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Chardet C, Payrastre C, Gerland B, Escudier JM. Convertible and Constrained Nucleotides: The 2'-Deoxyribose 5'-C-Functionalization Approach, a French Touch. Molecules 2021; 26:5925. [PMID: 34641475 PMCID: PMC8512084 DOI: 10.3390/molecules26195925] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2021] [Revised: 09/21/2021] [Accepted: 09/27/2021] [Indexed: 11/17/2022] Open
Abstract
Many strategies have been developed to modulate the biological or biotechnical properties of oligonucleotides by introducing new chemical functionalities or by enhancing their affinity and specificity while restricting their conformational space. Among them, we review our approach consisting of modifications of the 5'-C-position of the nucleoside sugar. This allows the introduction of an additional chemical handle at any position on the nucleotide chain without disturbing the Watson-Crick base-pairing. We show that 5'-C bromo or propargyl convertible nucleotides (CvN) are accessible in pure diastereoisomeric form, either for nucleophilic displacement or for CuAAC conjugation. Alternatively, the 5'-carbon can be connected in a stereo-controlled manner to the phosphate moiety of the nucleotide chain to generate conformationally constrained nucleotides (CNA). These allow the precise control of the sugar/phosphate backbone torsional angles. The consequent modulation of the nucleic acid shape induces outstanding stabilization properties of duplex or hairpin structures in accordance with the preorganization concept. Some biological applications of these distorted oligonucleotides are also described. Effectively, the convertible and the constrained approaches have been merged to create constrained and convertible nucleotides (C2NA) providing unique tools to functionalize and stabilize nucleic acids.
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Affiliation(s)
| | | | - Béatrice Gerland
- Laboratoire de Synthèse et Physico-Chimie de Molécules d′Intérêt Biologique, UMR CNRS 5068, Université Paul Sabatier, 118 Route de Narbonne, CEDEX 9, 31062 Toulouse, France; (C.C.); (C.P.)
| | - Jean-Marc Escudier
- Laboratoire de Synthèse et Physico-Chimie de Molécules d′Intérêt Biologique, UMR CNRS 5068, Université Paul Sabatier, 118 Route de Narbonne, CEDEX 9, 31062 Toulouse, France; (C.C.); (C.P.)
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2
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Kel'in AV, Zlatev I, Harp J, Jayaraman M, Bisbe A, O'Shea J, Taneja N, Manoharan RM, Khan S, Charisse K, Maier MA, Egli M, Rajeev KG, Manoharan M. Structural Basis of Duplex Thermodynamic Stability and Enhanced Nuclease Resistance of 5'-C-Methyl Pyrimidine-Modified Oligonucleotides. J Org Chem 2016; 81:2261-79. [PMID: 26940174 DOI: 10.1021/acs.joc.5b02375] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
Abstract
Although judicious use of chemical modifications has contributed to the success of nucleic acid therapeutics, poor systemic stability remains a major hurdle. The introduction of functional groups around the phosphate backbone can enhance the nuclease resistance of oligonucleotides (ONs). Here, we report the synthesis of enantiomerically pure (R)- and (S)-5'-C-methyl (C5'-Me) substituted nucleosides and their incorporation into ONs. These modifications generally resulted in a decrease in thermal stability of oligonucleotide (ON) duplexes in a manner dependent on the stereoconfiguration at C5' with greater destabilization characteristic of (R)-epimers. Enhanced stability against snake venom phosphodiesterase resulted from modification of the 3'-end of an ON with either (R)- or (S)-C5'-Me nucleotides. The (S)-isomers with different 2'-substituents provided greater resistance against 3'-exonucleases than the corresponding (R)-isomers. Crystal structure analyses of RNA octamers with (R)- or (S)-5'-C-methyl-2'-deoxy-2'-fluorouridine [(R)- or (S)-C5'-Me-2'-FU, respectively] revealed that the stereochemical orientation of the C5'-Me and the steric effects that emanate from the alkyl substitution are the dominant determinants of thermal stability and are likely molecular origins of resistance against nucleases. X-ray and NMR structural analyses showed that the (S)-C5'-Me epimers are spatially and structurally more similar to their natural 5' nonmethylated counterparts than the corresponding (R)-epimers.
