroedersstraat 10, 3000 Leuven, Belgium
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43
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Rapozzi V, Cogoi S, Xodo LE. Antisense locked nucleic acids efficiently suppress BCR/ABL and induce cell growth decline and apoptosis in leukemic cells. Mol Cancer Ther 2006; 5:1683-92. [PMID: 16891454 DOI: 10.1158/1535-7163.mct-06-0006] [Citation(s) in RCA: 16] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
Chronic myeloid leukemia (CML) develops when a hematopoietic stem cell acquires the Philadelphia chromosome carrying the BCR/ABL fusion gene. This gives the transformed cells a proliferative advantage over normal hematopoietic cells. Silencing the BCR/ABL oncogene by treatment with specific drugs remains an important therapeutic goal. In this work, we used locked nucleic acid (LNA)-modified oligonucleotides to silence BCR/ABL and reduce CML cell proliferation, as these oligonucleotides are resistant to nucleases and exhibit an exceptional affinity for cognate RNA. The anti-BCR/ABL oligonucleotides were designed as LNA-DNA gapmers, consisting of end blocks of 3/4 LNA monomers and a central DNA stretch of 13/14 deoxyribonucleotides. The gapmers were complementary to the b2a2 and b3a2 mRNA junctions with which they form hybrid duplexes that have melting temperatures of 79 degrees C and 75 degrees C, respectively, in a 20 mmol/L NaCl-buffered (pH 7.4) solution. Like DNA, the designed LNA-DNA gapmers were capable of activating RNase H and promote cleavage of the target b2a2 and b3a2 BCR/ABL mRNAs. The treatment of CML cells with junction-specific antisense gapmers resulted in a strong and specific reduction of the levels of BCR/ABL transcripts ( approximately 20% of control) and protein p210(BCR/ABL) ( approximately 30% of control). Moreover, the antisense oligonucleotides suppressed cell growth up to 40% of control and induced apoptosis, as indicated by the increase of caspase-3/7 activity in the treated cells. Finally, the b2a2-specific antisense gapmer used in combination with STI571 (imatinib mesylate), a tyrosine kinase inhibitor of p210(BCR/ABL), produced an enhanced antiproliferative effect in KYO-1 cells, which compared with K562 cells are refractory to STI571. The data of this study support the application of BCR/ABL antisense LNA-DNA gapmers, used either alone or in combination with STI571, as potential antileukemic agents.
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MESH Headings
- Antineoplastic Combined Chemotherapy Protocols/chemistry
- Antineoplastic Combined Chemotherapy Protocols/therapeutic use
- Apoptosis/genetics
- Benzamides
- Cell Proliferation/drug effects
- Fusion Proteins, bcr-abl/analysis
- Fusion Proteins, bcr-abl/antagonists & inhibitors
- Fusion Proteins, bcr-abl/genetics
- Humans
- Imatinib Mesylate
- Leukemia, Myelogenous, Chronic, BCR-ABL Positive/drug therapy
- Leukemia, Myelogenous, Chronic, BCR-ABL Positive/genetics
- Oligonucleotides
- Oligonucleotides, Antisense/chemistry
- Oligonucleotides, Antisense/therapeutic use
- Piperazines/therapeutic use
- Protein Kinase Inhibitors/therapeutic use
- Protein-Tyrosine Kinases/antagonists & inhibitors
- Pyrimidines/therapeutic use
- RNA, Messenger/antagonists & inhibitors
- Ribonuclease H/drug effects
- Transcription, Genetic/drug effects
- Tumor Cells, Cultured
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Affiliation(s)
- Valentina Rapozzi
- Department of Biomedical Sciences and Technologies, School of Medicine, P.le Kolbe 4, 33100 Udine, Italy
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44
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Lonkar PS, Kumar VA. trans-5-aminopipecolyl-aegPNA chimera: design, synthesis, and study of binding preferences with DNA/RNA in duplex/triplex mode. J Org Chem 2006; 70:6956-9. [PMID: 16095325 DOI: 10.1021/jo0506884] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
The design and synthesis of novel chiral PNA monomer based on trans-5-aminopipecolic acid is reported. The trans diequatorial disposition of the 1,4 ring substituents in six-membered 5-aminopipecolic acid derivative could be favorable over trans 1,3 axial-equatorial disposition in 4-aminopipecolic acid of PNA. Studies on the synthesis of trans-4/5-aminopipecolyl PNA-eagPNA chimeras and their binding preferences to DNA/RNA in duplex/triplex modes are described.
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Affiliation(s)
- Pallavi S Lonkar
- Division of Organic Chemistry (Synthesis), National Chemical Laboratory, Pune 411008, India.
