1
|
Li Y, Zhou Y, Zhou D, Jiang Y, Butt M, Yang H, Que Y, Li Z, Chen G. Regioselective Homolytic C 2-H Borylation of Unprotected Adenosine and Adenine Derivatives via Minisci Reaction. J Am Chem Soc 2024; 146:21428-21441. [PMID: 39051926 DOI: 10.1021/jacs.4c03865] [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: 07/27/2024]
Abstract
A Minisci-type borylation of unprotected adenosine, adenine nucleotide, and adenosine analogues was successfully achieved through photocatalysis or thermal activation. Despite the challenges posed by the presence of two potential reactive sites (C2 and C8) in the purine motif, the unique nucleophilic amine-ligated boryl radicals effortlessly achieved excellent C2 site selectivity and simultaneously avoided the formation of multifunctionalized products. This protocol proved effective for the late-stage borylation of some important biomolecules as well as a few antiviral and antitumor drug molecules, such as AMP, cAMP, Vidarabine, Cordycepin, Tenofovir, Adefovir, GS-441524, etc. Theoretical calculations shed light on the site selectivity, revealing that the free energy barriers for the C2-Minisci addition are further lowered through the chelation of additive Mg2+ to N3 and furyl oxygen. This phenomenon has been confirmed by an IGMH analysis. Preliminary antitumor evaluation, derivation of the C2-borylated adenosine to other analogues with high-value functionalities, along with the CuAAC click reactions, suggest the potential application of this methodology in drug molecular optimization studies and chemical biology.
Collapse
Affiliation(s)
- Yangyan Li
- Shanghai Key Laboratory for Molecular Engineering of Chiral Drugs, School of Chemistry and Chemical Engineering, Shanghai Jiao Tong University, Shanghai 200240, P. R. China
| | - Yutong Zhou
- Shanghai Key Laboratory for Molecular Engineering of Chiral Drugs, School of Chemistry and Chemical Engineering, Shanghai Jiao Tong University, Shanghai 200240, P. R. China
- Key Laboratory of Green and High-value Utilization of Salt Lake Resources, Qinghai Institute of Salt Lakes, Chinese Academy of Sciences, Xining 810008, Qinghai, P. R. China
| | - Dazhi Zhou
- Department of Chemistry, Fudan University, Shanghai 200438, P. R. China
| | - Yujie Jiang
- Shanghai Key Laboratory for Molecular Engineering of Chiral Drugs, School of Chemistry and Chemical Engineering, Shanghai Jiao Tong University, Shanghai 200240, P. R. China
| | - Madiha Butt
- Shanghai Key Laboratory for Molecular Engineering of Chiral Drugs, School of Chemistry and Chemical Engineering, Shanghai Jiao Tong University, Shanghai 200240, P. R. China
| | - Hui Yang
- Key Laboratory of Biocatalysis and Chiral Drug Synthesis of Guizhou Province, Generic Drug Research Center of Guizhou Province, Department of Pharmacy, Zunyi Medical University, Zunyi 563000, P. R. China
| | - Yingchuan Que
- Shanghai Key Laboratory for Molecular Engineering of Chiral Drugs, School of Chemistry and Chemical Engineering, Shanghai Jiao Tong University, Shanghai 200240, P. R. China
| | - Zhiming Li
- Department of Chemistry, Fudan University, Shanghai 200438, P. R. China
| | - Gang Chen
- Shanghai Key Laboratory for Molecular Engineering of Chiral Drugs, School of Chemistry and Chemical Engineering, Shanghai Jiao Tong University, Shanghai 200240, P. R. China
- Key Laboratory of Green and High-value Utilization of Salt Lake Resources, Qinghai Institute of Salt Lakes, Chinese Academy of Sciences, Xining 810008, Qinghai, P. R. China
| |
Collapse
|
2
|
Liu D, Shu X, Xiang S, Li T, Huang C, Cheng M, Cao J, Hua Y, Liu J. N4 -allyldeoxycytidine: A New DNA Tag with Chemical Sequencing Power for Pinpointing Labelling Sites, Mapping Epigenetic Mark, and in situ Imaging. Chembiochem 2022; 23:e202200143. [PMID: 35438823 DOI: 10.1002/cbic.202200143] [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: 03/11/2022] [Revised: 04/18/2022] [Indexed: 11/08/2022]
Abstract
DNA tagging with base analogs has found numerous applications. To precisely record the DNA labelling information, it will be highly beneficial to develop chemical sequencing tags that can be encoded into DNA as regular bases and decoded as mutant bases upon a mild, efficient and bioorthognal chemical treatment. Here we reported such a DNA tag, N4-allyldeoxycytidine (a4dC), to label and identify DNA by in vitro assays. The iodination of a4dC led to fast and complete formation of 3, N4-cyclized deoxycytidine, which induced base misincorporation during DNA replication and thus could be located at single base resolution. We explored the applications of a4dC in pinpointing DNA labelling sites at single base resolution, mapping epigenetic mark N4-methyldeoxycytidine, and imaging nucleic acids in situ. In addition, mammalian cellular DNA could be metabolically labelled with a4dC. Together,our study sheds light on the design of next generation DNA tags with chemical sequencing power.
