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Asanuma H, Kamiya Y, Kashida H, Murayama K. Xeno nucleic acids (XNAs) having non-ribose scaffolds with unique supramolecular properties. Chem Commun (Camb) 2022; 58:3993-4004. [DOI: 10.1039/d1cc05868a] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
DNA and RNA have significance as a genetic materials, therapeutic potential, and supramolecular properties. Advances in nucleic acid chemistry have enabled large-scale synthesis of DNA and RNA oligonucleotides and oligomers...
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2
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Nie P, Bai Y, Mei H. Synthetic Life with Alternative Nucleic Acids as Genetic Materials. Molecules 2020; 25:E3483. [PMID: 32751873 PMCID: PMC7435384 DOI: 10.3390/molecules25153483] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2020] [Revised: 07/29/2020] [Accepted: 07/29/2020] [Indexed: 12/20/2022] Open
Abstract
DNA, the fundamental genetic polymer of all living organisms on Earth, can be chemically modified to embrace novel functions that do not exist in nature. The key chemical and structural parameters for genetic information storage, heredity, and evolution have been elucidated, and many xenobiotic nucleic acids (XNAs) with non-canonical structures are developed as alternative genetic materials in vitro. However, it is still particularly challenging to replace DNAs with XNAs in living cells. This review outlines some recent studies in which the storage and propagation of genetic information are achieved in vivo by expanding genetic systems with XNAs.
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Affiliation(s)
| | | | - Hui Mei
- Shenzhen Key Laboratory of Synthetic Genomics, Guangdong Provincial Key Laboratory of Synthetic Genomics, CAS Key Laboratory of Quantitative Engineering Biology, Shenzhen Institute of Synthetic Biology, Shenzhen Institutes of Advanced Technology, Chinese Academy of Sciences, Shenzhen 518055, China; (P.N.); (Y.B.)
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3
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4
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Escudier JM, Payrastre C, Gerland B, Tarrat N. Convertible and conformationally constrained nucleic acids (C 2NAs). Org Biomol Chem 2019; 17:6386-6397. [PMID: 31210235 DOI: 10.1039/c9ob01150a] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Abstract
We introduce the concept of Convertible and Constrained Nucleic Acids (C2NAs). By means of the synthesis of a stereocontrolled N-propargyl dioxo-1,3,2-oxaza-phosphorinane as an internucleotidic linkage, the torsional angles α and β can adopt either the canonical (g-, t) set of values able to increase DNA duplex stability or the non-canonical (g+, t) set that stabilized the hairpin structure when installed within the loop moiety. With an appended propargyl function on the nitrogen atom of the six-membered ring, the copper catalysed Huisgen's cycloaddition (CuAAC click chemistry) allows for the introduction of new functionalities at any location on the nucleic acid chain while maintaining the properties brought by the geometrical constraint and the neutral internucleotidic linkage.
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Affiliation(s)
- Jean-Marc Escudier
- Laboratoire de Synthèse et Physico-Chimie de Molécules d'Intérêt Biologique, UMR CNRS 5068, Université Paul Sabatier, 118 route de Narbonne, 31062 Toulouse, France.
| | - Corinne Payrastre
- Laboratoire de Synthèse et Physico-Chimie de Molécules d'Intérêt Biologique, UMR CNRS 5068, Université Paul Sabatier, 118 route de Narbonne, 31062 Toulouse, France.
| | - Béatrice Gerland
- Laboratoire de Synthèse et Physico-Chimie de Molécules d'Intérêt Biologique, UMR CNRS 5068, Université Paul Sabatier, 118 route de Narbonne, 31062 Toulouse, France.
| | - Nathalie Tarrat
- CEMES, Université de Toulouse, CNRS, 29 rue Jeanne Marvig, Toulouse 31055, France
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Páv O, Barvík I, Liboska R, Petrová M, Šimák O, Rosenbergová Š, Novák P, Buděšínský M, Rosenberg I. Tuning the hybridization properties of modified oligonucleotides: from flexible to conformationally constrained phosphonate internucleotide linkages. Org Biomol Chem 2018; 15:701-707. [PMID: 27995239 DOI: 10.1039/c6ob02571d] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
The concept of conformational restriction leading to the preorganization of modified strands has proven to be successful and has afforded nucleic acid analogues with many interesting properties suitable for various biochemical applications. We utilized this concept to prepare a set of constrained oligonucleotides derived from 1,4-dioxane and 1,3-dioxolane-locked nucleoside phosphonates and evaluated their hybridization affinities towards their complementary RNA strands. With an increase of ΔTm per modification up to +5.2 °C, the hybridization experiments revealed the (S)-2',3'-O-phosphonomethylidene internucleotide linkage as one of the most Tm-increasing modifications reported to date. Moreover, we introduced a novel prediction tool for the pre-selection of potentially interesting chemical modifications of oligonucleotides.
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Affiliation(s)
- Ondřej Páv
- Institute of Organic Chemistry and Biochemistry of the CAS, Flemingovo náměstí 2, 16610 Prague, Czech Republic.
| | - Ivan Barvík
- Faculty of Mathematics and Physics, Institute of Physics, Charles University, Ke Karlovu 5, 12116 Prague, Czech Republic
| | - Radek Liboska
- Institute of Organic Chemistry and Biochemistry of the CAS, Flemingovo náměstí 2, 16610 Prague, Czech Republic.
| | - Magdalena Petrová
- Institute of Organic Chemistry and Biochemistry of the CAS, Flemingovo náměstí 2, 16610 Prague, Czech Republic.
| | - Ondřej Šimák
- Institute of Organic Chemistry and Biochemistry of the CAS, Flemingovo náměstí 2, 16610 Prague, Czech Republic. and Department of Chemistry of Natural Compounds, University of Chemistry and Technology, Technická 5, 16628 Prague, Czech Republic
| | - Šárka Rosenbergová
- Institute of Organic Chemistry and Biochemistry of the CAS, Flemingovo náměstí 2, 16610 Prague, Czech Republic.
| | - Pavel Novák
- Institute of Organic Chemistry and Biochemistry of the CAS, Flemingovo náměstí 2, 16610 Prague, Czech Republic.
| | - Miloš Buděšínský
- Institute of Organic Chemistry and Biochemistry of the CAS, Flemingovo náměstí 2, 16610 Prague, Czech Republic.
| | - Ivan Rosenberg
- Institute of Organic Chemistry and Biochemistry of the CAS, Flemingovo náměstí 2, 16610 Prague, Czech Republic.
