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Dong T, Yu P, Zhao J, Wang J. Site specifically probing the unfolding process of human telomere i-motif DNA using vibrationally enhanced alkynyl stretch. Phys Chem Chem Phys 2024; 26:3857-3868. [PMID: 38224126 DOI: 10.1039/d3cp05328h] [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: 01/16/2024]
Abstract
The microscopic unfolding process of a cytosine-rich DNA forming i-motif by hemi-protonated base pairs is related to gene regulation. However, the detailed thermal unfolding mechanism and the protonation/deprotonation status of site-specific cytosine in DNA in a physiological environment are still obscure. To address this issue, a vibration-enhanced CC probe tagged on 5'E terminal cytosine of human telomere i-motif DNA was examined using linear and nonlinear infrared (IR) spectroscopies and quantum-chemistry calculations. The CC probe extended into the major groove of the i-motif was found using nonlinear IR results only to introduce a minor steric effect on both steady-state structure and local structure dynamics; however, its IR absorption profile effectively reports the cleavage of the hemi-protonated base pair of C1-C13 upon the unfolding with C1 remaining protonated. The temperature mid-point (Tm) of the local transition reported using the CC tag was slightly lower than the Tm of global transition, and the enthalpy of the former exceeds 60% of the global transition. It is shown that the base-pair unraveling is noncooperative, with outer base pairs breaking first and being likely the rate limiting step. Our results offered an in-depth understanding of the macroscopic unfolding characteristics of the i-motif DNA and provided a nonlinear IR approach to monitoring the local structural transition and dynamics of DNA and its complexes.
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Affiliation(s)
- Tiantian Dong
- Beijing National Laboratory for Molecular Sciences, Molecular Reaction Dynamics Laboratory, CAS Research/Education Center for Excellence in Molecular Sciences, Institute of Chemistry, Chinese Academy of Sciences, Beijing, 100190, P. R. China.
- University of Chinese Academy of Sciences, Beijing 100049, P. R. China
| | - Pengyun Yu
- Beijing National Laboratory for Molecular Sciences, Molecular Reaction Dynamics Laboratory, CAS Research/Education Center for Excellence in Molecular Sciences, Institute of Chemistry, Chinese Academy of Sciences, Beijing, 100190, P. R. China.
- University of Chinese Academy of Sciences, Beijing 100049, P. R. China
| | - Juan Zhao
- Beijing National Laboratory for Molecular Sciences, Molecular Reaction Dynamics Laboratory, CAS Research/Education Center for Excellence in Molecular Sciences, Institute of Chemistry, Chinese Academy of Sciences, Beijing, 100190, P. R. China.
- University of Chinese Academy of Sciences, Beijing 100049, P. R. China
| | - Jianping Wang
- Beijing National Laboratory for Molecular Sciences, Molecular Reaction Dynamics Laboratory, CAS Research/Education Center for Excellence in Molecular Sciences, Institute of Chemistry, Chinese Academy of Sciences, Beijing, 100190, P. R. China.
- University of Chinese Academy of Sciences, Beijing 100049, P. R. China
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2
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Passow KT, Harki DA. 4-Isocyanoindole-2'-deoxyribonucleoside (4ICIN): An Isomorphic Indole Nucleoside Suitable for Inverse Electron Demand Diels-Alder Reactions. Tetrahedron Lett 2023; 132:154807. [PMID: 38009110 PMCID: PMC10673620 DOI: 10.1016/j.tetlet.2023.154807] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2023]
Abstract
Isomorphic nucleosides are powerful tool compounds for interrogating a variety of biological processes involving nucleosides and nucleic acids. We previously reported a fluorescent isomorphic indole nucleoside called 4CIN. A distinguishing molecular feature of 4CIN is the presence of a 4-cyano moiety on the indole that functions as the nucleobase. Given the known chemical reactivity of isonitriles with tetrazines through [4+1]-cycloaddition chemistry, we investigated whether conversion of 4CIN to the corresponding isonitrile would confer a useful chemical probe. Here we report the synthesis of 4-isocyanoindole-2'-deoxyribonucleoside (4ICIN) and the propensity of 4ICIN to undergo inverse electron demand Diels-Alder cycloaddition with a model tetrazine.
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Affiliation(s)
- Kellan T Passow
- Department of Medicinal Chemistry, University of Minnesota, 2231 6th Street SE, Minneapolis, MN 55455, United States
| | - Daniel A Harki
- Department of Medicinal Chemistry, University of Minnesota, 2231 6th Street SE, Minneapolis, MN 55455, United States
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3
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Bristiel A, Cadinot M, Pizzonero M, Taran F, Urban D, Guignard R, Guianvarc'h D. 2'-Modified Thymidines with Bioorthogonal Cyclopropene or Sydnone as Building Blocks for Copper-Free Postsynthetic Functionalization of Chemically Synthesized Oligonucleotides. Bioconjug Chem 2023; 34:1613-1621. [PMID: 37669427 DOI: 10.1021/acs.bioconjchem.3c00284] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 09/07/2023]
Abstract
The development of facile methods for conjugating relevant probes, ligands, or delivery agents onto oligonucleotides (ONs) is highly desirable both for fundamental studies in chemical biology and for improving the pharmacology of ONs in medicinal chemistry. Numerous efforts have been focused on the introduction of bioorthogonal groups onto phosphoramidite building blocks, allowing the controlled chemical synthesis of reactive ONs for postsynthetic modifications. Among these building blocks, alkyne, cyclooctynes, trans-cyclooctene, and norbornene have been proved to be compatible with automated solid-phase chemistry. Herein, we present the development of novel 2'-functionalized nucleoside phosphoramidite monomers comprising bioorthogonal methylcyclopropene or sydnone moieties and their introduction for the first time to ON solid-phase synthesis. Traceless ON postsynthetic modifications with reactive complementary probes were successfully achieved through either inverse electron-demand Diels-Alder (iEDDA) reactions or strain-promoted sydnone-alkyne cycloaddition (SPSAC). These results expand the set of bioorthogonal phosphoramidite building blocks to generate ONs for postsynthetic labeling.