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Affiliation(s)
- Alexander V Kel'in
- Alnylam Pharmaceuticals , 300 Third Street, Cambridge, Massachusetts 02142, United States
| | - Ivan Zlatev
- Alnylam Pharmaceuticals , 300 Third Street, Cambridge, Massachusetts 02142, United States
| | - Joel Harp
- Department of Biochemistry and Center for Structural Biology, Vanderbilt University, School of Medicine , Nashville, Tennessee 37232, United States
| | - Muthusamy Jayaraman
- Alnylam Pharmaceuticals , 300 Third Street, Cambridge, Massachusetts 02142, United States
| | - Anna Bisbe
- Alnylam Pharmaceuticals , 300 Third Street, Cambridge, Massachusetts 02142, United States
| | - Jonathan O'Shea
- Alnylam Pharmaceuticals , 300 Third Street, Cambridge, Massachusetts 02142, United States
| | - Nate Taneja
- Alnylam Pharmaceuticals , 300 Third Street, Cambridge, Massachusetts 02142, United States
| | - Rajar M Manoharan
- Alnylam Pharmaceuticals , 300 Third Street, Cambridge, Massachusetts 02142, United States
| | - Saeed Khan
- Department of Chemistry and Biochemistry, University of California , Los Angeles, California 90095, United States
| | - Klaus Charisse
- Alnylam Pharmaceuticals , 300 Third Street, Cambridge, Massachusetts 02142, United States
| | - Martin A Maier
- Alnylam Pharmaceuticals , 300 Third Street, Cambridge, Massachusetts 02142, United States
| | - Martin Egli
- Department of Biochemistry and Center for Structural Biology, Vanderbilt University, School of Medicine , Nashville, Tennessee 37232, United States
| | | | - Muthiah Manoharan
- Alnylam Pharmaceuticals , 300 Third Street, Cambridge, Massachusetts 02142, United States
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3
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Efficient synthesis, antioxidant and antimicrobial profiles of 2-(arylamino)- and 2-(heteroarylamino)- 1,3,4,2λ5-dioxazaphosphinin-2-ones. Chem Heterocycl Compd (N Y) 2015. [DOI: 10.1007/s10593-015-1680-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/23/2022]
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4
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Gerland B, Millard P, Dupouy C, Renard BL, Escudier JM. Stabilization of hairpins and bulged secondary structures of nucleic acids by single incorporation of α,β-D-CNA featuring a gauche(+) alpha torsional angle. RSC Adv 2014. [DOI: 10.1039/c4ra09639h] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/22/2023] Open
Abstract
A constrained dinucleotide unit featuring a gauche(+) alpha torsional angle configuration was used to stabilize DNA hairpin or bulged structures.
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Affiliation(s)
- Béatrice Gerland
- Laboratoire de Synthèse et Physico-Chimie de Molécules d'Intérêt Biologique
- UMR 5068 CNRS
- Université Paul Sabatier
- 31062 Toulouse Cedex 9, France
| | - Pierre Millard
- Laboratoire de Synthèse et Physico-Chimie de Molécules d'Intérêt Biologique
- UMR 5068 CNRS
- Université Paul Sabatier
- 31062 Toulouse Cedex 9, France
| | - Christelle Dupouy
- Laboratoire de Synthèse et Physico-Chimie de Molécules d'Intérêt Biologique
- UMR 5068 CNRS
- Université Paul Sabatier
- 31062 Toulouse Cedex 9, France
| | - Brice-Loïc Renard
- Laboratoire de Synthèse et Physico-Chimie de Molécules d'Intérêt Biologique
- UMR 5068 CNRS
- Université Paul Sabatier
- 31062 Toulouse Cedex 9, France
| | - Jean-Marc Escudier
- 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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5
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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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6
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Hanessian S, Wagger J, Merner BL, Giacometti RD, Ostergaard ME, Swayze EE, Seth PP. A constrained tricyclic nucleic acid analogue of α-L-LNA: investigating the effects of dual conformational restriction on duplex thermal stability. J Org Chem 2013; 78:9064-75. [PMID: 23937256 DOI: 10.1021/jo401170y] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
Abstract
A constrained tricyclic analogue of α-L-LNA (2), which contains dual modes of conformational restriction about the ribose sugar moiety, has been synthesized and characterized by X-ray crystallography. Thermal denaturation experiments of oligonucleotide sequences containing this tricyclic α-L-LNA analogue (α-L-TriNA 2, 5) indicate that this modification is moderately stabilizing when paired with complementary DNA and RNA, but less stabilizing than both α-L-LNA (2) and α-L-TriNA 1 (4).