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6
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Goyenvalle A, Leumann C, Garcia L. Therapeutic Potential of Tricyclo-DNA antisense oligonucleotides. J Neuromuscul Dis 2018; 3:157-167. [PMID: 27854216 PMCID: PMC5271482 DOI: 10.3233/jnd-160146] [Citation(s) in RCA: 25] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/16/2023]
Abstract
Oligonucleotide therapeutics hold great promise for the treatment of various diseases and the antisense field is constantly gaining interest due to the development of more potent and nuclease resistant chemistries. Despite a rather low success rate with only three antisense drugs being clinically approved, the frontiers of AON therapeutic applications have increased over the past three decades and continue to expand thanks to a steady increase in understanding the mechanisms of action of these molecules, progress in chemical modification and delivery. In this review, we will examine the recent advances obtained with the tricyclo-DNA chemistry which displays unique pharmacological properties and unprecedented uptake in many tissues after systemic administration. We will review their specific properties and their therapeutic applications mainly for neuromuscular disorders, including exon-skipping for Duchenne muscular dystrophy and exon-inclusion for spinal muscular atrophy, but also aberrant splicing correction for Pompe disease. Finally, we will discuss their advantages and potential limitations, with a focus on the need for careful toxicological screen early in the process of AON drug development.
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Affiliation(s)
- Aurelie Goyenvalle
- Université de Versailles St- Quentin, U1179 INSERM, UFR des Sciences de la Santé - LIA BAHN CSM, France
| | - Christian Leumann
- Department of Chemistry & Biochemistry, University of Bern, Switzerland
| | - Luis Garcia
- Université de Versailles St- Quentin, U1179 INSERM, UFR des Sciences de la Santé - LIA BAHN CSM, France
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7
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Plashkevych O, Li Q, Chattopadhyaya J. How RNase HI (Escherichia coli) promoted site-selective hydrolysis works on RNA in duplex with carba-LNA and LNA substituted antisense strands in an antisense strategy context? MOLECULAR BIOSYSTEMS 2018; 13:921-938. [PMID: 28352859 DOI: 10.1039/c6mb00762g] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
A detailed kinetic study of 36 single modified AON-RNA heteroduplexes shows that substitution of a single native nucleotide in the antisense strand (AON) by locked nucleic acid (LNA) or by diastereomerically pure carba-LNA results in site-dependent modulation of RNase H promoted cleavage of complementary mRNA strands by 2 to 5 fold at 5'-GpN-3' cleavage sites, giving up to 70% of the RNA cleavage products. The experiments have been performed using RNase HI of Escherichia coli. The 2nd best cleavage site, being the 5'-ApN-3' sites, cleaves up to 23%, depending upon the substitution site in 36 isosequential complementary AONs. A comparison of the modified AON promoted RNA cleavage rates with that of the native AON shows that sequence-specificity is considerably enhanced as a result of modification. Clearly, relatively weaker 5'-purine (Pu)-pyrimidine (Py)-3' stacking in the complementary RNA strand is preferred (giving ∼90% of total cleavage products), which plays an important role in RNase H promoted RNA cleavage. A plausible mechanism of RNase H mediated cleavage of the RNA has been proposed to be two-fold, dictated by the balancing effect of the aromatic character of the purine aglycone: first, the locally formed 9-guanylate ion (pKa 9.3, ∼18-20% N1 ionized at pH 8) alters the adjoining sugar-phosphate backbone around the scissile phosphate, transforming its sugar N/S conformational equilibrium, to preferential S-type, causing preferential cleavage at 5'-GpN-3' sites around the center of 20 mer complementary mRNA. Second, the weaker nearest-neighbor strength of 5'-Pu-p-Py-3' stacking promotes preferential 5'-GpN-3' and 5'-ApN-3' cleavage, providing ∼90% of the total products, compared to ∼50% in that of the native one, because of the cLNA/LNA substituent effect on the neighboring 5'-Pu-p-Py-3' sites, providing both local steric flexibility and additional hydration. This facilitates both the water and water/Mg2+ ion availability at the cleavage site causing sequence-specific hydrolysis of the phosphodiester bond of scissile phosphate. The enhancement of the total rate of cleavage of the complementary mRNA strand by up to 25%, presented in this work, provides opportunities to engineer a single modification site in appropriately substituted AONs to design an effective antisense strategy based on the nucleolytic stability of the AON strand versus RNase H capability to cleave the complementary RNA strand.
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Affiliation(s)
- Oleksandr Plashkevych
- Chemical Biology Program, Department of Cell and Molecular Biology, Biomedical Center, Uppsala University, Box 581, SE-751 23 Uppsala, Sweden.
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8
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Plashkevych O, Upadhayaya RS, Chattopadhyaya J. Carbocyclic C-C Bond Formation: Intramolecular Radical Ring Closure to Yield Diastereomerically Pure (7'S-Me- or 7'R-Me-) Carba-LNA Nucleotide Analogs. ACTA ACUST UNITED AC 2017. [PMID: 28628208 DOI: 10.1002/cpnc.29] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
Abstract
In light of the impressive gene-silencing properties of carba-LNA modified oligo DNA and RNA, both in antisense RNA and siRNA approaches, which have been confirmed as proof-of-concept for biochemical applications in post-transcriptional gene silencing, we envision the true potential of carba-LNA modifications to be revealed soon. Herein we provide detailed protocols for synthesis of carba-LNA-A, -G, -5-Me C, and -T nucleosides on a medium/large scale (gram scale), as well as important guidelines for incorporation of these modified carba-LNAs into DNA or RNA oligonucleotides. Creation of a stereoselective C-C bond during the 5-exo radical intramolecular cyclization involves trapping of a C2' radical intermediate intramolecularly by the vicinal double bond of a C4'-tethered ─CH2 -CH═CH2 group. All diastereomers of substituted carba-LNAs are now available in pure form. The present procedure allows carba-LNA to be commercialized for medicinal or biotechnological purposes. © 2017 by John Wiley & Sons, Inc.
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Affiliation(s)
| | - Ram Shankar Upadhayaya
- Department of Cell and Molecular Biology, Uppsala University, Uppsala, Sweden.,Bioimics AB, Uppsala, Sweden
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9
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Evéquoz D, Leumann CJ. Probing the Backbone Topology of DNA: Synthesis and Properties of 7',5'-Bicyclo-DNA. Chemistry 2017; 23:7953-7968. [PMID: 28262999 DOI: 10.1002/chem.201700435] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2017] [Indexed: 01/18/2023]
Abstract
We describe the synthesis and pairing properties of the novel DNA analogue 7',5'-bicyclo(bc)-DNA. In this analogue, the point of attachment of the connecting phosphodiester group is switched from the 3' to the 7' position of the underlying bicyclic sugar unit and is thus in a topological position that is inaccessible in natural DNA. The corresponding phosphoramidite building blocks carrying all natural nucleobases were synthesized and incorporated into oligonucleotides. From Tm experiments of duplexes with complementary DNA and RNA we find that single modifications are generally well tolerated with some variability as to the nature of the nucleobase. Fully modified oligonucleotides show low affinity for RNA and DNA complements. However, they form antiparallel homo-duplexes with similar thermal stability as DNA. CD spectra of the homo-duplexes show distinct changes in the helix conformation compared to natural DNA. A conformational analysis at the ab initio level of the mononucleosides revealed two minimal energy structures which primarily deviate in the conformation of the cyclopentane ring. Molecular dynamics simulation of a 7',5'-bc-DNA homo-duplex revealed a right-handed structure with a smaller helical rise and a significantly wider minor groove compared to DNA. Interestingly, this duplex is characterized by an atypical, alternating 6'-endo/6'-exo conformational pattern of consecutive nucleotides which seems to be responsible for the poor binding to natural nucleic acids.
