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Chen X, Xie L, Zhang C, Tian S, Tang Z, Xiang M, Tian W, Lu P, Yang X. Synthesis of Nucleotides Bearing the 2'-O-Trifluoromethyl Group and Their Application in RNA Analogs Preparation. Curr Protoc 2024; 4:e956. [PMID: 38230581 DOI: 10.1002/cpz1.956] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/18/2024]
Abstract
The integration of fluorine atoms into biologically active organic compounds has proved to be a vital technique in small molecule drugs. This technique can substantially enhance crucial properties, including metabolic stability, lipophilicity, and bioavailability, often with a mere addition of a single fluorine atom or a trifluoromethyl group. Over the past few decades, this concept has also been applied in nucleic acid chemistry. A commonly employed 2'-OH substitution is the introduction of a 2'-deoxy-2'-fluoro (2'-F) group. The strong electronegativity of fluorine prompts the modified siRNA to readily adopt a C3'-endo conformation, resulting in significant advantages in terms of binding affinity. To enrich the toolbox of chemical modification of oligonucleotides, the replacement of the 2'-OH with the 2'-O-trifluoromethyl group has been developed in RNA analog synthesis. Oligodeoxynucleotides containing the 2'-O-trifluoromethyl group can greatly increase the thermal stability of DNA/RNA duplexes depending on the position and amount of the modification. Moreover, 2'-O-trifluoromethylated oligodeoxynucleotide also exhibited a slightly higher resistance to snake venom phosphodiesterase than the unmodified oligodeoxynucleotide. The 2'-O-trifluoromethylated oligonucleotides can emerge as a label to study RNA structure and function as well, or to develop DNA/RNA-based diagnostics. Hence, it is necessary to report an effective method for the synthesis, deprotection, purification, and characterization of oligonucleotides bearing a 2'-O-trifluoromethyl group. © 2024 Wiley Periodicals LLC. Basic Protocol 1: Preparation of 6-N-benzoyl-5'-O-dimethoxytrityl-2'-O-trifluoromethyl adenosine 3'-(2-cyanoethyl N,N-diisopropyl)phosphoramidite Basic Protocol 2: Preparation of 4-N-acetyl-5'-O-dimethoxytrityl-2'-O-trifluoromethyl cytidine 3'-(2-cyanoethyl N,N-diisopropyl)phosphoramidite Basic Protocol 3: Preparation of 2-N-isobutyryl-5'-O-dimethoxytrityl-2'-O-trifluoromethyl guanine 3'-(2-cyanoethyl N,N-diisopropyl)phosphoramidite Basic Protocol 4: Preparation of 5'-O-dimethoxytrityl-2'-O-2-trifluoromethyl uridine 3'-(2-cyanoethyl N,N-diisopropyl) phosphoramidite Basic Protocol 5: Solid-phase synthesis of 2'-O-trifluoromethylated RNA analogs Basic Protocol 6: Deprotection and purification of 2'-O-trifluoromethyl-RNAs.
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2
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Chen X, Xie L, Zhang C, Tian S, Tang Z, Tian W, Lu P, Yang X. A Convenient Method for the Synthesis of 2'-O-Cyanoethylated Nucleotides and Their Application in the Solid-Phase Synthesis of Related RNA Analogs. Curr Protoc 2023; 3:e923. [PMID: 37962485 DOI: 10.1002/cpz1.923] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2023]
Abstract
Although small interfering RNA (siRNA) is a key player among gene inhibition therapeutics, there are many obstacles to the development of siRNA drugs due to inherent properties of oligonucleotides, including the unsatisfactory stability of unmodified siRNA, poor pharmacokinetic distribution, and the toxicity induced by off-target effects. To maximize treatment potency, chemical modification of siRNA has undoubtedly been the most successful strategy by far. Widely applied modifications include phosphorothioate linkages, 2'-O-methyl modifications, and 2'-fluoro modifications, among others. To extend the family of chemical modifications for oligonucleotides, 2'-O-cyanoethylated RNA analogs were developed through the replacement of the 2'-hydroxyl group with a 2'-O-cyanoethyl group (-OCH2 CH2 CN). This modification can provide several advantages over unmodified RNA, such as increased stability, improved binding affinity to complementary DNA or RNA strands, and resistance to degradation by cellular nucleases. The 2'-O-cyanoethyl-modified RNAs not only are applied in RNA silencing machinery but also act as research tools for studying RNA structure and function or for developing RNA-based diagnostics. Therefore, the efficient synthesis, deprotection, purification, and characterization of 2'-O-cyanoethylated RNAs deserves