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Affiliation(s)
- Alexandra Bristiel
- Université Paris-Saclay, CNRS, Institut de Chimie Moléculaire et des Matériaux d'Orsay (ICMMO), UMR 8182, 91405, Orsay, France
- Unité Drug Design Small Molecules, Institut de Recherche et Développement Servier Paris-Saclay, 22 route 128, Gif-sur-Yvette 91190, France
| | - Manon Cadinot
- Unité Drug Design Small Molecules, Institut de Recherche et Développement Servier Paris-Saclay, 22 route 128, Gif-sur-Yvette 91190, France
| | - Mathieu Pizzonero
- Unité Drug Design Small Molecules, Institut de Recherche et Développement Servier Paris-Saclay, 22 route 128, Gif-sur-Yvette 91190, France
| | - Frédéric Taran
- CEA, INRAE, Département Médicaments et Technologies pour la Santé (DMTS), SCBM, Université Paris-Saclay, Gif-sur-Yvette 91191, France
| | - Dominique Urban
- Université Paris-Saclay, CNRS, Institut de Chimie Moléculaire et des Matériaux d'Orsay (ICMMO), UMR 8182, 91405, Orsay, France
| | - Raphaël Guignard
- Unité Drug Design Small Molecules, Institut de Recherche et Développement Servier Paris-Saclay, 22 route 128, Gif-sur-Yvette 91190, France
| | - Dominique Guianvarc'h
- Université Paris-Saclay, CNRS, Institut de Chimie Moléculaire et des Matériaux d'Orsay (ICMMO), UMR 8182, 91405, Orsay, France
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4
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Huang K, Fang X. A review on recent advances in methods for site-directed spin labeling of long RNAs. Int J Biol Macromol 2023; 239:124244. [PMID: 37001783 DOI: 10.1016/j.ijbiomac.2023.124244] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2022] [Revised: 01/12/2023] [Accepted: 03/15/2023] [Indexed: 03/31/2023]
Abstract
RNAs are important biomolecules that play essential roles in various cellular processes and are crucially linked with many human diseases. The key to elucidate the mechanisms underlying their biological functions and develop RNA-based therapeutics is to investigate RNA structure and dynamics and their connections to function in detail using a variety of approaches. Magnetic resonance techniques including paramagnetic nuclear magnetic resonance (NMR) and electron magnetic resonance (EPR) spectroscopies have proved to be powerful tools to gain insights into such properties. The prerequisites for paramagnetic NMR and EPR studies on RNAs are to achieve site-specific spin labeling of the intrinsically diamagnetic RNAs, which however is not trivial, especially for long ones. In this review, we present some covalent labeling strategies that allow site-specific introduction of electron spins to long RNAs. Generally, these strategies include assembly of long RNAs via enzymatic ligation of short oligonucleotides, co- and post-transcriptional site-specific labeling empowered with the unnatural base pair system, and direct enzymatic functionalization of natural RNAs. We introduce a few case studies to discuss the advantages and limitations of each strategy, and to provide a vision for the future development.
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5
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Eyberg J, Ringenberg M, Richert C. Caging of a Strongly Pairing Fluorescent Thymidine Analog with Soft Nucleophiles. Chemistry 2023; 29:e202203289. [PMID: 36395348 PMCID: PMC10107337 DOI: 10.1002/chem.202203289] [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: 10/20/2022] [Revised: 11/15/2022] [Accepted: 11/16/2022] [Indexed: 11/18/2022]
Abstract
Controlling the pairing strength of nucleobases in DNA through reactions with compounds found inside the cell is a formidable challenge. Here we report how a thiazolyl substituent turns a strongly pairing ethynylpyridone C-nucleoside into a reactive residue in oligonucleotides. The thiazolyl-bearing pyridone reacts with soft nucleophiles, such as glutathione, but not with hard nucleophiles like hydroxide or carbonate. The addition products pair much more weakly with adenine in a complementary strand than the starting material, and also change their fluorescence. This makes oligonucleotides containing the new deoxynucleoside interesting for controlled release. Due to its reactivity toward N, P, S, and Se-nucleophiles, and the visual signal accompanying chemical conversion, the fluorescent nucleotide reported here may also have applications in chemical biology, sensing and diagnostics.
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Affiliation(s)
- Juri Eyberg
- Institute of Organic Chemistry, University of Stuttgart, 70569, Stuttgart, Germany
| | - Mark Ringenberg
- Institute of Organic Chemistry, University of Stuttgart, 70569, Stuttgart, Germany
| | - Clemens Richert
- Institute of Organic Chemistry, University of Stuttgart, 70569, Stuttgart, Germany
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6
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Dong T, Yu P, Zhao J, Wang J. Probing the local structure and dynamics of nucleotides using vibrationally enhanced alkynyl stretching. Phys Chem Chem Phys 2022; 24:29988-29998. [PMID: 36472165 DOI: 10.1039/d2cp03920f] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
Abstract
Monitoring the site-specific local structure and dynamics of polynucleotides and DNA is important for understanding their biological functions. However, structurally characterizing these biomolecules with high time resolution has been known to be experimentally challenging. In this work, several 5-silylethynyl-2'-deoxynucleosides and 5-substituted phenylethynyl-2'-deoxynucleosides on the basis of deoxycytidine (dC) and deoxythymidine (dT) were synthesized, in which the alkynyl group shows intensified CC stretching vibration with infrared transition dipole moment magnitude close to that of typical CO stretching, and exhibits structural sensitivities in both vibrational frequency and spectral width. In particular, 5-trimethylsilylethynyl-2'-dC (TMSEdC, molecule 1a) was examined in detail using femtosecond nonlinear IR spectroscopy. The solvent dependent CC stretching frequency of 1a can be reasonably interpreted mainly as the hydrogen-bonding effect between the solvent and cytosine base ring structure. Transient 2D IR and pump-probe IR measurements of 1a carried out comparatively in two aprotic solvents (DMSO and THF) and one protic solvent (MeOH) further reveal solvent dependent ultrafast vibrational properties, including diagonal anharmonicity, spectral diffusion, vibrational relaxation and anisotropy dynamics. These observed sensitivities are rooted in an extended π-conjugation of the base ring structure in which the CC group is actively involved. Our results show that the intensified CC stretching vibration can potentially provide a site-specific IR probe for monitoring the equilibrium and ultrafast structural dynamics of polynucleotides.