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Affiliation(s)
- Damien Evéquoz
- Department of Chemistry and Biochemistry, University of Bern, Freiestrasse 3, 3012, Bern, Switzerland
| | - Christian J Leumann
- Department of Chemistry and Biochemistry, University of Bern, Freiestrasse 3, 3012, Bern, Switzerland
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10
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Sontakke VA, Lawande PP, Kate AN, Khan A, Joshi R, Kumbhar AA, Shinde VS. Antiproliferative activity of bicyclic benzimidazole nucleosides: synthesis, DNA-binding and cell cycle analysis. Org Biomol Chem 2016; 14:4136-45. [DOI: 10.1039/c6ob00527f] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
Bicyclic benzimidazole nucleosides were synthesized from d-glucose as a starting material. DNA binding, antiproliferative activity and cell cycle analysis were performed.
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Affiliation(s)
- Vyankat A. Sontakke
- Department of Chemistry
- Savitribai Phule Pune University (formerly University of Pune)
- Pune-411007
- India
| | - Pravin P. Lawande
- Department of Chemistry
- Savitribai Phule Pune University (formerly University of Pune)
- Pune-411007
- India
| | - Anup N. Kate
- Department of Chemistry
- Savitribai Phule Pune University (formerly University of Pune)
- Pune-411007
- India
| | - Ayesha Khan
- Department of Chemistry
- Savitribai Phule Pune University (formerly University of Pune)
- Pune-411007
- India
| | - Rakesh Joshi
- Institute of Bioinformatics and Biotechnology
- Savitribai Phule Pune University
- Pune-411007
- India
| | - Anupa A. Kumbhar
- Department of Chemistry
- Savitribai Phule Pune University (formerly University of Pune)
- Pune-411007
- India
| | - Vaishali S. Shinde
- Department of Chemistry
- Savitribai Phule Pune University (formerly University of Pune)
- Pune-411007
- India
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11
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Sarkar R, Debnath M, Maji K, Haldar D. Solvent assisted structural diversity: supramolecular sheet and double helix of a short aromatic γ-peptide. RSC Adv 2015. [DOI: 10.1039/c5ra12831e] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022] Open
Abstract
Solvent interaction has a significant effect on the molecular motions, folding and self-assembly of short aromatic γ-peptides that leads to a change in initial helical conformation.
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Affiliation(s)
- Rajib Sarkar
- Department of Chemical Sciences
- Indian Institute of Science Education and Research Kolkata
- India
| | - Mintu Debnath
- Department of Chemical Sciences
- Indian Institute of Science Education and Research Kolkata
- India
| | - Krishnendu Maji
- Department of Chemical Sciences
- Indian Institute of Science Education and Research Kolkata
- India
| | - Debasish Haldar
- Department of Chemical Sciences
- Indian Institute of Science Education and Research Kolkata
- India
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12
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Dugovic B, Wagner M, Leumann CJ. Structure/affinity studies in the bicyclo-DNA series: Synthesis and properties of oligonucleotides containing bc(en)-T and iso-tricyclo-T nucleosides. Beilstein J Org Chem 2014; 10:1840-7. [PMID: 25161745 PMCID: PMC4142851 DOI: 10.3762/bjoc.10.194] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2014] [Accepted: 07/22/2014] [Indexed: 12/11/2022] Open
Abstract
We present the synthesis of the two novel nucleosides iso-tc-T and bc(en)-T, belonging to the bicyclo-/tricyclo-DNA molecular platform. In both modifications the torsion around C6'-C7' within the carbocyclic ring is planarized by either the presence of a C6'-C7' double bond or a cyclopropane ring. Structural analysis of these two nucleosides by X-ray analysis reveals a clear preference of torsion angle γ for the gauche orientation with the furanose ring in a near perfect 2'-endo conformation. Both modifications were incorporated into oligodeoxynucleotides and their thermal melting behavior with DNA and RNA as complements was assessed. We found that the iso-tc-T modification was significantly more destabilizing in duplex formation compared to the bc(en)-T modification. In addition, duplexes with complementary RNA were less stable as compared to duplexes with DNA as complement. A structure/affinity analysis, including the already known bc-T and tc-T modifications, does not lead to a clear correlation of the orientation of torsion angle γ with DNA or RNA affinity. There is, however, some correlation between furanose conformation (N- or S-type) and affinity in the sense that a preference for a 3'-endo like conformation is associated with a preference for RNA as complement. As a general rule it appears that T m data of single modifications with nucleosides of the bicyclo-/tricyclo-DNA platform within deoxyoligonucleotides are not predictive for the stability of fully modified oligonucleotides.
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Affiliation(s)
- Branislav Dugovic
- Department of Chemistry and Biochemistry, University of Bern, Freiestrasse 3, CH-3012 Bern, Switzerland
| | - Michael Wagner
- Department of Chemistry and Biochemistry, University of Bern, Freiestrasse 3, CH-3012 Bern, Switzerland
| | - Christian J Leumann
- Department of Chemistry and Biochemistry, University of Bern, Freiestrasse 3, CH-3012 Bern, Switzerland
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13
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Hollenstein M, Leumann CJ. Synthesis and biochemical characterization of tricyclothymidine triphosphate (tc-TTP). Chembiochem 2014; 15:1901-4. [PMID: 25044722 DOI: 10.1002/cbic.201402116] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2014] [Indexed: 01/03/2023]
Abstract
Tricyclo-DNA (tc-DNA) is a conformationally restricted oligonucleotide analogue that exhibits promising properties as a robust antisense agent. Here we report on the synthesis and biochemical characterization of tc-TTP, the triphosphate of a tc-DNA nucleoside containing the base thymine. Tc-TTP turned out to be a substrate for the Vent (exo(-) ) DNA polymerase, a polymerase that allows for multiple incorporations of tc-T nucleotides under primer extension reaction conditions. However, the substrate acceptance is rather low, as also observed for other sugar-modified analogues. Tc-TTP and tc-nucleotide-containing templates do not sustain enzymatic polymerization under physiological conditions; this indicates that tc-DNA-based antisense agents will not enter natural metabolic pathways that lead to long-term toxicity.
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Affiliation(s)
- Marcel Hollenstein
- Department of Chemistry and Biochemistry, University of Bern, Freiestrasse 3, 3012 Bern (Switzerland).