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Affiliation(s)
- Stephen Hanessian
- Department of Chemistry, Université de Montréal , Montréal, QC, H3C 3J7, Canada
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7
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Dioxaphosphorinane-constrained nucleic Acid dinucleotides as tools for structural tuning of nucleic acids. J Nucleic Acids 2012; 2012:215876. [PMID: 23150809 PMCID: PMC3488415 DOI: 10.1155/2012/215876] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2012] [Accepted: 08/02/2012] [Indexed: 01/03/2023] Open
Abstract
We describe a rational approach devoted to modulate the sugar-phosphate backbone geometry of nucleic acids. Constraints were generated by connecting one oxygen of the phosphate group to a carbon of the sugar moiety. The so-called dioxaphosphorinane rings were introduced at key positions along the sugar-phosphate backbone allowing the control of the six-torsion angles α to ζ defining the polymer structure. The syntheses of all the members of the D-CNA family are described, and we emphasize the effect on secondary structure stabilization of a couple of diastereoisomers of α,β-D-CNA exhibiting wether B-type canonical values or not.
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8
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Kumar S, Hansen MH, Albaek N, Steffansen SI, Petersen M, Nielsen P. Synthesis of functionalized carbocyclic locked nucleic acid analogues by ring-closing diene and enyne metathesis and their influence on nucleic acid stability and structure. J Org Chem 2009; 74:6756-69. [PMID: 19711996 DOI: 10.1021/jo9013657] [Citation(s) in RCA: 34] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
Abstract
A series of bicylic 2'-deoxynucleosides that are locked in the N-type conformation due to three-carbon linkages between the 2'- and 4'-positions have been prepared by ring-closing diene or enyne metathesis. The alkene or 1,3-diene hereby introduced in the bicyclic system is further derivatized, the latter showing the expected potential for Diels-Alder reactions. Four derivatives that are saturated or unsaturated as well as functionalized at the 2'-4'-linkage are incorporated into oligodeoxynucleotides, and the affinity of these for complementary RNA and DNA is studied. Substantially increased affinity for complementary RNA is observed, especially with additional hydroxyl groups attached to the bicyclic system. On the other hand, decreased affinity for complementary single-stranded DNA is obtained, whereas only a very small influence on a triplex-forming oligonucleotide sequence is found. Hence, a strong RNA-selective nucleic acid recognition is seen, and it can be concluded that the 2'-oxygen atom is less important for the formation of DNA:RNA duplexes than for the formation of DNA:DNA duplexes. However, the lack of a 2'-oxygen in the duplex formation can be partly compensated by other hydrophilic moieties around the 2'-4'-linkages indicating structural water binding to be of significant importance.
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Affiliation(s)
- Surender Kumar
- Nucleic Acid Center, Department of Physics and Chemistry, University of Southern Denmark, 5230 Odense M, Denmark
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9
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Zhou C, Plashkevych O, Chattopadhyaya J. Double sugar and phosphate backbone-constrained nucleotides: synthesis, structure, stability, and their incorporation into oligodeoxynucleotides. J Org Chem 2009; 74:3248-65. [PMID: 19348480 DOI: 10.1021/jo900391n] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Abstract
Two diastereomerically pure carba-LNA dioxaphosphorinane nucleotides [(S(p))- or (R(p))-D(2)-CNA], simultaneously conformationally locked at the sugar and the phosphate backbone, have been designed and synthesized. Structural studies by NMR as well as by ab initio calculations showed that in (S(p))- and (R(p))-D(2)-CNA the following occur: (i) the sugar is locked in extreme North-type conformation with P = 11 degrees and Phi(m) = 54 degrees ; (ii) the six-membered 1,3,2-dioxaphosphorinane ring adopts a half-chair conformation; (iii) the fixed phosphate backbone delta, epsilon, and zeta torsions were found to be delta [gauch(+)], epsilon (cis), zeta [anticlinal(+)] for (S(p))-D(2)-CNA, and delta [gauche(+)], epsilon (cis), zeta [anticlinal(-)] for (R(p))-D(2)-CNA. It has been found that F(-) ion can catalyze the isomerization of pure (S(p))-D(2)-CNA or (R(p))-D(2)-CNA to give an equilibrium mixture (K = 1.94). It turned out that at equilibrium concentration the (S(p))-D(2)-CNA isomer is preferred over the (R(p))-D(2)-CNA isomer by 0.39 kcal/mol. The chemical reactivity of the six-membered dioxaphosphorinane ring in D(2)-CNA was found to be dependent on the internucleotidic phosphate stereochemistry. Thus, both (S(p))- and (R(p))-D(2)-CNA dimers (17a and 17b) were very labile toward nucleophile attack in concentrated aqueous ammonia [t(1/2) = 12 and 6 min, respectively] to give carba-LNA-6',5'-phosphodiester (21) approximately 70-90%, carba-LNA-3',5'-phosphodiester (22) approximately 10%, and