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Affiliation(s)
- Tiantian Dong
- Beijing National Laboratory for Molecular Sciences, Molecular Reaction Dynamics Laboratory, CAS Research/Education Center for Excellence in Molecular Sciences, Institute of Chemistry, Chinese Academy of Sciences, Beijing, 100190, P. R. China. .,University of Chinese Academy of Sciences, Beijing 100049, P. R. China
| | - Pengyun Yu
- Beijing National Laboratory for Molecular Sciences, Molecular Reaction Dynamics Laboratory, CAS Research/Education Center for Excellence in Molecular Sciences, Institute of Chemistry, Chinese Academy of Sciences, Beijing, 100190, P. R. China. .,University of Chinese Academy of Sciences, Beijing 100049, P. R. China
| | - Juan Zhao
- Beijing National Laboratory for Molecular Sciences, Molecular Reaction Dynamics Laboratory, CAS Research/Education Center for Excellence in Molecular Sciences, Institute of Chemistry, Chinese Academy of Sciences, Beijing, 100190, P. R. China. .,University of Chinese Academy of Sciences, Beijing 100049, P. R. China
| | - Jianping Wang
- Beijing National Laboratory for Molecular Sciences, Molecular Reaction Dynamics Laboratory, CAS Research/Education Center for Excellence in Molecular Sciences, Institute of Chemistry, Chinese Academy of Sciences, Beijing, 100190, P. R. China. .,University of Chinese Academy of Sciences, Beijing 100049, P. R. China
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7
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Eyberg J, Göhringer D, Salihovic A, Richert C. Acid‐Stable Nucleobase Protection for a Strongly Pairing Pyridone C‐Nucleoside Suitable for Solid‐Phase Synthesis of Oligonucleotides. European J Org Chem 2022. [DOI: 10.1002/ejoc.202200611] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Affiliation(s)
| | | | - Amila Salihovic
- University of Stuttgart: Universitat Stuttgart Chemistry GERMANY
| | - Clemens Richert
- Universität Stuttgart Institut für Organische Chemie Pfaffenwaldring 55 70569 Stuttgart GERMANY
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8
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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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9
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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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10
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Tivon Y, Falcone G, Deiters A. Protein Labeling and Crosslinking by Covalent Aptamers. Angew Chem Int Ed Engl 2021. [DOI: 10.1002/ange.202101174] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/24/2023]
Affiliation(s)
- Yaniv Tivon
- Department of Chemistry University of Pittsburgh Pittsburgh PA 15260 USA
| | - Gianna Falcone
- Department of Chemistry University of Pittsburgh Pittsburgh PA 15260 USA
| | - Alexander Deiters
- Department of Chemistry University of Pittsburgh Pittsburgh PA 15260 USA
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11
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Tivon Y, Falcone G, Deiters A. Protein Labeling and Crosslinking by Covalent Aptamers. Angew Chem Int Ed Engl 2021; 60:15899-15904. [PMID: 33928724 PMCID: PMC8260448 DOI: 10.1002/anie.202101174] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2021] [Revised: 04/09/2021] [Indexed: 12/11/2022]
Abstract
We developed a new approach to selectively modify native proteins in their biological environment using electrophilic covalent aptamers. These aptamers are generated through introduction of a proximity-driven electrophile at specific nucleotide sites. Using thrombin as a proof-of-concept, we demonstrate that covalent aptamers can selectively transfer a variety of functional handles and/or irreversibly crosslink to the target protein. This approach offers broad programmability and high target specificity. Furthermore, it addresses issues common to aptamers such as instability towards endogenous nucleases and residence times during target engagement. Covalent aptamers are new tools that enable specific protein modification and sensitive protein detection. Moreover, they provide prolonged, nuclease-resistant enzyme inhibition.
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Affiliation(s)
- Yaniv Tivon
- Department of Chemistry, University of Pittsburgh, Pittsburgh, PA, 15260, USA
| | - Gianna Falcone
- Department of Chemistry, University of Pittsburgh, Pittsburgh, PA, 15260, USA
| | - Alexander Deiters
- Department of Chemistry, University of Pittsburgh, Pittsburgh, PA, 15260, USA
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12
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Fantoni NZ, El-Sagheer AH, Brown T. A Hitchhiker's Guide to Click-Chemistry with Nucleic Acids. Chem Rev 2021; 121:7122-7154. [PMID: 33443411 DOI: 10.1021/acs.chemrev.0c00928] [Citation(s) in RCA: 143] [Impact Index Per Article: 47.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Abstract
Click chemistry is an immensely powerful technique for the fast and efficient covalent conjugation of molecular entities. Its broad scope has positively impacted on multiple scientific disciplines, and its implementation within the nucleic acid field has enabled researchers to generate a wide variety of tools with application in biology, biochemistry, and biotechnology. Azide-alkyne cycloadditions (AAC) are still the leading technology among click reactions due to the facile modification and incorporation of azide and alkyne groups within biological scaffolds. Application of AAC chemistry to nucleic acids allows labeling, ligation, and cyclization of oligonucleotides efficiently and cost-effectively relative to previously used chemical and enzymatic techniques. In this review, we provide a guide to inexperienced and knowledgeable researchers approaching the field of click chemistry with nucleic acids. We discuss in detail the chemistry, the available modified-nucleosides, and applications of AAC reactions in nucleic acid chemistry and provide a critical view of the advantages, limitations, and open-questions within the field.