Collapse
Affiliation(s)
- Donghong Liu
- Zhejiang University, Department of polymer science and engineering, CHINA
| | - Xiao Shu
- Zhejiang University, Department of polymer science and engineering, CHINA
| | - Siying Xiang
- Zhejiang University, Department of polymer science and engineering, CHINA
| | - Tengwei Li
- Zhejiang University, Department of polymer science and engineering, CHINA
| | - Chenyang Huang
- Zhejiang University, Department of polymer science and engineering, CHINA
| | - Mohan Cheng
- Zhejiang University, Department of polymer science and engineering, CHINA
| | - Jie Cao
- Zhejiang University, Life Sciences Institute; Department of Polymer Science and Engineering, CHINA
| | - Yuejin Hua
- Zhejiang University, he MOE Key Laboratory of Biosystems Homeostasis & Protection; Department of Infectious Diseases, Sir Run Run Shaw Hospital, College of Medicine, CHINA
| | - Jianzhao Liu
- Zhejiang University, Department of Polymer Science and Engineering, Zheda road 38, 310007, hangzhou, CHINA
| |
Collapse
|
3
|
Chardet C, Payrastre C, Gerland B, Escudier JM. Convertible and Constrained Nucleotides: The 2'-Deoxyribose 5'-C-Functionalization Approach, a French Touch. Molecules 2021; 26:5925. [PMID: 34641475 PMCID: PMC8512084 DOI: 10.3390/molecules26195925] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2021] [Revised: 09/21/2021] [Accepted: 09/27/2021] [Indexed: 11/17/2022] Open
Abstract
Many strategies have been developed to modulate the biological or biotechnical properties of oligonucleotides by introducing new chemical functionalities or by enhancing their affinity and specificity while restricting their conformational space. Among them, we review our approach consisting of modifications of the 5'-C-position of the nucleoside sugar. This allows the introduction of an additional chemical handle at any position on the nucleotide chain without disturbing the Watson-Crick base-pairing. We show that 5'-C bromo or propargyl convertible nucleotides (CvN) are accessible in pure diastereoisomeric form, either for nucleophilic displacement or for CuAAC conjugation. Alternatively, the 5'-carbon can be connected in a stereo-controlled manner to the phosphate moiety of the nucleotide chain to generate conformationally constrained nucleotides (CNA). These allow the precise control of the sugar/phosphate backbone torsional angles. The consequent modulation of the nucleic acid shape induces outstanding stabilization properties of duplex or hairpin structures in accordance with the preorganization concept. Some biological applications of these distorted oligonucleotides are also described. Effectively, the convertible and the constrained approaches have been merged to create constrained and convertible nucleotides (C2NA) providing unique tools to functionalize and stabilize nucleic acids.
Collapse
Affiliation(s)
| | | | - Béatrice Gerland
- Laboratoire de Synthèse et Physico-Chimie de Molécules d′Intérêt Biologique, UMR CNRS 5068, Université Paul Sabatier, 118 Route de Narbonne, CEDEX 9, 31062 Toulouse, France; (C.C.); (C.P.)
| | - Jean-Marc Escudier
- Laboratoire de Synthèse et Physico-Chimie de Molécules d′Intérêt Biologique, UMR CNRS 5068, Université Paul Sabatier, 118 Route de Narbonne, CEDEX 9, 31062 Toulouse, France; (C.C.); (C.P.)
| |
Collapse
|
4
|
Towards the enzymatic synthesis of phosphorothioate containing LNA oligonucleotides. Bioorg Med Chem Lett 2021; 48:128242. [PMID: 34217829 DOI: 10.1016/j.bmcl.2021.128242] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2021] [Revised: 06/24/2021] [Accepted: 06/28/2021] [Indexed: 12/20/2022]
Abstract
Therapeutic oligonucleotides require the addition of multiple chemical modifications to the nucleosidic scaffold in order to improve their drug delivery efficiency, cell penetration capacity, biological stability, and pharmacokinetic properties. This chemical modification pattern is often accompanied by a synthetic burden and by limitations in sequence length. Here, we have synthesized a nucleoside triphosphate analog bearing two simultaneous modifications at the level of the sugar (LNA) and the backbone (thiophosphate) and have tested its compatibility with enzymatic DNA synthesis which could abrogate some of these synthetic limitations. While this novel analog is not as well tolerated by polymerases compared to the corresponding α-thio-dTTP or LNA-TTP, α -thio-LNA-TTP can readily be used for enzymatic synthesis on universal templates for the introduction of phosphorothioated LNA nucleotides.