carba-LNA-6',3'-phosphodiester (23) <10%. In contrast, the (S(p))-D(2)-CNA was about 2 times more stable than (R(p))-D(2)-CNA under hydrazine hydrate/pyridine/AcOH (pH = 5.6) [t(1/2) = 178 and 99 h, respectively], which was exploited in the deprotection of pure (S(p))-D(2)-CNA-incorporated antisense oligodeoxynucleotides (AON). Thus, after removal of the solid supports from the (S(p))-D(2)-CNA-modified AONs by BDU/MeCN, they were treated with hydrazine hydrate in pyridine/AcOH to give pure AONs in 35-40% yield, which was unequivocally characterized by MALDI-TOF to show that they have an intact six-membered dioxaphosphorinane ring. The effect of pure (S(p))-D(2)-CNA modification in the AONs was estimated by complexing to the complementary RNA and DNA strands by the thermal denaturation studies. This showed that this cyclic phosphotriester modification destabilizes the AON/DNA and AON/RNA duplex by about -6 to -9 degrees C/modification. Treatment of (S(p))-D(2)-CNA-modified AON with concentrated aqueous ammonia gave carba-LNA-6',5'-phosphodiester modified AON ( approximately 80%) plus a small amount of carba-LNA-3',5'-phosphodiester-modified AON ( approximately 20%). It is noteworthy that Carba-LNA-3',5'-phosphodiester modification stabilized the AON/RNA duplex by +4 degrees C/modification (J. Org. Chem. 2009, 74, 118), whereas carba-LNA-6', 5'-phosphodiester modification destabilizes both AON/RNA and AON/DNA significantly (by -10 to -19 degrees C/modification), which, as shown in our comparative CD studies, that the cyclic phosphotriester modified AONs as well as carba-LNA-6',5'-phosphodiester modified AONs are much more weakly stacked than carba-LNA-3',5'-phosphodiester-modified AONs.
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Affiliation(s)
- Chuanzheng Zhou
- Department of Bioorganic Chemistry, Box 581, ICM, Biomedical Center, Uppsala University, SE-751 23 Uppsala, Sweden
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10
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11
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Dupouy C, Lavedan P, Escudier JM. Synthesis and Structure of Dinucleotides with S-Type Sugar Puckering and Noncanonical ε and ζ Torsion Angle Combination (ν2,ε,ζ-D-CNA). European J Org Chem 2008. [DOI: 10.1002/ejoc.200701022] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
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12
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Abstract
The synthesis of modified nucleic acids has been the subject of much study ever since the structure of DNA was elucidated by Watson and Crick at Cambridge and Wilkins and Franklin at King's College over half a century ago. This review describes recent developments in the synthesis and application of these artificial nucleic acids, predominantly the phosphoramidites which allow for easy inclusion into oligonucleotides, and is divided into three separate sections. Firstly, modifications to the base portion will be discussed followed secondly by modifications to the sugar portion. Finally, changes in the type of nucleic acid linker will be discussed in the third section. Peptide Nucleic Acids (PNAs) are not discussed in this review as they represent a separate and large area of nucleic acid mimics.
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Affiliation(s)
- Alexander J A Cobb
- School of Pharmacy, University of Reading, Whiteknights, Reading, Berks RG6 6AD, UK.
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13
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Le Clézio I, Dupouy C, Lavedan P, Escudier JM. Synthesis and Structure of an α,β-D-CNA Featuring a Noncanonical α/β Torsion Angle Combination within a Tetranucleotide. European J Org Chem 2007. [DOI: 10.1002/ejoc.200700229] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
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14
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Albaek N, Petersen M, Nielsen P. Analogues of a locked nucleic acid with three-carbon 2',4'-linkages: synthesis by ring-closing metathesis and influence on nucleic acid duplex stability and structure. J Org Chem 2007; 71:7731-40. [PMID: 16995680 DOI: 10.1021/jo061225g] [Citation(s) in RCA: 65] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Two bicyclic 2'-deoxynucleoside analogues containing a saturated and an unsaturated three-carbon 2',4'-linkage, respectively, have been synthesized using a ring-closing metathesis-based linear strategy starting from uridine. Both analogues have been incorporated into oligodeoxynucleotide sequences and increased the stability of DNA:RNA hybrid duplexes (DeltaT(m) approximately 2.5-5.0 degrees C per modification) and decreased the stability of dsDNA duplexes (DeltaT(m) approximately 2.5-1.0 degrees C per modification). CD spectroscopy revealed that the bicyclic nucleosides induced formation of A-type-like duplexes albeit to a lesser degree than found for locked nucleic acid (LNA) monomers. From the CD data and UV melting analysis, we propose that the 2'-oxygen atom of the bicyclic moiety is essential for the formation of stabilized A-type-like dsDNA but not for the formation of a stabilized A-type DNA:RNA hybrid.