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45
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Herdewijn P. The interplay between antiviral activity, oligonucleotide hybridisation and nucleic acids incorporation studies. Antiviral Res 2006; 71:317-21. [PMID: 16690140 DOI: 10.1016/j.antiviral.2006.04.004] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2006] [Revised: 04/04/2006] [Accepted: 04/04/2006] [Indexed: 11/22/2022]
Abstract
Nucleoside analogues have been the most successful antiviral compounds. Likewise, they are the most intriguing antiviral compounds, because of their structural relationship to natural nucleosides. This is also the reason why the design process of a potential selective antiviral nucleoside is so difficult. Too many natural processes (from cellular uptake to DNA incorporation) and too many enzymes are involved in their biological effect (activity/toxicity/catabolism/anabolism) to make the design process readily predictable. The relationship between the physicochemical and biochemical properties of nucleoside analogues and their antiviral activity is very complex and could only be understood on a very long term basis. Here we try to explain some of the reasoning that was made during the design process leading to new potent antivirals with a phosphonate functionality.
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Affiliation(s)
- Piet Herdewijn
- Rega Institute for Medical Research, Laboratory of Medicinal Chemistry, Minderbroedersstraat 10, B-3000 Leuven, Belgium.
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46
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Gogoi K, Gunjal AD, Kumar VA. Sugar-thioacetamide backbone in oligodeoxyribonucleosides for specific recognition of nucleic acids. Chem Commun (Camb) 2006:2373-5. [PMID: 16733584 DOI: 10.1039/b603958h] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
The amide linkage being shorter than the natural phosphate linkage, an additional atom is introduced into oligodeoxyribonucleosides (ODNs) with sugar-thioacetamide backbone that show very good RNA recognition properties.
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Affiliation(s)
- Khirud Gogoi
- Division of Organic Chemistry (Synthesis), National Chemical Laboratory, Pune, 411008, India
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47
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Kumar VA, Ganesh KN. Conformationally constrained PNA analogues: structural evolution toward DNA/RNA binding selectivity. Acc Chem Res 2005; 38:404-12. [PMID: 15895978 DOI: 10.1021/ar030277e] [Citation(s) in RCA: 149] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Since its discovery 12 years ago, aminoethylglycyl peptide nucleic acid (aeg-PNA) has emerged as one of the successful DNA mimics for potential therapeutic and diagnostic applications. An important requisite for in vivo applications that has received inadequate attention is engineering PNA analogues for able discrimination between DNA and RNA as binding targets. Our approach toward this aim is based on structural preorganization of the backbone to hybridization-competent conformations to impart binding selectivity. This strategy has allowed us to design locked PNAs to achieve specific hybridization with DNA or RNA with aims to increase the binding strength without losing the binding specificity. This Account presents results of our rationale in design of different conformationally constrained PNA analogues, their synthesis, and evaluation of hybridization specificities.
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Affiliation(s)
- Vaijayanti A Kumar
- Division of Organic Synthesis, National Chemical Laboratory, Pune 411008, India.
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48
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Maier T, Przylas I, Strater N, Herdewijn P, Saenger W. Reinforced HNA backbone hydration in the crystal structure of a decameric HNA/RNA hybrid. J Am Chem Soc 2005; 127:2937-43. [PMID: 15740130 DOI: 10.1021/ja045843v] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
The crystal structure of a decameric HNA/RNA (HNA = 2',3'-dideoxy-1',5'-anhydro-d-arabinohexitol nucleic acid) hybrid with the RNA sequence 5'-GGCAUUACGG-3' is the first crystal structure of a hybrid duplex between a naturally occurring nucleic acid and a strand, which is fully modified to contain a six-membered ring instead of ribose. The presence of four duplex helices in the asymmetric unit allows for a detailed discussion of hydration, which revealed a tighter spinelike backbone hydration for the HNA- than for the RNA-strands. The reinforced backbone hydration is suggested to contribute significantly to the exceptional stability of HNA-containing duplexes and might be one of the causes for the evolutionary preference for ribose-derived nucleic acids.
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Affiliation(s)
- Timm Maier
- Institut für Chemie der Freien Universität Berlin, Takustrasse 6, 14195 Berlin, Germany
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49
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Lonkar PS, Kumar VA. Design and synthesis of conformationally frozen peptide nucleic acid backbone: chiral piperidine PNA as a hexitol nucleic acid surrogate. Bioorg Med Chem Lett 2004; 14:2147-9. [PMID: 15080997 DOI: 10.1016/j.bmcl.2004.02.034] [Citation(s) in RCA: 19] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2003] [Revised: 02/09/2004] [Accepted: 02/09/2004] [Indexed: 11/30/2022]
Abstract
The design and facile synthesis of novel chiral piperidine PNA from naturally occurring 4-hydroxy-L-proline is reported. The stereospecific ring-expansion reaction to get six-membered piperidine derivative from 5-membered pyrrolidine derivative is exploited for this synthesis. The resulting conformationally constrained PNA is utilized for the synthesis of PNA mixmers and the concept is substantiated by UV-Tm studies of the resulting PNA(2):DNA complexes.
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Affiliation(s)
- Pallavi S Lonkar
- Division of Organic Chemistry, Synthesis, National Chemical Laboratory, Pune 411008, India
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Shirude PS, Kumar VA, Ganesh KN. (2S,5R/2R,5S)-Aminoethylpipecolyl aepip-aegPNA chimera: synthesis and duplex/triplex stability. Tetrahedron 2004. [DOI: 10.1016/j.tet.2004.07.080] [Citation(s) in RCA: 15] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
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