more attention. This protocol describes the chemical synthesis of 2'-O-cyanoethylated nucleotides and the solid-phase synthesis, deprotection, and purification of 2'-O-cyanoethylated RNAs. © 2023 Wiley Periodicals LLC. Basic Protocol 1: Preparation of 6-N-dimethylformamidyl-5'-O-dimethoxytrityl-2'-O-cyanoethyl adenosine 3'-(2-cyanoethyl N,N-diisopropyl)phosphoramidite Basic Protocol 2: Preparation of 4-N-acetyl-5'-O-dimethoxytrityl-2'-O-cyanoethyl cytidine 3'-(2-cyanoethyl N,N-diisopropyl)phosphoramidite Basic Protocol 3: Preparation of 2-N-dimethylformamidyl-5'-O-dimethoxytrityl-2'-O-cyanoethyl guanine 3'-(2-cyanoethyl N,N-diisopropyl)phosphoramidite Basic Protocol 4: Preparation of 5'-O-dimethoxytrityl-2'-O-2-cyanoethyl uridine 3'-(2-cyanoethyl N,N-diisopropyl)phosphoramidite Basic Protocol 5: Solid-phase synthesis of 2'-O-cyanoethylated RNA analogs Basic Protocol 6: Deprotection and purification of synthesized 2'-O-cyanoethyl-RNAs.
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Affiliation(s)
- Xuan Chen
- Sirnaomics Ltd. Suzhou, Suzhou, China
| | - Long Xie
- Sirnaomics Ltd. Suzhou, Suzhou, China
| | | | - Shen Tian
- Sirnaomics Ltd. Suzhou, Suzhou, China
| | - Zeyu Tang
- Sirnaomics Ltd. Suzhou, Suzhou, China
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3
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Das G, Harikrishna S, Gore KR. Influence of Sugar Modifications on the Nucleoside Conformation and Oligonucleotide Stability: A Critical Review. CHEM REC 2022; 22:e202200174. [PMID: 36048010 DOI: 10.1002/tcr.202200174] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2022] [Revised: 08/16/2022] [Indexed: 12/15/2022]
Abstract
Ribofuranose sugar conformation plays an important role in the structure and dynamics of functional nucleic acids such as siRNAs, AONs, aptamers, miRNAs, etc. To improve their therapeutic potential, several chemical modifications have been introduced into the sugar moiety over the years. The stability of the oligonucleotide duplexes as well as the formation of stable and functional protein-oligonucleotide complexes are dictated by the conformation and dynamics of the sugar moiety. In this review, we systematically categorise various ribofuranose sugar modifications employed in DNAs and RNAs so far. We discuss different stereoelectronic effects imparted by different substituents on the sugar ring and how these effects control sugar puckering. Using this data, it would be possible to predict the precise use of chemical modifications and design novel sugar-modified nucleosides for therapeutic oligonucleotides that can improve their physicochemical properties.
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Affiliation(s)
- Gourav Das
- Department of Chemistry, Indian Institute of Technology Kharagpur, Kharagpur, West Bengal-721302, India
| | - S Harikrishna
- Department of Chemistry and Center for Structural Biology, Vanderbilt University, Nashville, TN 37240, USA
| | - Kiran R Gore
- Department of Chemistry, Indian Institute of Technology Kharagpur, Kharagpur, West Bengal-721302, India
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4
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Cabrero C, Martín-Pintado N, Mazzini S, Gargallo R, Eritja R, Aviñó A, González C. Structural Effects of Incorporation of 2'-Deoxy-2'2'-Difluorodeoxycytidine (Gemcitabine) in A- and B-Form Duplexes. Chemistry 2021; 27:7351-7355. [PMID: 33772916 DOI: 10.1002/chem.202100503] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2021] [Indexed: 11/06/2022]
Abstract
We report the structural effect of 2'-deoxy-2',2'-difluorocytidine (dFdC) insertions in the DNA strand of a DNA : RNA hybrid duplex and in a self-complementary DNA : DNA duplex. In both cases, the modification slightly destabilizes the duplex and provokes minor local distortions that are more pronounced in the case of the DNA : RNA hybrid. Analysis of the solution structures determined by NMR methods show that dFdC is an adaptable derivative that adopts North type sugar conformation when inserted in pure DNA, or a South sugar conformation in the context of DNA : RNA hybrids. In this latter context, South sugar pucker favors the formation of a 2'F⋅⋅H8 attractive interaction with a neighboring purine, which compensates the destabilizing effect of base pair distortions. These interactions share some features with pseudohydrogen bonds described previously in other nucleic acids structures with fluorine modified sugars.