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Affiliation(s)
- Nanna Albaek
- Nucleic Acid Center, Department of Chemistry, University of Southern Denmark, 5230 Odense M, Denmark
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15
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Christensen MS, Madsen CM, Nielsen P. Synthesis and modelling of DNA junction and minor groove zipper motifs incorporating the double-headed nucleoside 5'(S)-C-(thymine-1-ylmethyl)thymidine. Org Biomol Chem 2007; 5:1586-94. [PMID: 17571188 DOI: 10.1039/b700852j] [Citation(s) in RCA: 26] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
A nucleoside with two nucleobases, a so-called double-headed nucleoside, 5'(S)-C-(thymine-1-ylmethyl)thymidine 3, is synthesised and incorporated into oligonucleotides. The additional nucleobase is hereby positioned in the minor groove of the duplexes, which are formed with complementary DNA and RNA-sequences. Slight thermal destabilisation of these duplexes as compared to unmodified duplexes is observed. With other target sequences forming bulged duplexes or three-way junctions, no additional influence of the additional base on the thermal stability is observed. On the other hand, a base-base stacking interaction and subsequent stabilisation is observed when two double-headed nucleotide moieties are positioned in two complementary DNA-sequences forming a DNA-zipper motif.
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Affiliation(s)
- Mikkel S Christensen
- Nucleic Acid Center, Department of Chemistry and Physics, University of Southern Denmark, 5230, Odense M, Denmark
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16
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Le Clézio I, Vigroux A, Escudier JM. Diastereoselective and Regioselective Synthesis of Conformationally Restricted Thio-dioxa- and Oxo-oxathiaphosphorinane Dinucleotides Featuring Noncanonical α/β Torsion Angle Combinations (α,β-CNAs). European J Org Chem 2007. [DOI: 10.1002/ejoc.200601030] [Citation(s) in RCA: 15] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
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17
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Dupouy C, Le Clézio I, Lavedan P, Gornitzka H, Escudier JM, Vigroux A. Diastereoselective Synthesis of Conformationally Restricted Dinucleotides Featuring Canonical and Noncanonical α/β Torsion Angle Combinations(α,β-D-CNA). European J Org Chem 2006. [DOI: 10.1002/ejoc.200600593] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/02/2023]
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18
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19
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Kodama T, Greenberg MM. Preparation and analysis of oligonucleotides containing lesions resulting from C5'-oxidation. J Org Chem 2006; 70:9916-24. [PMID: 16292822 PMCID: PMC1657062 DOI: 10.1021/jo051666k] [Citation(s) in RCA: 35] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
[reaction: see text] Hydrogen atom abstraction from the C5'-position of nucleotides in DNA results in direct strand scission. The newly formed 5'-termini of the cleaved DNA consists of alkali-labile fragments of the oxidized nucleotide. One terminus contains a 5'-aldehyde as part of an otherwise undamaged nucleotide (T-al). A second more structurally distinct product that is produced in lower yields results from cleavage of the C4'-C5' carbon-carbon bond. The 1,4-dioxo-2-phosphorylbutane (DOB) is a precursor of the alkylating agent but-2-ene-1,4-dial. To facilitate studies on these lesions, methods for synthesizing oligodeoxynucleotides containing DOB or T-al at their 5'-termini were developed. The effects of these lesions on the UV-melting temperatures of duplex DNA, and their cleavage labilities were determined. T-al cleaves very slowly (t(1/2) = 100.7 h), whereas DOB has a half-life at 37 degrees C (pH 7.2) of less than 11 h. In addition, DOB forms a stable adduct very efficiently with Tris, which protects the abasic site against cleavage.