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Affiliation(s)
- Nicolò Zuin Fantoni
- Department of Chemistry, University of Oxford, Chemistry Research Laboratory, 12 Mansfield Road, Oxford OX1 3TA, U.K
| | - Afaf H El-Sagheer
- Department of Chemistry, University of Oxford, Chemistry Research Laboratory, 12 Mansfield Road, Oxford OX1 3TA, U.K.,Chemistry Branch, Department of Science and Mathematics, Faculty of Petroleum and Mining Engineering, Suez University, Suez 43721, Egypt
| | - Tom Brown
- Department of Chemistry, University of Oxford, Chemistry Research Laboratory, 12 Mansfield Road, Oxford OX1 3TA, U.K
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13
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Walter TJ, Richert C. A strongly pairing fifth base: oligonucleotides with a C-nucleoside replacing thymidine. Nucleic Acids Res 2019; 46:8069-8078. [PMID: 30085103 PMCID: PMC6144870 DOI: 10.1093/nar/gky669] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2018] [Accepted: 07/13/2018] [Indexed: 12/12/2022] Open
Abstract
There are five canonical bases in DNA and RNA. Each base has its particular molecular recognition properties and base pairing strength. Thymine and uracil form only two hydrogen bonds when pairing with adenine, and duplexes rich in A:T base pairs are more labile than duplexes rich in C and G, making some sequences difficult to detect via hybridization in a genomic context. Here we report the synthesis of an ethynylmethylpyridone C-nucleoside, abbreviated ‘W’, that presents a similar recognition surface as thymidine in the major groove but pairs with A about as strongly as C pairs with G. A phosphoramidite building block was synthesized that allows for incorporation of W residues via automated synthesis in high yield. Melting point increases over duplexes containing T:A pairs of up to 17.5°C, or up to 5.8°C per residue were measured for oligonucleotides containing W. Further, the new base shows excellent fidelity, with a single mismatched G opposite W causing a melting point depression of up to 20.5°C. The strongly pairing replacement for thymidine is only slightly larger than its natural counterpart and performs well in different sequence contexts. It can be used to target weakly pairing A-rich sequences in biological studies.
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Affiliation(s)
- Tanja J Walter
- Institute of Organic Chemistry, University of Stuttgart, 70569 Stuttgart, Germany
| | - Clemens Richert
- Institute of Organic Chemistry, University of Stuttgart, 70569 Stuttgart, Germany
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14
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Copper-Catalyzed Alkyne-Azide Cycloaddition on the Solid Phase for the Preparation of Fully Click-Modified Nucleic Acids. Methods Mol Biol 2019. [PMID: 31016702 DOI: 10.1007/978-1-4939-9216-4_11] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register]
Abstract
Click chemistry has become a widely used method to insert modifications into DNA. Due to its commercial availability, 5'-ethynyl-deoxyuridine (EdU) is commonly incorporated into the DNA for subsequent modification by click reaction. However, it is partially oxidized during deprotection during solid-phase synthesis, resulting in a ketone that is no longer accessible for click modification. To enable the high-fidelity solid-phase synthesis of EdU-containing DNA, this protocol describes a procedure to perform the click reaction on the solid phase before deprotection. Afterwards, the DNA can be deprotected and purified according to standard procedures, and the full modification of EdU with the azide of choice can be analyzed by HPLC and HPLC/MS.
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15
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Hilko DH, Bornaghi LF, Poulsen SA. Stereoselective Synthesis of Highly Functionalized Arabinosyl Nucleosides through Application of an N-Nitro Protecting Group. J Org Chem 2018; 83:11944-11955. [PMID: 30153729 DOI: 10.1021/acs.joc.8b01834] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
2'-Deoxy-2',5-disubstituted arabinosyl uridine derivatives bearing a halogen (Cl, Br or I) at C2' and an ethynyl group at C5 have been synthesized in 6 steps from 2',3',5'-tri- O-acetyl-5-iodo-uridine in overall yields of 61% (compound 3, Cl), 47% (compound 4, Br), and 19% (compound 5, I). Stabilization of a 2'- O-triflyl leaving group intermediate to overcome spontaneous intramolecular 2,2'-anhydro uridine formation was pivotal to the synthesis. Specifically, to favor SN2 reaction with a halogen nucleophile over intramolecular cyclization, the nucleophilicity of O-2 oxygen was reduced by incorporation of an adjacent electron withdrawing nitro substituent at N-3. The introduction of the 3- N-nitro group proceeded rapidly (nitronium trifluoroacetate, 1 min) and in quantitative yield. A one-pot method to remove the 3- N-nitro group by reductive nitration (zinc metal in acetic acid, 5 min) and the silyl protecting groups of the alkyne and 3',5' hydroxyls (fluoride reagent, 16 h) was established as the final synthetic step. This application of the 3- N-nitro protecting group addresses the significant shortfalls of the conventional approach to synthesis of 2' modified nucleosides, wherein condensation of a 2' modified sugar fragment with a pyrimidine base provides poor stereocontrol of N-glycosylation, low yields and incompatibility with 2' iodo sugars.
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Affiliation(s)
- David H Hilko
- Griffith Institute for Drug Discovery , Griffith University , Don Young Road , Nathan, Brisbane , Queensland 4111 , Australia
| | - Laurent F Bornaghi
- Griffith Institute for Drug Discovery , Griffith University , Don Young Road , Nathan, Brisbane , Queensland 4111 , Australia
| | - Sally-Ann Poulsen
- Griffith Institute for Drug Discovery , Griffith University , Don Young Road , Nathan, Brisbane , Queensland 4111 , Australia
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16
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Pfeiffer F, Gröber C, Blank M, Händler K, Beyer M, Schultze JL, Mayer G. Systematic evaluation of error rates and causes in short samples in next-generation sequencing. Sci Rep 2018; 8:10950. [PMID: 30026539 PMCID: PMC6053417 DOI: 10.1038/s41598-018-29325-6] [Citation(s) in RCA: 169] [Impact Index Per Article: 28.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2018] [Accepted: 07/09/2018] [Indexed: 01/08/2023] Open
Abstract
Next-generation sequencing (NGS) is the method of choice when large numbers of sequences have to be obtained. While the technique is widely applied, varying error rates have been observed. We analysed millions of reads obtained after sequencing of one single sequence on an Illumina sequencer. According to our analysis, the index-PCR for sample preparation has no effect on the observed error rate, even though PCR is traditionally seen as one of the major contributors to enhanced error rates in NGS. In addition, we observed very persistent pre-phasing effects although the base calling software corrects for these. Removal of shortened sequences abolished these effects and allowed analysis of the actual mutations. The average error rate determined was 0.24 ± 0.06% per base and the percentage of mutated sequences was found to be 6.4 ± 1.24%. Constant regions at the 5'- and 3'-end, e.g., primer binding sites used in in vitro selection procedures seem to have no effect on mutation rates and re-sequencing of samples obtains very reproducible results. As phasing effects and other sequencing problems vary between equipment and individual setups, we recommend evaluation of error rates and types to all NGS-users to improve the quality and analysis of NGS data.
