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Kanagawa T, Tachibana S, Masaki Y, Seio K. Synthesis and Conformational Analyses of Cyclonucleoside Having 13-Membered Ring Bridging Nucleobase and 5'-Position via a Linker Containing Sulfonamide. Org Lett 2023; 25:7868-7872. [PMID: 37857270 DOI: 10.1021/acs.orglett.3c03094] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/21/2023]
Abstract
A cyclic nucleoside has been designed and synthesized to serve as a conformationally fixed building block for the development of functional oligonucleotides. The bridge was introduced between the nucleobase and the 5'-position to fix the rotation around the C4'-C5' bond, the base orientation, and the sugar puckering all at once. The 13-membered cyclic structure was introduced using a sulfonamide linkage, which retains an N-H group that can be used to attach an additional nucleoside moiety. The sulfonamide linkage was formed through the end-to-end cyclization of an intermediate that contained both a sulfonyltriazole and amino groups. Both 1H NMR and computational studies revealed that the sugar conformation, base orientation, and γ torsion angle were S-type, anti, and trans, respectively. As such, cyclic nucleosides show promise for introducing these specific distorted conformations into functional nucleic acids.
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Affiliation(s)
- Takayuki Kanagawa
- Department of Life Sciences and Technology, Tokyo Institute of Technology, 4259 Nagatsuta-cho, Midori-ku, Yokohama Kanagawa 226-8501, Japan
| | - Shigetoshi Tachibana
- Department of Life Sciences and Technology, Tokyo Institute of Technology, 4259 Nagatsuta-cho, Midori-ku, Yokohama Kanagawa 226-8501, Japan
| | - Yoshiaki Masaki
- Department of Life Sciences and Technology, Tokyo Institute of Technology, 4259 Nagatsuta-cho, Midori-ku, Yokohama Kanagawa 226-8501, Japan
- JST PRESTO, Kawaguchi 332-0012, Japan
| | - Kohji Seio
- Department of Life Sciences and Technology, Tokyo Institute of Technology, 4259 Nagatsuta-cho, Midori-ku, Yokohama Kanagawa 226-8501, Japan
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Convertible and Constrained Nucleotides: The 2'-Deoxyribose 5'-C-Functionalization Approach, a French Touch. Molecules 2021; 26:molecules26195925. [PMID: 34641475 PMCID: PMC8512084 DOI: 10.3390/molecules26195925] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [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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Kano T, Katsuragi Y, Maeda Y, Ueno Y. Synthesis and properties of 4′-C-aminoalkyl-2′-fluoro-modified RNA oligomers. Bioorg Med Chem 2018; 26:4574-4582. [DOI: 10.1016/j.bmc.2018.08.001] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2018] [Revised: 07/30/2018] [Accepted: 08/01/2018] [Indexed: 01/16/2023]
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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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Stemper J, Isaac K, Pastor J, Frison G, Retailleau P, Voituriez A, Betzer J, Marinetti A. Development of Chiral Phosphoric Acids based on Ferrocene‐Bridged Paracyclophane Frameworks. Adv Synth Catal 2013. [DOI: 10.1002/adsc.201300697] [Citation(s) in RCA: 39] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
Affiliation(s)
- Jérémy Stemper
- Institut de Chimie des Substances Naturelles, CNRS UPR 2301, Centre de Recherche de Gif, 91198 Gif‐sur‐Yvette, France, Fax: (+33)‐1‐6907‐7247
| | - Kévin Isaac
- Institut de Chimie des Substances Naturelles, CNRS UPR 2301, Centre de Recherche de Gif, 91198 Gif‐sur‐Yvette, France, Fax: (+33)‐1‐6907‐7247
| | - Julien Pastor
- Laboratoire des Mécanismes Réactionnels, Department of Chemistry, Ecole Polytechnique and CNRS, 91128 Palaiseau, France
| | - Gilles Frison
- Laboratoire des Mécanismes Réactionnels, Department of Chemistry, Ecole Polytechnique and CNRS, 91128 Palaiseau, France
| | - Pascal Retailleau
- Institut de Chimie des Substances Naturelles, CNRS UPR 2301, Centre de Recherche de Gif, 91198 Gif‐sur‐Yvette, France, Fax: (+33)‐1‐6907‐7247
| | - Arnaud Voituriez
- Institut de Chimie des Substances Naturelles, CNRS UPR 2301, Centre de Recherche de Gif, 91198 Gif‐sur‐Yvette, France, Fax: (+33)‐1‐6907‐7247
| | - Jean‐François Betzer
- Institut de Chimie des Substances Naturelles, CNRS UPR 2301, Centre de Recherche de Gif, 91198 Gif‐sur‐Yvette, France, Fax: (+33)‐1‐6907‐7247
| | - Angela Marinetti
- Institut de Chimie des Substances Naturelles, CNRS UPR 2301, Centre de Recherche de Gif, 91198 Gif‐sur‐Yvette, France, Fax: (+33)‐1‐6907‐7247