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14
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Yueh H, Pal A, Chang K, Schlegel MK, McLaughlin LW. Synthesis and NMR assignment of the two diastereomers of 8,6'-cyclo-2',6'-dideoxyadenosine. NUCLEOSIDES NUCLEOTIDES & NUCLEIC ACIDS 2013; 32:320-32. [PMID: 23638925 DOI: 10.1080/15257770.2013.778997] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/26/2022]
Abstract
We herein present the first synthesis and characterization of the two C5' diastereomers of 8,6'-cyclo-2',6'-dideoxyadenosine. Starting from commercially available 2'-deoxyadenosine, the target cyclonucleosides were synthesized in 11 linear steps. Following a zinc-mediated cyclization reaction to form the seven-membered ring, the stereochemistry of the newly formed chiral center was established using two-dimensional NOESY NMR experiments.
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Affiliation(s)
- Han Yueh
- Department of Chemistry, Merkert Chemistry Center, Boston College, Chestnut Hill, Massachusetts 02467, USA
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15
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Hanessian S, Schroeder BR, Merner BL, Chen B, Swayze EE, Seth PP. Synthesis of cis- and trans-α-l-[4.3.0]bicyclo-DNA monomers for antisense technology: methods for the diastereoselective formation of bicyclic nucleosides. J Org Chem 2013; 78:9051-63. [PMID: 23937280 DOI: 10.1021/jo401166q] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Abstract
Two α-L-ribo-configured bicyclic nucleic acid modifications, represented by analogues 12 and 13, which are epimeric at C3' and C5' have been synthesized using a carbohydrate-based approach to build the bicyclic core structure. An intramolecular L-proline-mediated aldol reaction was employed to generate the cis-configured ring junction of analogue 12 and represents a rare application of this venerable organocatalytic reaction to a carbohydrate system. In the case of analogue 13, where a trans-ring junction was desired, an intermolecular diastereoselective Grignard reaction followed by ring-closing metathesis was used. In order to set the desired stereochemistry at the C5' positions of both nucleoside targets, a study of diastereoselective Lewis acid mediated allylation reactions on a common bicyclic aldehyde precursor was carried out. Analogue 12 was incorporated in oligonucleotide sequences, and thermal denaturation experiments indicate that it is destabilizing when paired with complementary DNA and RNA. However, this construct shows a significant improvement in nuclease stability relative to a DNA oligonucleotide.
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Affiliation(s)
- Stephen Hanessian
- Department of Chemistry, Université de Montréal , Montréal, Québec H3C 3J7, Canada
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16
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Gerber AB, Leumann CJ. Synthesis and properties of isobicyclo-DNA. Chemistry 2013; 19:6990-7006. [PMID: 23613358 DOI: 10.1002/chem.201300487] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2013] [Indexed: 11/11/2022]
Abstract
We present the synthesis of the isobicyclo-DNA building blocks with the nucleobases A, C, G and T, as well as biophysical and biological properties of oligonucleotides derived thereof. The synthesis of the sugar part was achieved in 5 steps starting from a known intermediate of the tricyclo-DNA synthesis. Dodecamers containing single isobicyclo-thymidine incorporations, fully modified A- and T-containing sequences, and fully modified oligonucleotides containing all four bases were synthesized and characterized. Isobicyclo-DNA forms stable duplexes with natural nucleic acids with a pronounced preference for DNA over RNA as complements. The most stable duplexes, however, arise by self-pairing. Isobicyclo-DNA forms preferentially B-DNA-like duplexes with DNA and A-like duplexes with complementary RNA as determined by circular dichroism (CD) spectroscopy. Self-paired duplexes show a yet unknown structure, as judged from CD spectroscopy. Biochemical tests revealed that isobicyclo-DNA is stable in fetal bovine serum and does not elicit RNaseH activity.
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Affiliation(s)
- Anna-Barbara Gerber
- Department of Chemistry & Biochemistry, University of Bern, Freiestrasse 3, 3012 Bern, Switzerland
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17
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Konar AD. Can a single pyridinedicarboxylic acid be ample enough to nucleate supramolecular double helices in enantiomeric pseudopeptides? CrystEngComm 2013. [DOI: 10.1039/c3ce26912d] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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18
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Zhou C, Chattopadhyaya J. Intramolecular free-radical cyclization reactions on pentose sugars for the synthesis of carba-LNA and carba-ENA and the application of their modified oligonucleotides as potential RNA targeted therapeutics. Chem Rev 2012; 112:3808-32. [PMID: 22530946 DOI: 10.1021/cr100306q] [Citation(s) in RCA: 39] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Affiliation(s)
- Chuanzheng Zhou
- Chemical Biology Program, Department of Cell and Molecular Biology, Biomedical Center, Uppsala University, Sweden
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19
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Abstract
The combined use of surface plasmon resonance (SPR) and modified or mimic oligonucleotides have expanded diagnostic capabilities of SPR-based biosensors and have allowed detailed studies of molecular recognition processes. This review summarizes the most significant advances made in this area over the past 15 years. Functional and conformationally restricted DNA analogs (e.g., aptamers and PNAs) when used as components of SPR biosensors contribute to enhance the biosensor sensitivity and selectivity. At the same time, the SPR technology brings advantages that allows forbetter exploration of underlying properties of non-natural nucleic acid structures such us DNAzymes, LNA and HNA.
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Affiliation(s)
- Roberta D'Agata
- Dipartimento di Scienze Chimiche, Università di Catania, Catania, Italy
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20
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Maity SK, Maity S, Jana P, Haldar D. Supramolecular double helix from capped γ-peptide. Chem Commun (Camb) 2012; 48:711-3. [DOI: 10.1039/c1cc15570a] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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21
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Eschenmoser A. Ätiologie potentiell primordialer Biomolekül-Strukturen: Vom Vitamin B12 zu den Nukleinsäuren und der Frage nach der Chemie der Entstehung des Lebens - ein Rückblick. Angew Chem Int Ed Engl 2011. [DOI: 10.1002/ange.201103672] [Citation(s) in RCA: 50] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
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22
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Eschenmoser A. Etiology of potentially primordial biomolecular structures: from vitamin B12 to the nucleic acids and an inquiry into the chemistry of life's origin: a retrospective. Angew Chem Int Ed Engl 2011; 50:12412-72. [PMID: 22162284 DOI: 10.1002/anie.201103672] [Citation(s) in RCA: 135] [Impact Index Per Article: 10.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2011] [Indexed: 11/10/2022]
Abstract
"We'll never be able to know" is a truism that leads to resignation with respect to any experimental effort to search for the chemistry of life's origin. But such resignation runs radically counter to the challenge imposed upon chemistry as a natural science. Notwithstanding the prognosis according to which the shortest path to understanding the metamorphosis of the chemical into the biological is by way of experimental modeling of "artificial chemical life", the scientific search for the route nature adopted in creating the life we know will arguably never truly end. It is, after all, part of the search for our own origin.
