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Jestřábová I, Poštová Slavětínská L, Hocek M. Arylethynyl- or Alkynyl-Linked Pyrimidine and 7-Deazapurine 2'-Deoxyribonucleoside 3'-Phosphoramidites for Chemical Synthesis of Hypermodified Hydrophobic Oligonucleotides. ACS OMEGA 2023; 8:39447-39453. [PMID: 37901526 PMCID: PMC10601081 DOI: 10.1021/acsomega.3c05202] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 07/19/2023] [Accepted: 09/28/2023] [Indexed: 10/31/2023]
Abstract
We designed and synthesized a set of 2'-deoxyribonucleoside 3'-phosphoramidites derived from 5-phenylethynyluracil, 5-(pentyn-1-yl)cytosine, 7-(indol-3-yl)ethynyl-7-deazaadenine, and 7-isopropylethynyl-7-deazaguanine. These nucleoside phosphoramidites were successfully used for automated solid-phase synthesis of oligonucleotides containing one or several modifications, including fully modified sequences where every nucleobase was displaying a modification, and their hybridization was studied. The phosphoramidite building blocks have potential for synthesis of hypermodified aptamers and other functional nucleic acid-based polymers, which sequence-specifically display amino acid-like hydrophobic substituents.
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Affiliation(s)
- Ivana Jestřábová
- Institute
of Organic Chemistry and Biochemistry, Czech
Academy of Sciences, Flemingovo nam. 2, CZ-16000 Prague 6, Czech Republic
- Department
of Organic Chemistry, Faculty of Science, Charles University, Hlavova 8, CZ-12843 Prague 2, Czech Republic
| | - Lenka Poštová Slavětínská
- Institute
of Organic Chemistry and Biochemistry, Czech
Academy of Sciences, Flemingovo nam. 2, CZ-16000 Prague 6, Czech Republic
| | - Michal Hocek
- Institute
of Organic Chemistry and Biochemistry, Czech
Academy of Sciences, Flemingovo nam. 2, CZ-16000 Prague 6, Czech Republic
- Department
of Organic Chemistry, Faculty of Science, Charles University, Hlavova 8, CZ-12843 Prague 2, Czech Republic
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2
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Ziemkiewicz K, Warminski M, Wojcik R, Kowalska J, Jemielity J. Quick Access to Nucleobase-Modified Phosphoramidites for the Synthesis of Oligoribonucleotides Containing Post-Transcriptional Modifications and Epitranscriptomic Marks. J Org Chem 2022; 87:10333-10348. [PMID: 35857285 PMCID: PMC9361293 DOI: 10.1021/acs.joc.2c01390] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
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Herein, we report a straightforward one-step procedure
for modifying N-nucleophilic groups in the nucleobases
of commercially
available nucleoside phosphoramidites. This method involves the deprotonation
of amide groups under phase-transfer conditions and subsequent reaction
with electrophilic molecules such as alkyl halides or organic isocyanates.
Using this approach, we obtained 10 different classes of modified
nucleoside phosphoramidites suitable for the synthesis of oligonucleotides,
including several noncanonical nucleotides found in natural RNA or
DNA (e.g., m6A, i6A, m1A, g6A, m3C, m4C, m3U, m1G,
and m2G). Such modification of nucleobases is a common
mechanism for post-transcriptional regulation of RNA stability and
translational activity in various organisms. To better understand
this process, relevant cellular recognition partners (e.g., proteins)
must be identified and characterized. However, this step has been
impeded by limited access to molecular tools containing such modified
nucleotides.