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Affiliation(s)
- Cristina Cabrero
- Instituto de Química Física Rocasolano, CSIC, Serrano, 119, 28006, Madrid, Spain
| | - Nerea Martín-Pintado
- Instituto de Química Física Rocasolano, CSIC, Serrano, 119, 28006, Madrid, Spain
| | - Stefania Mazzini
- Department of Food, Environmental and Nutritional Sciences (DEFENS), Università degli Studi di Milano, Via Celoria 2, 20133, Milano, Italy
| | - Raimundo Gargallo
- Dept. of Chemical Engineering and Analytical Chemistry, University of Barcelona, Marti i Franquès 1, 08028, Barcelona, Spain.,BIOESTRAN associated unit UB-CSIC, 08028, Barcelona, Spain
| | - Ramon Eritja
- Institute for Advanced Chemistry of Catalonia (IQAC-CSIC) CIBER-BBN, Jordi, Girona 18-26, 08034, Barcelona, Spain
| | - Anna Aviñó
- Institute for Advanced Chemistry of Catalonia (IQAC-CSIC) CIBER-BBN, Jordi, Girona 18-26, 08034, Barcelona, Spain
| | - Carlos González
- Instituto de Química Física Rocasolano, CSIC, Serrano, 119, 28006, Madrid, Spain.,BIOESTRAN associated unit UB-CSIC, 08028, Barcelona, Spain
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5
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Varley AJ, Desaulniers JP. Chemical strategies for strand selection in short-interfering RNAs. RSC Adv 2021; 11:2415-2426. [PMID: 35424193 PMCID: PMC8693850 DOI: 10.1039/d0ra07747j] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2020] [Accepted: 12/24/2020] [Indexed: 12/13/2022] Open
Abstract
Therapeutic small interfering RNAs (siRNAs) are double stranded RNAs capable of potent and specific gene silencing through activation of the RNA interference (RNAi) pathway. The potential of siRNA drugs has recently been highlighted by the approval of multiple siRNA therapeutics. These successes relied heavily on chemically modified nucleic acids and their impact on stability, delivery, potency, and off-target effects. Despite remarkable progress, clinical trials still face failure due to off-target effects such as off-target gene dysregulation. Each siRNA strand can downregulate numerous gene targets while also contributing towards saturation of the RNAi machinery, leading to the upregulation of miRNA-repressed genes. Eliminating sense strand uptake effectively reduces off-target gene silencing and helps limit the disruption to endogenous regulatory mechanisms. Therefore, our understanding of strand selection has a direct impact on the success of future siRNA therapeutics. In this review, the approaches used to improve strand uptake are discussed and effective methods are summarized.
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Affiliation(s)
- Andrew J Varley
- Faculty of Science, University of Ontario Institute of Technology Oshawa Ontario L1G 0C5 Canada +1 905 721 3304 +1 905 721 8668 (ext. 3621)
| | - Jean-Paul Desaulniers
- Faculty of Science, University of Ontario Institute of Technology Oshawa Ontario L1G 0C5 Canada +1 905 721 3304 +1 905 721 8668 (ext. 3621)
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6
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Hofmeister A, Jahn-Hofmann K, Krack A, Müller A, Kurz M, Scheidler S. Novel Dioxane and Morpholino Nucleotide Analogues: Syntheses and RNA-Hybridization Properties. Chembiochem 2020; 22:1072-1078. [PMID: 33112485 DOI: 10.1002/cbic.202000693] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2020] [Revised: 10/26/2020] [Indexed: 11/09/2022]
Abstract
A novel class of nucleotide analogues with a dioxane ring as central scaffold has been developed. Synthetic routes in two diastereomeric series were realized, and the final thymidine analogues were synthesized with common functionalities for the automated oligonucleotide synthesis. The chemical space of the initially derived nucleotides was expanded by changing the central dioxane to analogous morpholine derivatives. This opens up the possibility for further derivatization by attaching different substituents at the morpholine nitrogen. The novel nucleotide building blocks were incorporated into double-stranded RNA sequences, and their hybridization properties investigated by melting-temperature analysis. Both scaffolds, dioxanes and morpholines, had an equal impact on double-strand stability, but Tm values differed depending on the chirality in the six-membered ring.