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Affiliation(s)
- Albert Eschenmoser
- Organisch-chemisches Laboratorium der ETH Zürich, Hönggerberg, Wolfgang-Pauli-Str. 10, CHI H309, CH-8093 Zürich, Switzerland
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23
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Terrazas M, Ocampo SM, Perales JC, Marquez VE, Eritja R. Effect of north bicyclo[3.1.0]hexane 2'-deoxy-pseudosugars on RNA interference: a novel class of siRNA modification. Chembiochem 2011; 12:1056-65. [PMID: 21452187 DOI: 10.1002/cbic.201000791] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/27/2010] [Indexed: 01/15/2023]
Abstract
North bicyclo methanocarba thymidine (T(N)) nucleosides were substituted into siRNAs to investigate the effect of bicyclo[3.1.0]hexane 2'-deoxy-pseudosugars on RNA interference activity. Here we provide evidence that these modified siRNAs are compatible with the intracellular RNAi machinery. We studied the effect of the T(N) modification in a screen involving residue-specific changes in an siRNA targeting Renilla luciferase and we applied the most effective pattern of modification to the knockdown of murine tumor necrosis factor (TNF-α). We also showed that incorporation of T(N) units into siRNA duplexes increased their thermal stabilities, substantially enhanced serum stabilities, and decreased innate immunostimulation. Comparative RNAi studies involving the T(N) substitution and locked nucleic acids (LNAs) showed that the gene-silencing activities of T(N) -modified siRNAs were comparable to those obtained with the LNA modification. An advantage of the North 2'-deoxy-methanocarba modification is that it may be explored further in the future by changing the 2'-position. The results from these studies suggest that this modification might be valuable for the development of siRNAs for therapeutic applications.
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Affiliation(s)
- Montserrat Terrazas
- Institute for Research in Biomedicine, CIBER-BBN, Spanish Research Council, Barcelona, Spain.
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24
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Lebreton J, Escudier JM, Arzel L, Len C. Synthesis of Bicyclonucleosides Having a C−C Bridge. Chem Rev 2010; 110:3371-418. [DOI: 10.1021/cr800465j] [Citation(s) in RCA: 54] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Affiliation(s)
- Jacques Lebreton
- Université de Nantes, CNRS, Laboratoire CEISAM-UMR-CNRS 6230, Faculté des Sciences et des Techniques, 2 rue de la Houssinière, BP 92208, 44322 Nantes Cedex 3, France, Université Paul Sabatier Laboratoire de Synthèse et Physicochimie des Molécules d’Intérêt Biologique - UMR-CNRS 5068, 31062 Toulouse Cedex, France, and Université de Technologie de Compiègne, Ecole Supérieure de Chimie Organique Minérale, EA 4297, Transformations Intégrées de la Matière Renouvelable, 1 allée du Réseau Jean-Marie Buckmaster,
| | - Jean-Marc Escudier
- Université de Nantes, CNRS, Laboratoire CEISAM-UMR-CNRS 6230, Faculté des Sciences et des Techniques, 2 rue de la Houssinière, BP 92208, 44322 Nantes Cedex 3, France, Université Paul Sabatier Laboratoire de Synthèse et Physicochimie des Molécules d’Intérêt Biologique - UMR-CNRS 5068, 31062 Toulouse Cedex, France, and Université de Technologie de Compiègne, Ecole Supérieure de Chimie Organique Minérale, EA 4297, Transformations Intégrées de la Matière Renouvelable, 1 allée du Réseau Jean-Marie Buckmaster,
| | - Laurence Arzel
- Université de Nantes, CNRS, Laboratoire CEISAM-UMR-CNRS 6230, Faculté des Sciences et des Techniques, 2 rue de la Houssinière, BP 92208, 44322 Nantes Cedex 3, France, Université Paul Sabatier Laboratoire de Synthèse et Physicochimie des Molécules d’Intérêt Biologique - UMR-CNRS 5068, 31062 Toulouse Cedex, France, and Université de Technologie de Compiègne, Ecole Supérieure de Chimie Organique Minérale, EA 4297, Transformations Intégrées de la Matière Renouvelable, 1 allée du Réseau Jean-Marie Buckmaster,
| | - Christophe Len
- Université de Nantes, CNRS, Laboratoire CEISAM-UMR-CNRS 6230, Faculté des Sciences et des Techniques, 2 rue de la Houssinière, BP 92208, 44322 Nantes Cedex 3, France, Université Paul Sabatier Laboratoire de Synthèse et Physicochimie des Molécules d’Intérêt Biologique - UMR-CNRS 5068, 31062 Toulouse Cedex, France, and Université de Technologie de Compiègne, Ecole Supérieure de Chimie Organique Minérale, EA 4297, Transformations Intégrées de la Matière Renouvelable, 1 allée du Réseau Jean-Marie Buckmaster,
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25
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Stauffiger A, Leumann CJ. Screening the Structural Space of Bicyclo-DNA: Synthesis and Thermal Melting Properties of bc4,3-DNA. European J Org Chem 2009. [DOI: 10.1002/ejoc.200801034] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
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26
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Luisier S, Leumann CJ. Screening the structural and functional properties of bicyclo-DNA: bc(ox)-DNA. Chembiochem 2009; 9:2244-53. [PMID: 18756553 DOI: 10.1002/cbic.200800322] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
The synthesis of two novel pyrimidine bicyclonucleosides (bc(ox)-nucleosides) has been accomplished. These bicyclonucleosides each carry a lipophilic benzyloxime substituent on the carbocyclic ring and show improved conformational similarity to 2'-deoxyribonucleosides as shown by their X-ray structures. The thymine-containing bc(ox)-nucleoside was converted into the corresponding phosphoramidite building block and incorporated into oligodeoxyribonucleotides by standard phosphoramidite chemistry. T(m) data with complementary RNA and DNA were measured and compared to corresponding cases of natural and unfunctionalized bc-DNA. It was found that single incorporations of bc(ox) residues destabilize duplexes by roughly 5 degrees C per modification. The destabilization was found to be due to the oxime substituent and not to the bicyclic scaffold itself. No significant alteration of the base-pairing selectivity as a function of the modification was observed. With RNA (but not with DNA) as a complement the relative thermal destabilization of bc(ox)-oligothymidylates was gradually reduced and converted into a stabilizing interaction with increasing numbers of consecutive modifications. While no cellular uptake of bc(ox)-oligonucleotides into HeLa cells occurred without transfecting agents, a significant increase in the transfection rate relative to unmodified DNA was observed in complexation with lipofectamine.