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Affiliation(s)
- Kamil Ziemkiewicz
- Centre of New Technologies, University of Warsaw, Banacha 2c, Warsaw 02-097, Poland
| | - Marcin Warminski
- Division of Biophysics, Institute of Experimental Physics, Faculty of Physics, University of Warsaw, Pasteura 5, Warsaw 02-093, Poland
| | - Radoslaw Wojcik
- Centre of New Technologies, University of Warsaw, Banacha 2c, Warsaw 02-097, Poland
| | - Joanna Kowalska
- Division of Biophysics, Institute of Experimental Physics, Faculty of Physics, University of Warsaw, Pasteura 5, Warsaw 02-093, Poland
| | - Jacek Jemielity
- Centre of New Technologies, University of Warsaw, Banacha 2c, Warsaw 02-097, Poland
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3
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Chakrapani A, Ruiz‐Larrabeiti O, Pohl R, Svoboda M, Krásný L, Hocek M. Glucosylated 5‐Hydroxymethylpyrimidines as Epigenetic DNA Bases Regulating Transcription and Restriction Cleavage. Chemistry 2022; 28:e202200911. [DOI: 10.1002/chem.202200911] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2022] [Indexed: 12/13/2022]
Affiliation(s)
- Aswathi Chakrapani
- Institute of Organic Chemistry and Biochemistry Czech Academy of Sciences Flemingovo nam. 2 16610 Prague 6 Czech Republic
- Department of Organic Chemistry, Faculty of Science Charles University Hlavova 8 CZ-12843 Prague 2 Czech Republic
| | - Olatz Ruiz‐Larrabeiti
- Dept. of Microbial Genetics and Gene Expression Institute of Microbiology Czech Academy of Sciences 14220 Prague 4 Czech Republic
| | - Radek Pohl
- Institute of Organic Chemistry and Biochemistry Czech Academy of Sciences Flemingovo nam. 2 16610 Prague 6 Czech Republic
| | - Martin Svoboda
- Institute of Organic Chemistry and Biochemistry Czech Academy of Sciences Flemingovo nam. 2 16610 Prague 6 Czech Republic
| | - Libor Krásný
- Dept. of Microbial Genetics and Gene Expression Institute of Microbiology Czech Academy of Sciences 14220 Prague 4 Czech Republic
| | - Michal Hocek
- Institute of Organic Chemistry and Biochemistry Czech Academy of Sciences Flemingovo nam. 2 16610 Prague 6 Czech Republic
- Department of Organic Chemistry, Faculty of Science Charles University Hlavova 8 CZ-12843 Prague 2 Czech Republic
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An Improved Approach for Practical Synthesis of 5-Hydroxymethyl-2′-deoxycytidine (5hmdC) Phosphoramidite and Triphosphate. Molecules 2022; 27:molecules27030749. [PMID: 35164012 PMCID: PMC8839764 DOI: 10.3390/molecules27030749] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2022] [Revised: 01/19/2022] [Accepted: 01/20/2022] [Indexed: 11/16/2022] Open
Abstract
5-Hydroxymethyl-2′-deoxycytidine (5hmdC) phosphoramidite and triphosphate are important building blocks in 5hmdC-containing DNA synthesis for epigenetic studies. However, efficient and practical methods for the synthesis of these compounds are still limited. The current research provides an intensively improved synthetic method that enables the preparation of commercially available cyanoethyl-protected 5hmdC phosphoramidite with an overall yield of 39% on 5 g scale. On the basis of facile and efficient accesses to cyanoethyl protected-5hmdU and 5hmdC intermediates, two efficient synthetic routes for 5hmdC triphosphate were also developed.
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Gracias F, Ruiz-Larrabeiti O, Vaňková Hausnerová V, Pohl R, Klepetářová B, Sýkorová V, Krásný L, Hocek M. Homologues of epigenetic pyrimidines: 5-alkyl-, 5-hydroxyalkyl and 5-acyluracil and -cytosine nucleotides: synthesis, enzymatic incorporation into DNA and effect on transcription with bacterial RNA polymerase. RSC Chem Biol 2022; 3:1069-1075. [PMID: 35975001 PMCID: PMC9347353 DOI: 10.1039/d2cb00133k] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2022] [Accepted: 06/23/2022] [Indexed: 12/17/2022] Open
Abstract