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Affiliation(s)
- Tetsuya Kodama
- Department of Chemistry, Johns Hopkins University, 3400 N. Charles St., Baltimore, Maryland 21218, USA
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20
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Sahabuddin S, Roy A, Drew MGB, Roy BG, Achari B, Mandal SB. Sequential Ring-Closing Metathesis and Nitrone Cycloaddition on Glucose-Derived Substrates: A Divergent Approach to Analogues of Spiroannulated Carbanucleosides and Conformationally Locked Nucleosides. J Org Chem 2006; 71:5980-92. [PMID: 16872180 DOI: 10.1021/jo0606554] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
The carbohydrate-derived substrate 3-C-allyl-1,2:5,6-di-O-isopropylidene-alpha-D-allofuranose was judiciously manipulated for preparing suitable synthons, which could be converted to a variety of isoxazolidino-spirocycles and -tricycles through the application of ring-closing metathesis (RCM) and intramolecular nitrone cycloaddition (INC) reactions. Cleavage of the isoxazolidine rings of some of these derivatives by transfer hydrogenolysis followed by coupling of the generated amino functionalities with 5-amino-4,6-dichloropyrimidine furnished the corresponding chloropyrimidine nucleosides, which were elaborated to spiroannulated carbanucleosides and conformationally locked bicyclo[2.2.1]heptane/oxa-bicyclo[3.2.1]octane nucleosides. However, use of higher temperature for the cyclization of one of the chloropyrimidines led to the dimethylaminopurine analogue as a sole product, formed via nucleophilic displacement of the chloro group by dimethylamine generated from DMF.
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Affiliation(s)
- Sk Sahabuddin
- Department of Chemistry, Indian Institute of Chemical Biology, Jadavpur, 4, Raja S. C. Mullick Road, Kolkata 700 032, India
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21
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Sharma PK, Mikkelsen BH, Christensen MS, Nielsen KE, Kirchhoff C, Pedersen SL, Sørensen AM, Ostergaard K, Petersen M, Nielsen P. A cyclic dinucleotide with a four-carbon 5'-C-to-5'-C connection; synthesis by RCM, NMR-examination and incorporation into secondary nucleic acid structures. Org Biomol Chem 2006; 4:2433-45. [PMID: 16763689 DOI: 10.1039/b603830a] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
A 5'-C-allylthymidine derivative was prepared from thymidine by the application of a stereoselective allylation procedure and its 5'(S)-configuration was confirmed. From this nucleoside derivative, appropriately protected building blocks were prepared and coupled using standard phosphoramidite chemistry to afford a dinucleotide with two 5'-C-allylgroups. This molecule was used as a substrate for a ring-closing metathesis (RCM) reaction and after deprotection, a 1 : 1 mixture of E- and Z-isomers of a cyclic dinucleotide with an unsaturated 5'-C-to-5'-C connection was obtained. Alternatively, a hydrogenation of the double bond and deprotection afforded a saturated cyclic dinucleotide. An advanced NMR-examination confirmed the constitution of this molecule and indicated a restriction in its overall conformational freedom. After variation of the protecting group strategy, a phosphoramidite building block of the saturated cyclic dinucleotide with the 5'-O-position protected as a pixyl ether and the phosphate protected as a methyl phosphotriester was obtained. This building block was used in the preparation of two 14-mer oligonucleotides with a central artificial bend due to the cyclic dinucleotide moiety. These were found to destabilise duplexes, slightly destabilise bulged duplexes but, to some extent, stabilise a three-way junction in high Mg(2+)-concentrations.
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Affiliation(s)
- Pawan K Sharma
- Nucleic Acid Center, Department of Chemistry, University of Southern Denmark
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Børsting P, Christensen MS, Steffansen SI, Nielsen P. Synthesis of dinucleotides with 2′-C to phosphate connections by ring-closing metathesis. Tetrahedron 2006. [DOI: 10.1016/j.tet.2005.10.074] [Citation(s) in RCA: 17] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
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23
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Steffansen SI, Christensen MS, Børsting P, Nielsen P. Synthesis of conformationally restricted nucleic acid fragments using ring-closing alkene and enyne metathesis reactions. NUCLEOSIDES NUCLEOTIDES & NUCLEIC ACIDS 2005; 24:1015-8. [PMID: 16248082 DOI: 10.1081/ncn-200060347] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/03/2022]
Abstract
In the aim of constructing conformationally restricted nucleic acid fragments for the recognition of secondary RNA structures, we have synthesized different mono- and dinucleotides containing extra rings. These rings were prepared by ring-closing alkene or enyne metathesis reactions from nucleotide substrates in which double or triple bonds have been introduced.
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Affiliation(s)
- Signe I Steffansen
- Nucleic Acid Center, Department of Chemistry, University of Southern Denmark, Odense, Denmark
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Nielsen P, Børsting P. Ring-closing metathesis reactions in nucleic acid chemistry-cyclic dinucleotides for targeting secondary nucleic acid structures. NUCLEOSIDES NUCLEOTIDES & NUCLEIC ACIDS 2005; 24:349-52. [PMID: 16247950 DOI: 10.1081/ncn-200059776] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/03/2022]
Abstract
Cyclic dinucleotides are synthesized using a ring-closing metathesis protocol and incorporated into oligonucleotides. A stabilization of a three-way junction is observed by an oligodeoxynucleotide containing a central 2'-C to 3'-phosphate connection.