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Affiliation(s)
- Samuel Luisier
- Department of Chemistry and Biochemistry, University of Bern, Switzerland
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27
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Schlegel M, Xie X, Zhang L, Meggers E. Insight into the High Duplex Stability of the Simplified Nucleic Acid GNA. Angew Chem Int Ed Engl 2009; 48:960-3. [DOI: 10.1002/anie.200803472] [Citation(s) in RCA: 38] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
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28
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Schlegel M, Xie X, Zhang L, Meggers E. Insight into the High Duplex Stability of the Simplified Nucleic Acid GNA. Angew Chem Int Ed Engl 2009. [DOI: 10.1002/ange.200803472] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
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29
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Abstract
There is a general interest in designing biomimetic materials, such as the double helical structures of biopolymers, by the self-assembly of synthetic organic moieties. This interest stems from their structural versatility, biocompatibility, robustness and a relative experimental simplicity. The self-assembly process requires a combination of several non-covalent interactions between two intertwined strands. Besides the combination of metal-ligand binding, base pair interactions and peptide stacking interactions, in the last few years, hybridized synthetic foldamers have proven to be useful in this context. The molecular rigidity and the extent of intra- vs. intermolecular interactions within the strand play an important role in the intertwining processes. A dynamic equilibrium exists between the monomer and the dimer. In general, the combination of the enthalpic gain (from the interaction of the two strands) and entropic loss (upon hybridization) controls the duplex formation. There are now a variety of metal-free double helices from abiotic backbones, with potential applications in antigene therapy, studies on evolution and conducting materials. A tutorial review of some general guidelines and illustrative examples is presented.
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Affiliation(s)
- Debasish Haldar
- Institut für Organische Chemie, Fachbereich Chemie, Universität Duisburg-Essen, Universitätsstrasse 2, 45141 Essen, Germany
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30
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Dupouy C, Iché-Tarrat N, Durrieu MP, Vigroux A, Escudier JM. Alpha,beta-D-CNA induced rigidity within oligonucleotides. Org Biomol Chem 2008; 6:2849-51. [PMID: 18688476 DOI: 10.1039/b809775e] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Introduction of alpha,beta-D-CNA featuring canonical values of the torsional angles alpha and beta within oligonucleotides leads to an overall stabilization and improved rigidity of the duplex DNA as demonstrated by UV experiments, circular dichroism and corroborated by molecular dynamics simulations.
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Affiliation(s)
- Christelle Dupouy
- Laboratoire de Synthèse et Physico-Chimie de Molécules d'Intérêt Biologique UMR 5068 CNRS, Université Paul Sabatier, 31062, Toulouse Cedex 9, France
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31
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Nakane M, Ichikawa S, Matsuda A. Triazole-linked dumbbell oligodeoxynucleotides with NF-kappaB binding ability as potential decoy molecules. J Org Chem 2008; 73:1842-51. [PMID: 18237187 DOI: 10.1021/jo702459b] [Citation(s) in RCA: 59] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Triazole-cross-linked oligodeoxynucleotides were synthesized with use of the Cu(I) catalyzed alkyne-azide cycloaddition (CuAAC) with oligodeoxynucleotides possessing N-3-(azidoethyl)thymidine and N-3-(propargyl)thymidine at the 3'- and 5'-termini. The newly synthesized oligodeoxynucleotides were thermally stable and their global structures retained those of non-cross-linked oligodeoxynucleotides. The newly synthesized dumbbell oligodeoxynucleotides showed excellent stability against snake venom phosphodiesterase (3'-exonuclease) and high thermal stability, which are necessary for decoy molecules to achieve biological responses leading to alteration of gene expression. Moreover, dumbbell oligodeoxynucleotides have the ability to bind to NF-kappaB p50 homodimer within a similar range to that of a control double-stranded decoy oligodeoxynucleotide. This strategy allows us to prepare triazole-linked dumbbell oligodeoxynucleotides with a range of loop lengths, and we found that the greater the number of the thymidine residues constituting the loop region, the higher the binding affinity of the dumbbell oligodeoxynucleotides to the nuclear factor kappaB. This means that a protein binding ability of the dumbbell oligodeoxynucleotides could be modulated by altering the loop size. This study clearly shows that cross-linking by the triazole structure does not prevent the dumbbell oligodeoxynucleotides from binding to the nuclear factor kappaB transcription factor. Therefore, the results obtained conclusively demonstrate that the triazole cross-linked dumbbell oligodeoxynucleotides could be proposed as powerful decoy molecules.
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Affiliation(s)
- Masanori Nakane
- Faculty of Pharmaceutical Sciences, Hokkaido University, Sapporo 060-0812, Japan
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32
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Dupouy C, Iché-Tarrat N, Durrieu MP, Rodriguez F, Escudier JM, Vigroux A. Watson-Crick base-pairing properties of nucleic acid analogues with stereocontrolled alpha and beta torsion angles (alpha,beta-D-CNAs). Angew Chem Int Ed Engl 2007; 45:3623-7. [PMID: 16639765 DOI: 10.1002/anie.200504475] [Citation(s) in RCA: 32] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Affiliation(s)
- Christelle Dupouy
- Laboratoire de Synthèse et Physico-Chimie de Molécules d'Intérêt Biologique, UMR 5068 CNRS, Université Paul Sabatier, 31062 Toulouse Cedex 9, France
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33
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Schlegel MK, Peritz AE, Kittigowittana K, Zhang L, Meggers E. Duplex formation of the simplified nucleic acid GNA. Chembiochem 2007; 8:927-32. [PMID: 17465439 DOI: 10.1002/cbic.200600435] [Citation(s) in RCA: 72] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Abstract
Glycol nucleic acid (GNA) has an acyclic backbone of propylene glycol nucleosides that are connected by phosphodiester bonds. This paper characterizes the duplex-formation properties of this simplified nucleic acid. Although single and multiple GNA nucleotides are highly destabilizing if incorporated into DNA duplexes, the two enantiomeric oligomers (S)-GNA and (R)-GNA form antiparallel homoduplexes that are thermally and thermodynamically significantly more stable than analogous duplexes of DNA and RNA. The salt-dependence and Watson-Crick-pairing fidelity of GNA duplexes are similar to those of DNA duplexes, but, apparently, the 2'-deoxyribonucleotide and the propylene glycol backbones are not compatible with each other. This conclusion is further supported by cross-pairing experiments. Accordingly, both (S)- and (R)-GNA strands do not generally pair with DNA. However, (S)-GNA, but not (R)-GNA, forms stable heteroduplexes with RNA in sequences that are low in G:C content. Altogether, the high stability and fidelity of GNA duplex formation in combination with the economical accessibility of propylene glycol building blocks for oligonucleotide synthesis render GNA an attractive candidate for the design of self-assembling materials. They further suggest that GNA could be considered as a potential candidate for a predecessor of RNA during the evolution of life on Earth.