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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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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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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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Sekine M, Kurasawa O, Shohda KI, Seio K, Wada T. Essential Factors for Stabilization of the Predominant C3′-endo Conformation in Dinucleoside Phosphotriester Derivatives with Cyclonucleotide Bridge Structures at the Downstream 3′-Position. European J Org Chem 2001. [DOI: 10.1002/1099-0690(200105)2001:10<1989::aid-ejoc1989>3.0.co;2-h] [Citation(s) in RCA: 15] [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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11
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Groziak MP, Lin R. The 5′,6-Oxomethylene Transglycosidic Tether for Conformational Restriction of Pyrimidine Ribonucleosides. Investigation of 6-Formyl- and 6-(Hydroxymethyl)uridine 5′-Carboxaldehydes. Tetrahedron 2000. [DOI: 10.1016/s0040-4020(00)00970-4] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
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12
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Sekine M, Kurasawa O, Shohda K, Seio K, Wada T. Synthesis and properties of oligonucleotides having a phosphorus chiral center by incorporation of conformationally rigid 5'-cyclouridylic acid derivatives. J Org Chem 2000; 65:6515-24. [PMID: 11052096 DOI: 10.1021/jo0002588] [Citation(s) in RCA: 30] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
This paper describes the design and synthesis of a conformationally rigid dimer building block Umpc3Um as a chiral center at the phosphate group with the S/N junction where c3 refers to a propylene bridge linked between the uracil 5-position and 5'-phosphate group of pUm. The extensive H1 NMR analysis of Umpc3Um suggests that the 5'-upstream Um has predominantly a C2'-endo conformation and the pc3Um moiety exists almost exclusively in a C3'-endo conformation. The absolute configuration of the diastereomers Umpc3Um(fast) (8a) and Umpc3Um(slow) (8b) was determined by CD spectroscopy as well as computer simulations. The oligonucleotides U4[Umpc3Um(fast)]U4 (13a) and U4[Umpc3Um(slow)]U4 (13b) incorporating 8a and 8b were synthesized by use of the phosphoramidite building blocks 11a and 11b, respectively. The Tm experiments of the duplexes formed between these modified oligomers and the complementary oligomers imply that the modified oligomer 13a having Umpc3Um(fast) has the Sp configuration at the chiral phosphoryl group.
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Affiliation(s)
- M Sekine
- Department of Life Science, Tokyo Institute of Technology, Yokohama, Japan.
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13
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Sekine M, Kurasawa O, Shohda KI, Seio K, Wada T. Synthesis and properties of oligodeoxynucleotides incorporating a conformationally rigid uridine unit having a cyclic structure at the 5'-terminal site. J Org Chem 2000; 65:3571-8. [PMID: 10864738 DOI: 10.1021/jo991374h] [Citation(s) in RCA: 19] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
A 2'-O-methyluridylic acid derivative 3 having a cyclic structure linked between the 5-position of the uracil residue and the 5'-phosphate group was synthesized. The NMR analysis suggests that this cyclouridylic acid derivative has exclusively the C3'-endo conformation that is in favor of duplex formation with RNA. Two oligonucleotides ¿pc3Um(pT)(9) and pc3Um(pU)(9) incorporating this cyclouridylic acid unit at the 5'-terminal site were synthesized by using the fully protected cyclouridylic acid 3'-phosphoramidite derivative 11 in the solid-phase synthesis. To examine the actual effect of this cyclic structure on the thermal stability of duplexes between the modified oligonucleotides and their complementary oligonucleotides, two oligonucleotides ¿pUm(pT)(9) and pUm(pU)(9) having an acyclic structure were also synthesized. As the complementary oligonucleotides, dA(pdA)(9) and A(pA)(9) were used for T(m) experiments with these 5'-terminal modified oligonucleotides. The T(m) values of all the possible duplexes were measured. These results clearly show that the duplex of pc3Um(pT)(9)-A(pA)(9) has a higher T(m) value by 5.5 degrees C than that of A(pA)(9)-T(pT)(9). This is rather significant compared with all other cases. Moreover, the T(m) value of pc3Um(pT)(9)-A(pA)(9) is 4.5 degrees C higher than that of pUm(pT)(9)-A(pA)(9). This result suggests that the cyclic structure can considerably contribute to stabilization of the duplex only in the case of the modified oligomer (DNA) and decaadenylate (RNA).
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Affiliation(s)
- M Sekine
- Department of Life Science, Tokyo Institute of Technology, Nagatsuta, Midoriku, Yokohama 226-8501, Japan
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