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Affiliation(s)
- Armin Hofmeister
- Sanofi R&D, Industrial Park Hoechst, G838, 65926, Frankfurt am Main, Germany
| | | | - Arne Krack
- Sanofi R&D, Industrial Park Hoechst, G838, 65926, Frankfurt am Main, Germany
| | - Armin Müller
- Sanofi R&D, Industrial Park Hoechst, G838, 65926, Frankfurt am Main, Germany
| | - Michael Kurz
- Sanofi R&D, Industrial Park Hoechst, G838, 65926, Frankfurt am Main, Germany
| | - Sabine Scheidler
- Sanofi R&D, Industrial Park Hoechst, G838, 65926, Frankfurt am Main, Germany
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7
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Frei S, Katolik AK, Leumann CJ. Synthesis, biophysical properties, and RNase H activity of 6'-difluoro[4.3.0]bicyclo-DNA. Beilstein J Org Chem 2019; 15:79-88. [PMID: 30680042 PMCID: PMC6334804 DOI: 10.3762/bjoc.15.9] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2018] [Accepted: 12/13/2018] [Indexed: 12/25/2022] Open
Abstract
Here we present the synthesis, the biophysical properties, and the RNase H profile of 6'-difluorinated [4.3.0]bicyclo-DNA (6'-diF-bc4,3-DNA). The difluorinated thymidine phosphoramidite building block was synthesized starting from an already known gem-difluorinated tricyclic glycal. This tricyclic siloxydifluorocyclopropane was converted into the [4.3.0]bicyclic nucleoside via cyclopropane ring-opening through the addition of an electrophilic iodine during the nucleosidation step followed by reduction. The gem-difluorinated bicyclic nucleoside was then converted into the corresponding phosphoramidite building block which was incorporated into oligonucleotides. Thermal denaturation experiments of these oligonucleotides hybridized to complementary DNA or RNA disclosed a significant destabilization of both duplex types (ΔT m/mod = -1.6 to -5.5 °C). However, in the DNA/RNA hybrid the amount of destabilization could be reduced by multiple insertions of the modified unit. In addition, CD spectroscopy of the oligonucleotides hybridized to RNA showed a similar structure than the natural DNA/RNA duplex. Furthermore, since the structural investigation on the nucleoside level by X-ray crystallography and ab initio calculations pointed to a furanose conformation in the southern region, a RNase H cleavage assay was conducted. This experiment revealed that the oligonucleotide containing five modified units was able to elicit the RNase H-mediated cleavage of the complementary RNA strand.
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Affiliation(s)
- Sibylle Frei
- Department of Chemistry and Biochemistry, University of Bern, Freiestrasse 3, 3012 Bern, Switzerland
| | - Adam K Katolik
- 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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8
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Istrate A, Katolik A, Istrate A, Leumann CJ. 2'β-Fluoro-Tricyclo Nucleic Acids (2'F-tc-ANA): Thermal Duplex Stability, Structural Studies, and RNase H Activation. Chemistry 2017; 23:10310-10318. [PMID: 28477335 DOI: 10.1002/chem.201701476] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2017] [Indexed: 01/16/2023]
Abstract
We describe the synthesis, thermal stability, structural and RNase H activation properties of 2'β-fluoro-tricyclo nucleic acids (2'F-tc-ANA). Three 2'F-tc-ANA nucleosides (T, 5Me C and A) were synthesized starting from a previously described fluorinated tricyclo sugar intermediate. NMR analysis and quantum mechanical calculations indicate that 2'F-tc-ANA nucleosides prefer sugar conformations in the East and South regions of the pseudorotational cycle. UV-melting experiments revealed that non-consecutive insertions of 2'F-tc-ANA units in DNA reduce the affinity to DNA and RNA complements. However, an oligonucleotide with five contiguous 2'F-tc-ANA-T insertions exhibits increased affinity to complementary RNA. Moreover, a fully modified 10-mer 2'F-tc-ANA oligonucleotide paired to both DNA (+1.6 °C/mod) and RNA (+2.5 °C/mod) with significantly higher affinity compared to corresponding unmodified DNA, and similar affinity compared to corresponding tc-DNA. In addition, CD spectroscopy and molecular dynamics simulations indicate that the conformation of the 2'F-tc-ANA/RNA duplex is similar to that of a DNA/RNA duplex. Moreover, in some sequence contexts, 2'F-tc-ANA promotes RNase H-mediated cleavage of a complementary RNA strand. Taken together, 2'F-tc-ANA represents a nucleic acid analogue that offers the advantage of high RNA affinity while maintaining the ability to activate RNase H, and can be considered a prospective candidate for gene silencing applications.