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Affiliation(s)
- Franziska Pfeiffer
- University of Bonn, LIMES Institute, Chemical Biology, Gerhard-Domagk-Str. 1, 53121, Bonn, Germany
| | - Carsten Gröber
- AptaIT GmbH, Am Klopferspitz 19A, 82152, Planegg, Germany
| | - Michael Blank
- AptaIT GmbH, Am Klopferspitz 19A, 82152, Planegg, Germany
| | - Kristian Händler
- University of Bonn, LIMES Institute, Genomics and Immunoregulation, Carl-Troll-Str. 31, 53115, Bonn, Germany
- German Center for Neurodegenerative Diseases (DZNE) and University of Bonn, Platform for Single Cell Genomics and Epigenomics, Sigmund-Freud-Str. 25, 53127, Bonn, Germany
| | - Marc Beyer
- University of Bonn, LIMES Institute, Genomics and Immunoregulation, Carl-Troll-Str. 31, 53115, Bonn, Germany
- German Center for Neurodegenerative Diseases (DZNE) and University of Bonn, Platform for Single Cell Genomics and Epigenomics, Sigmund-Freud-Str. 25, 53127, Bonn, Germany
- DZNE, Molecular Immunology in Neurodegeneration, Sigmund-Freud-Str. 27, 53127, Bonn, Germany
| | - Joachim L Schultze
- University of Bonn, LIMES Institute, Genomics and Immunoregulation, Carl-Troll-Str. 31, 53115, Bonn, Germany
- German Center for Neurodegenerative Diseases (DZNE) and University of Bonn, Platform for Single Cell Genomics and Epigenomics, Sigmund-Freud-Str. 25, 53127, Bonn, Germany
| | - Günter Mayer
- University of Bonn, LIMES Institute, Chemical Biology, Gerhard-Domagk-Str. 1, 53121, Bonn, Germany.
- Center of Aptamer Research and Development, Gerhard-Domagk-Str. 1, 53121, Bonn, Germany.
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17
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Panattoni A, Pohl R, Hocek M. Flexible Alkyne-Linked Thymidine Phosphoramidites and Triphosphates for Chemical or Polymerase Synthesis and Fast Postsynthetic DNA Functionalization through Copper-Catalyzed Alkyne–Azide 1,3-Dipolar Cycloaddition. Org Lett 2018; 20:3962-3965. [DOI: 10.1021/acs.orglett.8b01533] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Affiliation(s)
- Alessandro Panattoni
- Institute of Organic Chemistry and Biochemistry, Czech Academy of Sciences, Flemingovo namesti 2, CZ-16610 Prague 6, Czech Republic
- Department of Organic Chemistry, Faculty of Science, Charles University in Prague, Hlavova 8, CZ-12843 Prague 2, Czech Republic
| | - Radek Pohl
- Institute of Organic Chemistry and Biochemistry, Czech Academy of Sciences, Flemingovo namesti 2, CZ-16610 Prague 6, Czech Republic
| | - Michal Hocek
- Institute of Organic Chemistry and Biochemistry, Czech Academy of Sciences, Flemingovo namesti 2, CZ-16610 Prague 6, Czech Republic
- Department of Organic Chemistry, Faculty of Science, Charles University in Prague, Hlavova 8, CZ-12843 Prague 2, Czech Republic
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18
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Kerzhner M, Matsuoka H, Wuebben C, Famulok M, Schiemann O. High-Yield Spin Labeling of Long RNAs for Electron Paramagnetic Resonance Spectroscopy. Biochemistry 2018; 57:2923-2931. [PMID: 29715006 DOI: 10.1021/acs.biochem.8b00040] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
Site-directed spin labeling is a powerful tool for investigating the conformation and dynamics of biomacromolecules such as RNA. Here we introduce a spin labeling strategy based on click chemistry in solution that, in combination with enzymatic ligation, allows highly efficient labeling of complex and long RNAs with short reaction times and suppressed RNA degradation. With this approach, a 34-nucleotide aptamer domain of the preQ1 riboswitch and an 81-nucleotide TPP riboswitch aptamer could be labeled with two labels in several positions. We then show that conformations of the preQ1 aptamer and its dynamics can be monitored in the absence and presence of Mg2+ and a preQ1 ligand by continuous wave electron paramagnetic resonance spectroscopy at room temperature and pulsed electron-electron double resonance spectroscopy (PELDOR or DEER) in the frozen state.
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Affiliation(s)
- Mark Kerzhner
- Life & Medical Sciences Institute Chemical Biology & Medicinal Chemistry Unit c/o Kekulé-Institut für Organische Chemie und Biochemie University of Bonn , Gerhard-Domagk-Strasse 1 , 53121 Bonn , Germany
| | - Hideto Matsuoka
- Institute of Physical and Theoretical Chemistry , University of Bonn , Wegelerstrasse 12 , 53115 Bonn , Germany
| | - Christine Wuebben
- Institute of Physical and Theoretical Chemistry , University of Bonn , Wegelerstrasse 12 , 53115 Bonn , Germany
| | - Michael Famulok
- Life & Medical Sciences Institute Chemical Biology & Medicinal Chemistry Unit c/o Kekulé-Institut für Organische Chemie und Biochemie University of Bonn , Gerhard-Domagk-Strasse 1 , 53121 Bonn , Germany.,Max Planck Fellowship Chemical Biology Group , Stiftung caesar , Ludwig-Erhard-Allee 2 , 53175 Bonn , Germany
| | - Olav Schiemann
- Institute of Physical and Theoretical Chemistry , University of Bonn , Wegelerstrasse 12 , 53115 Bonn , Germany
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19
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Identification and characterization of nucleobase-modified aptamers by click-SELEX. Nat Protoc 2018; 13:1153-1180. [PMID: 29700486 DOI: 10.1038/nprot.2018.023] [Citation(s) in RCA: 50] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
Abstract
Aptamers are single-stranded oligonucleotides that are in vitro-selected to recognize their target molecule with high affinity and specificity. As they consist of the four canonical nucleobases, their chemical diversity is limited, which in turn limits the addressable target spectrum. Introducing chemical modifications into nucleic acid libraries increases the interaction capabilities of the DNA and thereby the target spectrum. Here, we describe a protocol to select nucleobase-modified aptamers by using click chemistry (CuAAC) to introduce the preferred chemical modification. The use of click chemistry to modify the DNA library enables the introduction of a wide range of possible functionalities, which can be customized to the requirements of the target molecule and the desired application. This protocol yields modified DNA aptamers with extended interaction properties that are not accessible with the canonical set of nucleotides. After synthesis of the starting library containing a commercially available, alkyne-modified uridine (5-ethynyl-deoxyuridine (EdU)) instead of thymidine, the library is functionalized with the modification of choice by CuAAC. The thus-modified DNA is incubated with the target molecule and the best binding sequences are recovered. The chemical modification is removed during the amplification process. Therefore, this protocol is compatible with conventional amplification procedures and avoids enzymatic incompatibility problems associated with more extensive nucleobase modifications. After single-strand generation, the modification is reintroduced into the enriched library, which can then be subjected to the subsequent selection cycle. The duration of each selection cycle as outlined in the protocol is ∼1 d.