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Affiliation(s)
- Poul Nielsen
- Nucleic Acid Center, Department of Chemistry, University of Southern Denmark, Odense M, Denmark
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Pedersen SL, Nielsen P. Stabilisation of nucleic acid secondary structures by oligonucleotides with an additional nucleobase; synthesis and incorporation of 2'-deoxy-2'-C-(2-(thymine-1-yl)ethyl)uridine. Org Biomol Chem 2005; 3:3570-5. [PMID: 16172696 DOI: 10.1039/b510167k] [Citation(s) in RCA: 38] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
A nucleoside with two nucleobases is incorporated into oligonucleotides. The synthetic building block, 2'-deoxy-2'-C-(2-(thymine-1-yl)ethyl)uridine, 2, is prepared from uridine via 5',3'-TIPDS-protected 2'-deoxy-2'-C-allyluridine by an oxidative cleavage of the allyl group, a Mitsunobu reaction for the introduction of thymine and appropriate deprotection reactions. This compound is converted into a DMT-protected phosphoramidite and incorporated once into a 13-mer oligodeoxynucleotide sequence, once in an isosequential LNA-modified oligodeoxynucleotide and four times in the middle of a 12-mer oligodeoxynucleotide. These sequences are mixed with different complementary DNA and RNA sequences in order to study the effect of the additional nucleobase in duplexes, in bulged duplexes and in three-way junctions. The first additional thymine is found to be well-accommodated in a DNA-RNA duplex, whereas a DNA-DNA duplex was slightly destabilised. A three-way junction with the additional thymine in the branching point is found to be stabilised in both a DNA-DNA and a DNA-RNA context but destabilised where the modified LNA-sequence is used. In a Mg2+-containing buffer, however, the relative stability of the three-way junctions is found to be opposite with especially the LNA-modified DNA-DNA complex being significantly stabilised by the additional nucleobase.
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Affiliation(s)
- Søren Ljungberg Pedersen
- Nucleic Acid Center, Department of Chemistry, University of Southern Denmark, 5230, Odense M, Denmark
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Børsting P, Nielsen KE, Nielsen P. Stabilisation of a nucleic acid three-way junction by an oligonucleotide containing a single 2'-C to 3'-O-phosphate butylene linkage prepared by a tandem RCM-hydrogenation method. Org Biomol Chem 2005; 3:2183-90. [PMID: 15917908 DOI: 10.1039/b502720a] [Citation(s) in RCA: 30] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
A cyclic dinucleotide with a butylene linker between the upper 2'-C position and the 3'-O-phosphate linkage was synthesised from simple nucleoside building blocks via a tandem ring-closing metathesis and hydrogenation procedure. The major of two phosphorus epimers was incorporated into an oligodeoxynucleotide, as well as into an LNA-DNA mixmer oligonucleotide. These were evaluated as parts in three different secondary structures, a duplex, a bulged duplex and a three-way junction, with both DNA and RNA complements. In the DNA:RNA hybrid molecule, the oligodeoxynucleotide containing this single 2'-C to 3'-O-phosphate butylene linkage was found to stabilise a three-way junction.
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Affiliation(s)
- Philip Børsting
- Nucleic Acid Center, Department of Chemistry, University of Southern Denmark, 5230 Odense M, Denmark
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Børsting P, Freitag M, Nielsen P. Dinucleotides containing two allyl groups by combinations of allyl phosphotriesters, 5-allyl-, 2′-O-allyl- and 2′-arabino-O-allyl uridine derivatives as substrates for ring-closing metathesis. Tetrahedron 2004. [DOI: 10.1016/j.tet.2004.09.023] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/26/2022]
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McReynolds MD, Dougherty JM, Hanson PR. Synthesis of Phosphorus and Sulfur Heterocycles via Ring-Closing Olefin Metathesis. Chem Rev 2004; 104:2239-58. [PMID: 15137790 DOI: 10.1021/cr020109k] [Citation(s) in RCA: 501] [Impact Index Per Article: 25.1] [Reference Citation Analysis] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
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30
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The first example of ring-closing olefin metathesis of dehydroamino acids: an application to the synthesis of azabicyclo[X.Y.0]alkanes. Tetrahedron Lett 2004. [DOI: 10.1016/j.tetlet.2004.01.126] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
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Børsting P, Nielsen P. Conformationally restricted dinucleotides: tandem ring-closing metathesis and hydrogenation approach. NUCLEOSIDES NUCLEOTIDES & NUCLEIC ACIDS 2003; 22:1139-41. [PMID: 14565364 DOI: 10.1081/ncn-120022820] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/03/2022]
Abstract
Cyclic dinucleotides with saturated connections between a nucleobase and the phosphate are synthesised using a tandem ring-closing metathesis (RCM) and hydrogenation protocol and found to be significantly stabilised towards ammonia.