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Affiliation(s)
- Alena Istrate
- Department of Chemistry and Biochemistry, University of Bern, Freiestrasse 3, 3012, Bern, Switzerland
| | - Adam Katolik
- Department of Chemistry and Biochemistry, University of Bern, Freiestrasse 3, 3012, Bern, Switzerland
| | - Andrei Istrate
- 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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9
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Ingale SA, Leonard P, Tran QN, Seela F. Duplex DNA and DNA-RNA hybrids with parallel strand orientation: 2'-deoxy-2'-fluoroisocytidine, 2'-deoxy-2'-fluoroisoguanosine, and canonical nucleosides with 2'-fluoro substituents cause unexpected changes on the double helix stability. J Org Chem 2015; 80:3124-38. [PMID: 25742047 DOI: 10.1021/acs.joc.5b00040] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Oligonucleotides with parallel or antiparallel strand orientation incorporating 2'-fluorinated 2'-deoxyribonucleosides with canonical nucleobases or 2'-deoxy-2'-fluoroisocytidine ((F)iCd, 1c) and 2'-deoxy-2'-fluoroisoguanosine ((F)iGd, 3c) were synthesized. To this end, the nucleosides 1c and 3c as well as the phosphoramidite building blocks 19 and 23 were prepared and employed in solid-phase oligonucleotide synthesis. Unexpectedly, (F)iCd is not stable during oligonucleotide deprotection (55 °C, aq NH3) and was converted to a cyclonucleoside (14). Side product formation was circumvented when oligonucleotides were deprotected under mild conditions (aq ammonia-EtOH, rt). Oligonucleotides containing 2'-fluoro substituents ((F)iCd, (F)iGd and fluorinated canonical 2'-deoxyribonucleosides) stabilize double-stranded DNA, RNA, and DNA-RNA hybrids with antiparallel strand orientation. Unexpected strong stability changes are observed for oligonucleotide duplexes with parallel chains. While fluorinated oligonucleotides form moderately stable parallel stranded duplexes with complementary DNA, they do not form stable hybrids with RNA. Furthermore, oligoribonucleotide duplexes with parallel strand orientation are extremely unstable. It is anticipated that nucleic acids with parallel chains might be too rigid to accept sugar residues in the N-conformation as observed for ribonucleosides or 2'-deoxy-2'-fluororibonucleosides. These observations might explain why nature has evolved the principle of antiparallel chain orientation and has not used the parallel chain alignment.
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Affiliation(s)
- Sachin A Ingale
- †Laboratory of Bioorganic Chemistry and Chemical Biology, Center for Nanotechnology, Heisenbergstrasse 11, 48149 Münster, Germany
| | - Peter Leonard
- †Laboratory of Bioorganic Chemistry and Chemical Biology, Center for Nanotechnology, Heisenbergstrasse 11, 48149 Münster, Germany
| | - Quang Nhat Tran
- †Laboratory of Bioorganic Chemistry and Chemical Biology, Center for Nanotechnology, Heisenbergstrasse 11, 48149 Münster, Germany
| | - Frank Seela
- †Laboratory of Bioorganic Chemistry and Chemical Biology, Center for Nanotechnology, Heisenbergstrasse 11, 48149 Münster, Germany.,‡Laboratorium für Organische und Bioorganische Chemie, Institut für Chemie neuer Materialien, Universität Osnabrück, Barbarastrasse 7, 49069 Osnabrück, Germany
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10
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Jung ME, Dwight TA, Vigant F, Østergaard ME, Swayze EE, Seth PP. Synthesis and duplex-stabilizing properties of fluorinated N-methanocarbathymidine analogues locked in the C3'-endo conformation. Angew Chem Int Ed Engl 2014; 53:9893-7. [PMID: 25044699 DOI: 10.1002/anie.201405283] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2014] [Indexed: 11/11/2022]
Abstract
The efficient synthesis, antiviral activity, and duplex-stabilizing properties of both isomers of the 2'-fluoro analogue of Northern methanocarbathymidine (N-MCT), 2 and 3, are reported. We show that 2'-F incorporation on the N-MCT scaffold has a strong stabilizing effect on duplex thermal stability.