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20
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Mei H, Chaput JC. Expanding the chemical diversity of TNA with tUTP derivatives that are substrates for a TNA polymerase. Chem Commun (Camb) 2018; 54:1237-1240. [PMID: 29340357 DOI: 10.1039/c7cc09130c] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/25/2023]
Abstract
Expanding the chemical diversity of threose nucleic acid (TNA) beyond the natural bases would enable the development of TNA polymers with enhanced physicochemical properties. Here, we describe a versatile approach for increasing the chemical diversity of TNA using 5-alkynyl-modified α-l-threofuranosyl uridine triphosphates that are substrates for a TNA polymerase.
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Affiliation(s)
- Hui Mei
- Departments of Pharmaceutical Sciences, Chemistry, Molecular Biology and Biochemistry, University of California, Irvine, CA 92697-3958, USA.
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21
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Pfeiffer F, Rosenthal M, Siegl J, Ewers J, Mayer G. Customised nucleic acid libraries for enhanced aptamer selection and performance. Curr Opin Biotechnol 2017; 48:111-118. [PMID: 28437710 DOI: 10.1016/j.copbio.2017.03.026] [Citation(s) in RCA: 35] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2017] [Revised: 03/28/2017] [Accepted: 03/30/2017] [Indexed: 12/24/2022]
Abstract
Aptamers are short single-stranded oligo(deoxy)nucleotides that are selected to bind to target molecules with high affinity and specificity. Because of their sophisticated characteristics and versatile applicability, aptamers are thought to become universal molecular probes in biotechnological and therapeutic applications. However, the variety of possible interactions with a putative target molecule is limited by the chemical repertoire of the natural nucleobases. Consequently, many desired targets are not addressable by aptamers. This obstacle is overcome by broadening the chemical diversity of aptamers, mainly achieved by nucleobase-modifications and the introduction of novel bases or base pairs. We discuss these achievements and the characteristics of the respective modified aptamers, reflected by SOMAmers (slow off-rate modified aptamers), clickmers, and aptamers bearing an expanded genetic alphabet.
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Affiliation(s)
- Franziska Pfeiffer
- Life and Medical Sciences Institute, University of Bonn, Gerhard-Domagk-Str. 1, 53121 Bonn, Germany
| | - Malte Rosenthal
- Life and Medical Sciences Institute, University of Bonn, Gerhard-Domagk-Str. 1, 53121 Bonn, Germany
| | - Julia Siegl
- Life and Medical Sciences Institute, University of Bonn, Gerhard-Domagk-Str. 1, 53121 Bonn, Germany
| | - Jörg Ewers
- Life and Medical Sciences Institute, University of Bonn, Gerhard-Domagk-Str. 1, 53121 Bonn, Germany
| | - Günter Mayer
- Life and Medical Sciences Institute, University of Bonn, Gerhard-Domagk-Str. 1, 53121 Bonn, Germany; Center of Aptamer Research and Development, University of Bonn, Gerhard-Domagk-Str. 1, 53121 Bonn, Germany.
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22
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Yang H, Seela F. "Bis-Click" Ligation of DNA: Template-Controlled Assembly, Circularisation and Functionalisation with Bifunctional and Trifunctional Azides. Chemistry 2017; 23:3375-3385. [PMID: 27869337 DOI: 10.1002/chem.201604857] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2016] [Indexed: 12/14/2022]
Abstract
Ligation and circularisation of oligonucleotides containing terminal triple bonds was performed with bifunctional or trifunctional azides. Both reactions are high yielding. Template-assisted bis-click ligation of two individual non-complementary oligonucleotide strands was accomplished to yield heterodimers exclusively. In this context, the template fulfils two functions: it accelerates the ligation reaction and controls product assembly (heterodimer vs. homodimer formation). Intermolecular bis-click circularisation of one oligonucleotide strand took place without template assistance. For construction of oligonucleotides with terminal triple bonds in the nucleobase side chain, 7- or 5-functionalised 7-deaza-dA and dU residues were used. These oligonucleotides are directly accessible by solid-phase synthesis. When trifunctional azides were employed instead of bifunctional linkers, functionalisation of the remaining azido group was performed with small molecules such as 1-ethynyl pyrene, biotin propargyl amide or with ethynylated oligonucleotides. By this means, branched DNA was constructed.
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Affiliation(s)
- Haozhe Yang
- 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
| | - 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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23
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Röthlisberger P, Levi-Acobas F, Hollenstein M. New synthetic route to ethynyl-dUTP: A means to avoid formation of acetyl and chloro vinyl base-modified triphosphates that could poison SELEX experiments. Bioorg Med Chem Lett 2017; 27:897-900. [PMID: 28089700 DOI: 10.1016/j.bmcl.2017.01.009] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2016] [Revised: 01/04/2017] [Accepted: 01/05/2017] [Indexed: 01/10/2023]
Abstract
5-Ethynyl-2'-deoxyuridine is a common base-modified nucleoside analogue that has served in various applications including selection experiments for potent aptamers and in biosensing. The synthesis of the corresponding triphosphates involves a mild acidic deprotection step. Herein, we show that this deprotection leads to the formation of other nucleoside analogs which are easily converted to triphosphates. The modified nucleoside triphosphates are excellent substrates for numerous DNA polymerases under both primer extension and PCR conditions and could thus poison selection experiments by blocking sites that need to be further modified. The formation of these nucleoside analogs can be circumvented by application of a new synthetic route that is described herein.