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Affiliation(s)
- Philip Børsting
- Nucleic Acid Center, Department of Chemistry, University of Southern Denmark, Odense M, Denmark
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Chen X, Wiemer DF. Alpha-phosphono lactone analogues of cytidine and cytosine arabinoside diphosphates: synthesis via ring closing metathesis. J Org Chem 2003; 68:6597-604. [PMID: 12919022 DOI: 10.1021/jo0300136] [Citation(s) in RCA: 26] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
alpha-Phosphono lactone derivatives of the nucleosides cytidine and cytosine arabinoside have been prepared from the corresponding nucleoside aldehydes. The stereochemical outcome of allylation reactions with these aldehydes was found to be dependent upon both the choice of protecting groups for the 2'- and 3'-hydroxyl groups and, to some extent, the nature of the Lewis acid catalyst employed. Ultimately, conditions were found that favored either the 5'R or 5'S diastereomer from different cytidine aldehydes, and gave some stereoselectivity in additions to an aldehyde derivative of ara-C. The resulting homoallylic alcohols were used as substrates in attempted Knovenagel and Horner-Wadsworth-Emmons condensations, but elimination was found to predominate over lactone formation under the conditions employed. The desired alpha-phosphono lactones could be prepared through a reaction sequence that included ring-closing metathesis on acrylate esters of the homoallylic alcohols, followed by reduction of the resulting alpha,beta-unsaturated lactones and carbon-phosphorus bond formation on enolates generated from the saturated lactones.
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Affiliation(s)
- Xuemei Chen
- Department of Chemistry, University of Iowa, Iowa City, Iowa 52242-1294, USA
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Kirchhoff C, Nielsen P. Dinucleotides of 4′-C-vinyl- and 5′-C-allylthymidine as substrates for ring-closing metathesis reactions. Tetrahedron Lett 2003. [DOI: 10.1016/s0040-4039(03)01584-3] [Citation(s) in RCA: 19] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/27/2022]
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34
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Whitehead A, Moore JD, Hanson PR. A convenient approach to cyclic enol phosphates via ring-closing metathesis. Tetrahedron Lett 2003. [DOI: 10.1016/s0040-4039(03)00873-6] [Citation(s) in RCA: 32] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/27/2022]
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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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Grubbs RH, Trnka TM, Sanford MS. Transition Metal–Carbene Complexes in Olefin Metathesis and Related Reactions. CURRENT METHODS IN INORGANIC CHEMISTRY 2003. [DOI: 10.1016/s1873-0418(03)80006-4] [Citation(s) in RCA: 32] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/20/2023]
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Børsting P, Nielsen P. Tandem ring-closing metathesis and hydrogenation towards cyclic dinucleotides. Chem Commun (Camb) 2002:2140-1. [PMID: 12357814 DOI: 10.1039/b206560f] [Citation(s) in RCA: 47] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Cyclic dinucleotides containing a butylene nucleobase-phophotriester connection are synthesised by a tandem ring-closing metathesis and hydrogenation reaction.
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Affiliation(s)
- Philip Børsting
- Nucleic Acid Center, Department of Chemistry, University of Southern Denmark, DK-5230, Odense M, Denmark
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Herndon JW. The chemistry of the carbontransition metal double and triple bond: annual survey covering the year 2000. Coord Chem Rev 2002. [DOI: 10.1016/s0010-8545(01)00445-3] [Citation(s) in RCA: 20] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
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39
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Sørensen AM, Nielsen KE, Vogg B, Jacobsen JP, Nielsen P. Synthesis and NMR-studies of dinucleotides with conformationally restricted cyclic phosphotriester linkages. Tetrahedron 2001. [DOI: 10.1016/s0040-4020(01)01047-x] [Citation(s) in RCA: 38] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
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40
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Timmer MS, Ovaa H, Filippov DV, van der Marel GA, van Boom JH. Synthesis of phosphorus mono- and bicycles by catalytic ring-closing metathesis. Tetrahedron Lett 2001. [DOI: 10.1016/s0040-4039(01)01740-3] [Citation(s) in RCA: 45] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
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