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Affiliation(s)
- Mark K Schlegel
- Department of Chemistry, University of Pennsylvania, Philadelphia, PA 19104, USA
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34
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Dupouy C, Iché-Tarrat N, Durrieu MP, Rodriguez F, Escudier JM, Vigroux A. Watson–Crick Base-Pairing Properties of Nucleic Acid Analogues with Stereocontrolled α and β Torsion Angles (α,β-D-CNAs). Angew Chem Int Ed Engl 2006. [DOI: 10.1002/ange.200504475] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022]
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35
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Bonache MC, Chamorro C, Cordeiro A, Camarasa MJ, Jimeno ML, San-Félix A. Synthesis of Novel Bi-, Tri-, and Tetracyclic Nucleosides by Reaction of a Common Cyclic Enamine Derived from TSAO-T with Nucleophiles. J Org Chem 2004; 69:8758-66. [PMID: 15575754 DOI: 10.1021/jo048706p] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
We report here the efficient regio- and stereoselective synthesis of new polycyclic nucleosides using a common cyclic enamine (7) as the starting material. In fact, the reaction of 7, easily prepared by reaction of 5'-O-Tosyl TSAO-T under basic nonnucleophilic conditions (potassium carbonate), with different classes of nucleophiles, for example, nitrogen-, oxygen-, sulfur-, and carbon-based nucleophiles, or with amino acids afforded, with total regio- and stereoselectivity, new bi-, tri-, and tetracyclic nucleosides. This straighforward route represents an original and unambiguously regio- and stereoselective pathway to these compounds. Some of these polycyclic nucleosides may be useful intermediates for a second series of reactions that may lead to the generation of structurally new nucleosides.
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Affiliation(s)
- María-Cruz Bonache
- Instituto de Química Médica, CSIC, Juan de la Cierva 3, 28006 Madrid, Spain
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36
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Tarköy M, Bolli M, Leumann C. Nucleic-Acid Analogues with Restricted Conformational Flexibility in the Sugar-Phosphate Backbone (‘bicyclo-DNA’). Part 3. Synthesis, pairing properties, and calorimetric determination of duplex and triplex stability of decanucleotides from [(3′S,5′R)-2′-. Helv Chim Acta 2004. [DOI: 10.1002/hlca.19940770315] [Citation(s) in RCA: 96] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
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37
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Chamorro C, Luengo SM, Bonache MC, Velázquez S, Pérez-Pérez MJ, Camarasa MJ, Gago F, Jimeno ML, San-Félix A. Synthesis and structural characterization of pyrimidine bi- and tricyclic nucleosides with sugar puckers conformationally locked into the eastern region of the pseudorotational cycle. J Org Chem 2003; 68:6695-704. [PMID: 12919035 DOI: 10.1021/jo034088l] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Reaction of 5'-O-tosyl TSAO-m(3)T (1) with amines has led to the synthesis of new classes of bi- and tricyclic nucleosides. Full details about the synthesis of these compounds and a plausible mechanism to explain their obtention are reported. In addition, we describe the development of a second, more efficient, and higher yielding synthetic route as a general approach for the synthesis of some of these bicyclic nucleosides. To study the conformational behavior of the bi- and tricyclic nucleosides described in this paper, intensive NMR investigations and molecular modeling studies were performed. Conformational analysis indicates that the furanose ring of the compounds described here prefers the eastern side of the pseudorotation cycle with the base substituents preferentially in the anti range. The torsion angle gamma describing the C-4'[bond]C-5' is found to prefer the +sc range. These compounds represent a novel class of E-type conformationally restricted bicyclic ribo-nucleosides containing a [3.3.0]-fused carbohydrate moiety. The bicyclic nucleosides described herein present an interesting potential for diverse and selective chemical treatments on the 2'-hydroxyl and/or the functionalities incorporated at the bridge between C-3' and C-5'.
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Affiliation(s)
- Cristina Chamorro
- Instituto de Química Médica (CSIC), Juan de la Cierva 3, 28006 Madrid, Spain
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38
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Le Clézio I, Escudier JM, Vigroux A. Diastereoselective synthesis of a conformationally restricted dinucleotide with predefined alpha and beta torsional angles for the construction of alpha,beta-constrained nucleic acids (alpha,beta-CNA). Org Lett 2003; 5:161-4. [PMID: 12529130 DOI: 10.1021/ol027222h] [Citation(s) in RCA: 37] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
Abstract
[reaction: see text] The synthesis of a diastereopure 1,3,2-dioxaphosphorinane linkage in which two, alpha and beta, out of six torsion angles of the natural phosphodiester backbone are constrained with predefined values of ca. +60 degrees (g(+)) and 180 degrees (t), respectively, is described. The stable and unstrained six-membered cyclic phosphotriester structure represents the smallest possible ring allowing the conformational locking of the alpha torsion angle at a significant positive value that is typical of many bulged regions of nucleic acids.
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Affiliation(s)
- Ingrid Le Clézio
- Laboratoire de Synthèse et Physico-Chimie de Molécules d'Intérêt Biologique (UMR 5068), Université Paul Sabatier, 118 Route de Narbonne, 31062 Toulouse Cedex 4, France
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39
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Abstract
Mainly driven by the needs of antisense research, a large number of oligonucleotide analogues have been prepared and evaluated over the last 15 years. Besides minor structural modifications of the building blocks of DNA and RNA itself, a considerable effort has been devoted to the de novo design of nucleoside analogues with improved binding properties. A particularly successful concept turned out to be that of conformational restriction. This review focuses on recent advances in this area and tries to summarize scope and limitations of this design principle.
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Affiliation(s)
- Christian J Leumann
- Department of Chemistry and Biochemistry, University of Bern, Freiestrasse 3, CH-3012, Bern, Switzerland.
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40
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41
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Affiliation(s)
- D J Hill
- Department of Chemistry and Materials Science & Engineering, The Beckman Institute for Advanced Science and Technology, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, USA
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42
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Obika S, Uneda T, Sugimoto T, Nanbu D, Minami T, Doi T, Imanishi T. 2'-O,4'-C-Methylene bridged nucleic acid (2',4'-BNA): synthesis and triplex-forming properties. Bioorg Med Chem 2001; 9:1001-11. [PMID: 11354656 DOI: 10.1016/s0968-0896(00)00325-4] [Citation(s) in RCA: 124] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
Abstract
For development of ideal antisense and antigene molecules, various chemical modifications of oligonucleotides have been studied. However, despite their importance, there is only limited information available on the triplex-forming ability of the conformationally restricted or locked oligonucleotides. We report herein that 2'-O,4'-C-methylene bridged nucleic acid (2',4'-BNA) modification of triplex-forming oligonucleotide (TFO) significantly enhances the binding affinity towards target dsDNA. On Tm measurements, the triplex with the 2',4'-BNA oligonucleotides were found to be stabilized with deltaTm/modification of +4.3 to +5 degrees C at pH 6.6 compared to the triplexes with the unmodified oligonucleotide. By means of gel-retardation assay, the binding constant of the 2',4'-BNA oligonucleotide at pH 7.0 was at least 300-fold higher than that of the natural oligonucleotide. In addition, the 2',4'-BNA oligonucleotide clearly showed the inhibition of the NF-kappaB transcription factor (p50)-target dsDNA binding by forming a stable triplex at pH 7.0.