Homologues of natural epigenetic pyrimidine nucleosides and nucleotides were designed and synthesized. They included 5-ethyl-, 5-propyl-, 5-(1-hydroxyethyl)-, 5-(1-hydroxypropyl)- and 5-acetyl- and 5-propionylcytosine and -uracil 2′-deoxyribonucleosides and their corresponding 5′-O-triphosphates (dNXTPs). The epimers of 5-(1-hydroxyethyl)- and 5-(1-hydroxypropyl)pyrimidine nucleosides were separated and their absolute configuration was determined by a combination of X-ray and NMR analysis. The modified dNXTPs were used as substrates for PCR synthesis of modified DNA templates used for the study of transcription with bacterial RNA polymerase. Fundamental differences in transcription efficiency were observed, depending on the various modifications. The most notable effects included pronounced stimulation of transcription from 5-ethyluracil-bearing templates (200% transcription yield compared to natural thymine) and an enhancing effect of 5-acetylcytosine versus inhibiting effect of 5-acetyluracil. In summary, these results reveal that RNA polymerase copes with dramatically altered DNA structure and suggest that these nucleobases could potentially play roles as artificial epigenetic DNA nucleobases. Nucleotides derived from homologues of epigenetic pyrimidine bases were prepared and used for polymerase synthesis of modified DNA templates. Interesting effects of the substituents on PCR and transcription have been observed.![]()
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Affiliation(s)
- Filip Gracias
- Institute of Organic Chemistry and Biochemistry, Czech Academy of Sciences, Flemingovo nam. 2, CZ-16000, Prague 6, Czech Republic
| | - Olatz Ruiz-Larrabeiti
- Lab. of Microbial Genetics and Gene Expression, Institute of Microbiology, Czech Academy of Sciences, Vídeňská 1083, CZ-14220, Prague 4, Czech Republic
| | - Viola Vaňková Hausnerová
- Lab. of Microbial Genetics and Gene Expression, Institute of Microbiology, Czech Academy of Sciences, Vídeňská 1083, CZ-14220, Prague 4, Czech Republic
| | - Radek Pohl
- Institute of Organic Chemistry and Biochemistry, Czech Academy of Sciences, Flemingovo nam. 2, CZ-16000, Prague 6, Czech Republic
| | - Blanka Klepetářová
- Institute of Organic Chemistry and Biochemistry, Czech Academy of Sciences, Flemingovo nam. 2, CZ-16000, Prague 6, Czech Republic
| | - Veronika Sýkorová
- Institute of Organic Chemistry and Biochemistry, Czech Academy of Sciences, Flemingovo nam. 2, CZ-16000, Prague 6, Czech Republic
| | - Libor Krásný
- Lab. of Microbial Genetics and Gene Expression, Institute of Microbiology, Czech Academy of Sciences, Vídeňská 1083, CZ-14220, Prague 4, Czech Republic
| | - Michal Hocek
- Institute of Organic Chemistry and Biochemistry, Czech Academy of Sciences, Flemingovo nam. 2, CZ-16000, Prague 6, Czech Republic
- Department of Organic Chemistry, Faculty of Science, Charles University, Hlavova 8, CZ-12843, Prague 2, Czech Republic
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Klimek R, Donlin-Asp PG, Polisseni C, Hanff V, Schuman EM, Heckel A. Visible light-activatable Q-dye molecular beacons for long-term mRNA monitoring in neurons. Chem Commun (Camb) 2021; 57:12683-12686. [PMID: 34780585 DOI: 10.1039/d1cc05664f] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Herein, we present a new class of Q-dye molecular beacons (MBs) that can be locally activated with visible light in hippocampal neurons. Our novel architecture increases the available monitoring time for neuronal mRNA from several minutes to 14 hours, since a lower light-sampling rate is required for tracking.
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Affiliation(s)
- Robin Klimek
- Institute of Organic Chemistry and Chemical Biology, Goethe-University Frankfurt, Max-von-Laue-Straße 9, Frankfurt am Main 60438, Germany.
| | - Paul G Donlin-Asp
- Max Planck Institute for Brain Research, Max-von-Laue Str. 4, Frankfurt am Main 60438, Germany.
| | - Claudio Polisseni
- Max Planck Institute for Brain Research, Max-von-Laue Str. 4, Frankfurt am Main 60438, Germany.
| | - Vanessa Hanff
- Institute of Organic Chemistry and Chemical Biology, Goethe-University Frankfurt, Max-von-Laue-Straße 9, Frankfurt am Main 60438, Germany.
| | - Erin M Schuman
- Max Planck Institute for Brain Research, Max-von-Laue Str. 4, Frankfurt am Main 60438, Germany.
| | - Alexander Heckel
- Institute of Organic Chemistry and Chemical Biology, Goethe-University Frankfurt, Max-von-Laue-Straße 9, Frankfurt am Main 60438, Germany.
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