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Affiliation(s)
- Pascal Röthlisberger
- Laboratory for Bioorganic Chemistry of Nucleic Acids, Institut Pasteur, 28 rue du Dr. Roux, 75724 Paris Cedex 15, France; CNRS UMR3523 Institut Pasteur, 28 rue du Dr. Roux, 75724 Paris Cedex 15, France
| | - Fabienne Levi-Acobas
- Laboratory for Bioorganic Chemistry of Nucleic Acids, Institut Pasteur, 28 rue du Dr. Roux, 75724 Paris Cedex 15, France; CNRS UMR3523 Institut Pasteur, 28 rue du Dr. Roux, 75724 Paris Cedex 15, France
| | - Marcel Hollenstein
- Laboratory for Bioorganic Chemistry of Nucleic Acids, Institut Pasteur, 28 rue du Dr. Roux, 75724 Paris Cedex 15, France; CNRS UMR3523 Institut Pasteur, 28 rue du Dr. Roux, 75724 Paris Cedex 15, France.
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24
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Guo X, Ingale SA, Yang H, He Y, Seela F. MercuryII-mediated base pairs in DNA: unexpected behavior in metal ion binding and duplex stability induced by 2′-deoxyuridine 5-substituents. Org Biomol Chem 2017; 15:870-883. [PMID: 28045181 DOI: 10.1039/c6ob02560a] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023]
Abstract
DNA accepts small substituents at the 5-position of 2′-deoxyuridine residues within mercury ion mediated dU–HgII–dU base pairs, while triple bonds interact with mercury ions and those with space demanding aromatic side chains block metal ion mediated base pair formation.
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Affiliation(s)
- Xiurong Guo
- Precision Medicine Research Laboratory
- West China Hospital
- West China School of Medicine
- Sichuan University
- 610041 Chengdu
| | - Sachin A. Ingale
- Laboratory of Bioorganic Chemistry and Chemical Biology
- Center for Nanotechnology
- 48149 Münster
- Germany
- Laboratorium für Organische und Bioorganische Chemie
| | - Haozhe Yang
- Laboratory of Bioorganic Chemistry and Chemical Biology
- Center for Nanotechnology
- 48149 Münster
- Germany
- Laboratorium für Organische und Bioorganische Chemie
| | - Yang He
- Precision Medicine Research Laboratory
- West China Hospital
- West China School of Medicine
- Sichuan University
- 610041 Chengdu
| | - Frank Seela
- Laboratory of Bioorganic Chemistry and Chemical Biology
- Center for Nanotechnology
- 48149 Münster
- Germany
- Laboratorium für Organische und Bioorganische Chemie
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25
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Ingale SA, Seela F. 7-Deaza-2′-deoxyguanosine: Selective Nucleobase Halogenation, Positional Impact of Space-Occupying Substituents, and Stability of DNA with Parallel and Antiparallel Strand Orientation. J Org Chem 2016; 81:8331-42. [DOI: 10.1021/acs.joc.6b01498] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Sachin A. Ingale
- 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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26
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Tolle F, Rosenthal M, Pfeiffer F, Mayer G. Click Reaction on Solid Phase Enables High Fidelity Synthesis of Nucleobase-Modified DNA. Bioconjug Chem 2016; 27:500-3. [PMID: 26850226 DOI: 10.1021/acs.bioconjchem.5b00668] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
The post-synthetic functionalization of nucleic acids via click chemistry (CuAAC) has seen tremendous implementation, extending the applicability of nucleobase-modified nucleic acids in fields like fluorescent labeling, nanotechnology, and in vitro selection. However, the production of large quantities of high-density functionalized material via solid phase synthesis has been hampered by oxidative by-product formation associated with the alkaline workup conditions. Herein, we describe a rapid and cost-effective protocol for the high fidelity large-scale production of nucleobase-modified nucleic acids, exemplified with a recently described nucleobase-modified aptamer.
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Affiliation(s)
- Fabian Tolle
- Life and Medical Sciences Institute, University of Bonn , Gerhard-Domagk-Str. 1, 53121 Bonn, Germany
| | - Malte Rosenthal
- Life and Medical Sciences Institute, University of Bonn , Gerhard-Domagk-Str. 1, 53121 Bonn, Germany
| | - Franziska Pfeiffer
- Life and Medical Sciences Institute, University of Bonn , Gerhard-Domagk-Str. 1, 53121 Bonn, Germany
| | - Günter Mayer
- Life and Medical Sciences Institute, University of Bonn , Gerhard-Domagk-Str. 1, 53121 Bonn, Germany
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27
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Yang H, Seela F. Circular DNA by "Bis-Click" Ligation: Template-Independent Intramolecular Circularization of Oligonucleotides with Terminal Alkynyl Groups Utilizing Bifunctional Azides. Chemistry 2015; 22:1435-44. [PMID: 26685101 DOI: 10.1002/chem.201503615] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2015] [Indexed: 12/19/2022]
Abstract
A highly effective and convenient "bis-click" strategy was developed for the template-independent circularization of single-stranded oligonucleotides by employing copper(I)-assisted azide-alkyne cycloaddition. Terminal triple bonds were incorporated at both ends of linear oligonucleotides. Alkynylated 7-deaza-2'-deoxyadenosine and 2'-deoxyuridine residues with different side chains were used in solid-phase synthesis with phosphoramidite chemistry. The bis-click ligation of linear 9- to 36-mer oligonucleotides with 1,4-bis(azidomethyl)benzene afforded circular DNA in a simple and selective way; azido modification of the oligonucleotide was not necessary. Short ethynyl side chains were compatible with the circularization of longer oligonucleotides, whereas octadiynyl residues were used for short 9-mers. Compared with linear duplexes, circular bis-click constructs exhibit a significantly increased duplex stability over their linear counterparts. The intramolecular bis-click ligation protocol is not limited to DNA, but may also be suitable for the construction of other macrocycles, such as circular RNAs, peptides, or polysaccharides.
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Affiliation(s)
- Haozhe Yang
- 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), Fax: (+49) 251-53406857
| | - 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), Fax: (+49) 251-53406857.