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Affiliation(s)
- Michael E Jung
- Department of Chemistry and Biochemistry, University of California, Los Angeles, CA 90095 (USA).
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11
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Jung ME, Dwight TA, Vigant F, Østergaard ME, Swayze EE, Seth PP. Synthesis and Duplex-Stabilizing Properties of FluorinatedN-Methanocarbathymidine Analogues Locked in the C3′-endoConformation. Angew Chem Int Ed Engl 2014. [DOI: 10.1002/ange.201405283] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
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12
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Kröner C, Thunemann M, Vollmer S, Kinzer M, Feil R, Richert C. Endless: a purine-binding RNA motif that can be expressed in cells. Angew Chem Int Ed Engl 2014; 53:9198-202. [PMID: 25045108 DOI: 10.1002/anie.201403579] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2014] [Revised: 04/29/2014] [Indexed: 01/16/2023]
Abstract
It is becoming increasingly clear that nature uses RNAs extensively for regulating vital functions of the cell, and short sequences are frequently used to suppress gene expression. However, controlling the concentration of small molecules intracellularly through designed RNA sequences that fold into ligand-binding structures is difficult. The development of "endless", a triplex-based folding motif that can be expressed in mammalian cells and binds the second messenger 3',5'-cyclic guanosine monophosphate (cGMP), is described. In vitro, DNA or RNA versions of endless show low micromolar to nanomolar dissociation constants for cGMP. To test its functionality in vivo, four endless RNA motifs arranged in tandem were co-expressed with a fluorescent cGMP sensor protein in murine vascular smooth muscle cells. Nitric oxide induced endogenous cGMP signals were suppressed in endless-expressing cells compared to cells expressing a control motif, which suggests that endless can act as a genetically encoded cGMP sink to modulate signal transduction in cells.
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Affiliation(s)
- Christoph Kröner
- Institut für Organische Chemie, Universität Stuttgart, 70569 Stuttgart (Germany)
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13
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Kröner C, Thunemann M, Vollmer S, Kinzer M, Feil R, Richert C. Endless: A Purine-Binding RNA Motif that Can Be Expressed in Cells. Angew Chem Int Ed Engl 2014. [DOI: 10.1002/ange.201403579] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
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14
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N'Go I, Golten S, Ardá A, Cañada J, Jiménez-Barbero J, Linclau B, Vincent SP. Tetrafluorination of sugars as strategy for enhancing protein-carbohydrate affinity: application to UDP-Galp mutase inhibition. Chemistry 2013; 20:106-12. [PMID: 24311368 DOI: 10.1002/chem.201303693] [Citation(s) in RCA: 60] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2013] [Indexed: 01/16/2023]
Abstract
Tetrafluorinated analogues of both UDP-galactopyranose and UDP-galactofuranose have been synthesized and assayed against UDP-galactopyranose mutase, a key enzyme for Mycobacterium tuberculosis cell wall biosynthesis. Competition assays and STD-NMR spectroscopy techniques have evidenced not only the first unambiguous case of affinity enhancement through local sugar polyfluorination, but also showed that tetrafluorination can still have a beneficial effect on binding when monofluorination at the same position does not.