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Affiliation(s)
- S Obika
- Graduate School of Pharmaceutical Sciences, Osaka University, Suita, Japan
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43
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Urata H, Miyagoshi H, Kumashiro T, Mori K, Shoji K, Akagi M. Basis for the right-handed helical sense of double-stranded DNA: formation of the right-handed helix by L-oligonucleotides fixed in low-anti glycosyl conformation. J Am Chem Soc 2001; 123:4845-6. [PMID: 11457299 DOI: 10.1021/ja003028j] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- H Urata
- Osaka University of Pharmaceutical Sciences 4-20-1 Nasahara, Takatsuki, Osaka 569-1094, Japan
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44
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Nielsen P, Petersen M, Jacobsen JP. Synthesis and NMR-analysis of tricyclic nucleosides. NUCLEOSIDES, NUCLEOTIDES & NUCLEIC ACIDS 2001; 20:1309-12. [PMID: 11563010 DOI: 10.1081/ncn-100002543] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/03/2022]
Abstract
Two anomeric tricyclic nucleosides have been synthesised from diacetone-D-glucose using oxidation, stereoselective Grignard-addition of a vinyl-group, a stereoselective dihydroxylation followed by a tandem ring closing reaction, and finally a nucleobase coupling. The main beta-configured product was examined and its configuration confirmed using NMR-spectroscopy in connection to ab initio calculations. The preferred conformation of this tricyclic nucleoside was described.
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Affiliation(s)
- P Nielsen
- Department of Chemistry, University of Southern Denmark, 5230 Odense M, Denmark
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45
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Sørensen AM, Nielsen P. Synthesis of conformationally restricted dinucleotides by ring-closing metathesis. Org Lett 2000; 2:4217-9. [PMID: 11150203 DOI: 10.1021/ol0067639] [Citation(s) in RCA: 45] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
[reaction:see text] The ring-closing metathesis reaction has been used in the synthesis of conformationally restricted dinucleotides as well as a 3'-nucleotide analogue. From bis-allylic nucleoside phosphates obtained from simple nucleoside precursors, the synthesis of unsaturated cyclophosphates has been accomplished using either Grubbs' catalyst or an improved analogue. Hereby, the conformational freedom of the nucleic acid phosphordiester linkage has been efficiently constrained.
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Affiliation(s)
- A M Sørensen
- Department of Chemistry, University of Southern Denmark, Odense University, 5230 Odense M, Denmark
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46
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Wahlestedt C, Salmi P, Good L, Kela J, Johnsson T, Hökfelt T, Broberger C, Porreca F, Lai J, Ren K, Ossipov M, Koshkin A, Jakobsen N, Skouv J, Oerum H, Jacobsen MH, Wengel J. Potent and nontoxic antisense oligonucleotides containing locked nucleic acids. Proc Natl Acad Sci U S A 2000; 97:5633-8. [PMID: 10805816 PMCID: PMC25880 DOI: 10.1073/pnas.97.10.5633] [Citation(s) in RCA: 444] [Impact Index Per Article: 18.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 02/17/2000] [Indexed: 11/18/2022] Open
Abstract
Insufficient efficacy and/or specificity of antisense oligonucleotides limit their in vivo usefulness. We demonstrate here that a high-affinity DNA analog, locked nucleic acid (LNA), confers several desired properties to antisense agents. Unlike DNA, LNA/DNA copolymers were not degraded readily in blood serum and cell extracts. However, like DNA, the LNA/DNA copolymers were capable of activating RNase H, an important antisense mechanism of action. In contrast to phosphorothioate-containing oligonucleotides, isosequential LNA analogs did not cause detectable toxic reactions in rat brain. LNA/DNA copolymers exhibited potent antisense activity on assay systems as disparate as a G-protein-coupled receptor in living rat brain and an Escherichia coli reporter gene. LNA-containing oligonucleotides will likely be useful for many antisense applications.
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Affiliation(s)
- C Wahlestedt
- Center for Genomics Research and Department of Neuroscience, Karolinska Institutet, S-171 77 Stockholm, Sweden.
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Lescop C, Huet F. Synthesis of Novel Nucleosides with a Fused Cyclopropane Ring Substituted by a Hydroxymethyl Group. Tetrahedron 2000. [DOI: 10.1016/s0040-4020(00)00174-5] [Citation(s) in RCA: 21] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/17/2022]
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Katagiri N, Morishita Y, Oosawa I, Yamaguchi M. Artificial oligonucleotides consisting of an analog of nucleoside antibiotics, carbocyclic oxetanocins. Tetrahedron Lett 1999. [DOI: 10.1016/s0040-4039(99)01410-0] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/17/2022]
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Koshkin AA, Nielsen P, Meldgaard M, Rajwanshi VK, Singh SK, Wengel J. LNA (Locked Nucleic Acid): An RNA Mimic Forming Exceedingly Stable LNA:LNA Duplexes. J Am Chem Soc 1998. [DOI: 10.1021/ja9822862] [Citation(s) in RCA: 248] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Alexei A. Koshkin
- Center for Synthetic Bioorganic Chemistry Department of Chemistry, University of Copenhagen Universitetsparken 5 DK-2100 Copenhagen, Denmark Department of Chemistry, Odense University DK-5230 Odense M, Denmark
| | - Poul Nielsen
- Center for Synthetic Bioorganic Chemistry Department of Chemistry, University of Copenhagen Universitetsparken 5 DK-2100 Copenhagen, Denmark Department of Chemistry, Odense University DK-5230 Odense M, Denmark
| | - Michael Meldgaard
- Center for Synthetic Bioorganic Chemistry Department of Chemistry, University of Copenhagen Universitetsparken 5 DK-2100 Copenhagen, Denmark Department of Chemistry, Odense University DK-5230 Odense M, Denmark
| | - Vivek K. Rajwanshi
- Center for Synthetic Bioorganic Chemistry Department of Chemistry, University of Copenhagen Universitetsparken 5 DK-2100 Copenhagen, Denmark Department of Chemistry, Odense University DK-5230 Odense M, Denmark
| | - Sanjay K. Singh
- Center for Synthetic Bioorganic Chemistry Department of Chemistry, University of Copenhagen Universitetsparken 5 DK-2100 Copenhagen, Denmark Department of Chemistry, Odense University DK-5230 Odense M, Denmark
| | - Jesper Wengel
- Center for Synthetic Bioorganic Chemistry Department of Chemistry, University of Copenhagen Universitetsparken 5 DK-2100 Copenhagen, Denmark Department of Chemistry, Odense University DK-5230 Odense M, Denmark
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Singh SK, Kumar R, Wengel J. Synthesis of 2‘-Amino-LNA: A Novel Conformationally Restricted High-Affinity Oligonucleotide Analogue with a Handle. J Org Chem 1998. [DOI: 10.1021/jo9814445] [Citation(s) in RCA: 116] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
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