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28
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Mačková M, Boháčová S, Perlíková P, Poštová Slavětínská L, Hocek M. Polymerase Synthesis and Restriction Enzyme Cleavage of DNA Containing 7-Substituted 7-Deazaguanine Nucleobases. Chembiochem 2015; 16:2225-36. [PMID: 26382079 DOI: 10.1002/cbic.201500315] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2015] [Indexed: 01/06/2023]
Abstract
Previous studies of polymerase synthesis of base-modified DNAs and their cleavage by restriction enzymes have mostly related only to 5-substituted pyrimidine and 7-substituted 7-deazaadenine nucleotides. Here we report the synthesis of a series of 7-substituted 7-deazaguanine 2'-deoxyribonucleoside 5'-O-triphosphates (dG(R) TPs), their use as substrates for polymerase synthesis of modified DNA and the influence of the modification on their cleavage by type II restriction endonucleases (REs). The dG(R) TPs were generally good substrates for polymerases but the PCR products could not be visualised on agarose gels by intercalator staining, due to fluorescence quenching. The presence of 7-substituted 7-deazaguanine residues in recognition sequences of REs in most cases completely blocked the cleavage.
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Affiliation(s)
- Michaela Mačková
- Institute of Organic Chemistry and Biochemistry, Academy of Sciences of the Czech Republic, Gilead Sciences and IOCB Research Center, Flemingovo nám. 2, 16610, Prague 6, Czech Republic
| | - Soňa Boháčová
- Institute of Organic Chemistry and Biochemistry, Academy of Sciences of the Czech Republic, Gilead Sciences and IOCB Research Center, Flemingovo nám. 2, 16610, Prague 6, Czech Republic
| | - Pavla Perlíková
- Institute of Organic Chemistry and Biochemistry, Academy of Sciences of the Czech Republic, Gilead Sciences and IOCB Research Center, Flemingovo nám. 2, 16610, Prague 6, Czech Republic
| | - Lenka Poštová Slavětínská
- Institute of Organic Chemistry and Biochemistry, Academy of Sciences of the Czech Republic, Gilead Sciences and IOCB Research Center, Flemingovo nám. 2, 16610, Prague 6, Czech Republic
| | - Michal Hocek
- Institute of Organic Chemistry and Biochemistry, Academy of Sciences of the Czech Republic, Gilead Sciences and IOCB Research Center, Flemingovo nám. 2, 16610, Prague 6, Czech Republic. .,Department of Organic Chemistry, Faculty of Science, Charles University in Prague, Hlavova 8, 12843, Prague 2, Czech Republic.
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29
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Ingale SA, Leonard P, Yang H, Seela F. 5-Nitroindole oligonucleotides with alkynyl side chains: universal base pairing, triple bond hydration and properties of pyrene "click" adducts. Org Biomol Chem 2015; 12:8519-32. [PMID: 25236942 DOI: 10.1039/c4ob01478b] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
Oligonucleotides with 3-ethynyl-5-nitroindole and 3-octadiynyl-5-nitroindole 2'-deoxyribonucleosides were prepared by solid-phase synthesis. To this end, nucleoside phosphoramidites with clickable side chains were synthesized. The 3-ethynylated 5-nitroindole nucleoside was hydrated during automatized DNA synthesis to 3-acetyl-5-nitroindole 2'-deoxyribonucleoside. Side product formation was circumvented by triisopropylsilyl protection of the ethynyl side chain and was removed with TBAF after oligonucleotide synthesis. All compounds with a clickable 5-nitroindole skeleton show universal base pairing and can be functionalized with almost any azide in any position of the DNA chain. Functionalization of the side chain with 1-azidomethylpyrene afforded click adducts in which the fluorescence was quenched by the 5-nitroindole moieties. However, fluorescence was slightly recovered during duplex formation. Oligonucleotides with a pyrene residue and a long linker arm are stabilized over those with non-functionalized side chains. From the UV red shift of the pyrene residue in oligonucleotides and modelling studies, pyrene intercalation was established for the long linker adduct showing increased duplex stability over those with a short side chain.
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Affiliation(s)
- Sachin A Ingale
- Laboratory of Bioorganic Chemistry and Chemical Biology, Center for Nanotechnology, Heisenbergstrasse 11, 48149 Münster, Germany
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30
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Winz ML, Linder EC, André T, Becker J, Jäschke A. Nucleotidyl transferase assisted DNA labeling with different click chemistries. Nucleic Acids Res 2015; 43:e110. [PMID: 26013812 PMCID: PMC4787804 DOI: 10.1093/nar/gkv544] [Citation(s) in RCA: 35] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2015] [Accepted: 05/12/2015] [Indexed: 01/19/2023] Open
Abstract
Here, we present a simple, modular and efficient strategy that allows the 3′-terminal labeling of DNA, regardless of whether it has been chemically or enzymatically synthesized or isolated from natural sources. We first incorporate a range of modified nucleotides at the 3′-terminus, using terminal deoxynucleotidyl transferase. In the second step, we convert the incorporated nucleotides, using either of four highly efficient click chemistry-type reactions, namely copper-catalyzed azide-alkyne cycloaddition, strain-promoted azide-alkyne cycloaddition, Staudinger ligation or Diels-Alder reaction with inverse electron demand. Moreover, we create internal modifications, making use of either ligation or primer extension, after the nucleotidyl transferase step, prior to the click reaction. We further study the influence of linker variants on the reactivity of azides in different click reactions. We find that different click reactions exhibit distinct substrate preferences, a fact that is often overlooked, but should be considered when labeling oligonucleotides or other biomolecules with click chemistry. Finally, our findings allowed us to extend our previously published RNA labeling strategy to the use of a different copper-free click chemistry, namely the Staudinger ligation.
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Affiliation(s)
- Marie-Luise Winz
- Heidelberg University, Institute of Pharmacy and Molecular Biotechnology, Im Neuenheimer Feld 364, D-69120 Heidelberg, Germany
| | - Eva Christina Linder
- Heidelberg University, Institute of Pharmacy and Molecular Biotechnology, Im Neuenheimer Feld 364, D-69120 Heidelberg, Germany
| | - Timon André
- Heidelberg University, Institute of Pharmacy and Molecular Biotechnology, Im Neuenheimer Feld 364, D-69120 Heidelberg, Germany
| | - Juliane Becker
- Heidelberg University, Institute of Pharmacy and Molecular Biotechnology, Im Neuenheimer Feld 364, D-69120 Heidelberg, Germany
| | - Andres Jäschke
- Heidelberg University, Institute of Pharmacy and Molecular Biotechnology, Im Neuenheimer Feld 364, D-69120 Heidelberg, Germany
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