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Affiliation(s)
- Inès N'Go
- Department of Chemistry, University of Namur, Rue de Bruxelles 61, 5000 Namur (Belgium)
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15
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Deleavey GF, Frank F, Hassler M, Wisnovsky S, Nagar B, Damha MJ. The 5′ Binding MID Domain of Human Argonaute2 Tolerates Chemically Modified Nucleotide Analogues. Nucleic Acid Ther 2013; 23:81-7. [DOI: 10.1089/nat.2012.0393] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022] Open
Affiliation(s)
| | - Filipp Frank
- Department of Biochemistry, McGill University, Montréal, Canada
| | - Matthew Hassler
- Department of Chemistry, McGill University, Montréal, Canada
| | - Simon Wisnovsky
- Department of Chemistry, McGill University, Montréal, Canada
| | - Bhushan Nagar
- Department of Biochemistry, McGill University, Montréal, Canada
| | - Masad J. Damha
- Department of Chemistry, McGill University, Montréal, Canada
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16
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Seth PP, Pallan PS, Swayze EE, Egli M. Synthesis, duplex stabilization and structural properties of a fluorinated carbocyclic LNA analogue. Chembiochem 2012. [PMID: 23193103 DOI: 10.1002/cbic.201200669] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
DNA oligonucleotides modified with nucleoside monomers which have an electron withdrawing group (EWG) at the 2'-position of the furanose ring form more stable duplexes with complementary RNA as compared to unmodified DNA. Here we show that an anti-periplanar orientation of the nucleobase and the 2'-EWG is important for optimal duplex stabilization even for nucleic acid analogues with conformationally locked furanose rings.
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Affiliation(s)
- Punit P Seth
- Department of Medicinal Chemistry, Isis Pharmaceuticals, 2855 Gazelle Court, Carlsbad, CA 92010, USA.
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17
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Patra A, Paolillo M, Charisse K, Manoharan M, Rozners E, Egli M. 2'-Fluoro RNA shows increased Watson-Crick H-bonding strength and stacking relative to RNA: evidence from NMR and thermodynamic data. Angew Chem Int Ed Engl 2012; 51:11863-6. [PMID: 23055396 PMCID: PMC3757553 DOI: 10.1002/anie.201204946] [Citation(s) in RCA: 68] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2012] [Revised: 08/21/2012] [Indexed: 11/06/2022]
Affiliation(s)
- Amritraj Patra
- Department of Biochemistry, Vanderbilt University School of Medicine, Nashville, TN 37232-0146 (USA)
| | - Michael Paolillo
- Department of Chemistry, State University of New York at Binghamton, Binghamton, NY 13902 (USA)
| | - Klaus Charisse
- Alnylam Pharmaceuticals, 300 Third Street, Cambridge, MA 02142 (USA)
| | - Muthiah Manoharan
- Alnylam Pharmaceuticals, 300 Third Street, Cambridge, MA 02142 (USA)
| | - Eriks Rozners
- Department of Chemistry, State University of New York at Binghamton, Binghamton, NY 13902 (USA)
| | - Martin Egli
- Department of Biochemistry, Vanderbilt University School of Medicine, Nashville, TN 37232-0146 (USA)
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Patra A, Paolillo M, Charisse K, Manoharan M, Rozners E, Egli M. 2′-Fluoro RNA Shows Increased Watson-Crick H-Bonding Strength and Stacking Relative to RNA: Evidence from NMR and Thermodynamic Data. Angew Chem Int Ed Engl 2012. [DOI: 10.1002/ange.201204946] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
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19
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Egetenmeyer S, Richert C. A 5'-cap for DNA probes binding RNA target strands. Chemistry 2011; 17:11813-27. [PMID: 21932288 DOI: 10.1002/chem.201101828] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2011] [Indexed: 11/09/2022]
Abstract
Detecting short RNA strands with high fidelity at any of the bases of their sequence, including the termini, can be challenging, since fraying, wobbling, and refolding all compete with canonical base pairing. We performed a search for 5'-substituents of oligodeoxynucleotides that increase base pairing fidelity at the terminus of duplexes with RNA target strands. From a total of over 70 caps, differing in stacking moiety and linker, a phosphodiester-linked sequence of the residues of L-prolinol, glycine, and oxolinic acid, dubbed ogOA, was identified as a 5'-cap that stabilizes any of the four canonical base pairs, with ΔT(m) values of up to +13.1 °C for an octamer. At the same time, the cap increases discrimination against any of the 12 possible terminal mismatches, including mismatches that are more stable than their perfectly matched counterparts in the control duplex, such as A:A. A probe with the cap also showed increased selectivity in the detection of two closely related microRNAs, let7c and let7a, with a ΔT(m) value of 9.2 °C. Melting curves also yielded thermodynamic data that shed light on the uniformity of molecular recognition in the sequence space of DNA:DNA and DNA:RNA duplexes. Hybridization probes with fidelity-enhancing caps should find applications in the individual and parallel detection of biologically active RNA species.
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Affiliation(s)
- Simone Egetenmeyer
- Institut für Organische Chemie, Universität Stuttgart, 70569 Stuttgart, Germany
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