Collapse
|
5
|
Krömer M, Brunderová M, Ivancová I, Poštová Slavětínská L, Hocek M. 2-Formyl-dATP as Substrate for Polymerase Synthesis of Reactive DNA Bearing an Aldehyde Group in the Minor Groove. Chempluschem 2021; 85:1164-1170. [PMID: 32496002 DOI: 10.1002/cplu.202000287] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2020] [Revised: 05/15/2020] [Indexed: 12/16/2022]
Abstract
2-Formyl-2'-deoxyadenosine triphosphate (dCHO ATP) was synthesized and tested as a substrate in enzymatic synthesis of DNA modified in the minor groove with a reactive aldehyde group. The multistep synthesis of dCHO ATP was based on the preparation of protected 2-dihydroxyethyl-2'-deoxyadenosine intemediate, which was triphosphorylated and converted to aldehyde through oxidative cleavage. The dCHO ATP triphosphate was a moderate substrate for KOD XL DNA polymerase, and was used for enzymatic synthesis of some sequences using primer extension (PEX). On the other hand, longer sequences (31-mer) with higher number of modifications, or sequences with modifications at adjacent positions did not give full extension. Single-nucleotide extension followed by PEX was used for site-specific incorporation of one aldehyde-linked adenosine into a longer 49-mer sequence. The reactive formyl group was used for cross-linking with peptides and proteins using reductive amination and for fluorescent labelling through oxime formation with an AlexaFluor647-linked hydroxylamine.
Collapse
Affiliation(s)
- Matouš Krömer
- Institute of Organic Chemistry and Biochemistry, Czech Academy of Sciences, Flemingovo namesti 2, 16610, Prague 6, Czech Republic.,Department of Organic Chemistry, Faculty of Science, Charles University in Prague, Hlavova 8, Prague-2, 12843, Czech Republic
| | - Mária Brunderová
- Institute of Organic Chemistry and Biochemistry, Czech Academy of Sciences, Flemingovo namesti 2, 16610, Prague 6, Czech Republic.,Department of Organic Chemistry, Faculty of Science, Charles University in Prague, Hlavova 8, Prague-2, 12843, Czech Republic
| | - Ivana Ivancová
- Institute of Organic Chemistry and Biochemistry, Czech Academy of Sciences, Flemingovo namesti 2, 16610, Prague 6, Czech Republic.,Department of Organic Chemistry, Faculty of Science, Charles University in Prague, Hlavova 8, Prague-2, 12843, Czech Republic
| | - Lenka Poštová Slavětínská
- Institute of Organic Chemistry and Biochemistry, Czech Academy of Sciences, Flemingovo namesti 2, 16610, Prague 6, Czech Republic
| | - Michal Hocek
- Institute of Organic Chemistry and Biochemistry, Czech Academy of Sciences, Flemingovo namesti 2, 16610, Prague 6, Czech Republic.,Department of Organic Chemistry, Faculty of Science, Charles University in Prague, Hlavova 8, Prague-2, 12843, Czech Republic
| |
Collapse
|
6
|
Abstract
Labeling of nucleic acids is required for many studies aiming to elucidate their functions and dynamics in vitro and in cells. Out of the numerous labeling concepts that have been devised, covalent labeling provides the most stable linkage, an unrivaled choice of small and highly fluorescent labels and - thanks to recent advances in click chemistry - an incredible versatility. Depending on the approach, site-, sequence- and cell-specificity can be achieved. DNA and RNA labeling are rapidly developing fields that bring together multiple areas of research: on the one hand, synthetic and biophysical chemists develop new fluorescent labels and isomorphic nucleobases as well as faster and more selective bioorthogonal reactions. On the other hand, the number of enzymes that can be harnessed for post-synthetic and site-specific labeling of nucleic acids has increased significantly. Together with protein engineering and genetic manipulation of cells, intracellular and cell-specific labeling has become possible. In this review, we provide a structured overview of covalent labeling approaches for nucleic acids and highlight notable developments, in particular recent examples. The majority of this review will focus on fluorescent labeling; however, the principles can often be readily applied to other labels. We will start with entirely chemical approaches, followed by chemo-enzymatic strategies and ribozymes, and finish with metabolic labeling of nucleic acids. Each section is subdivided into direct (or one-step) and two-step labeling approaches and will start with DNA before treating RNA.
Collapse
Affiliation(s)
- Nils Klöcker
- Institute of Biochemistry, University of Muenster, Corrensstraße 36, D-48149 Münster, Germany.
| | | | | |
Collapse
|
7
|
Bhoge BA, Mala P, Kurian JS, Srinivasan V, Saraogi I. Selective functionalization at N 2-position of guanine in oligonucleotides via reductive amination. Chem Commun (Camb) 2020; 56:13832-13835. [PMID: 33084637 DOI: 10.1039/d0cc05492e] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
Chemo- and site-specific modifications in oligonucleotides have wide applicability as mechanistic probes in chemical biology. However, methods that label specific sites in nucleic acids are scarce, especially for labeling DNA/RNA from biological or enzymatic sources rather than synthetic ones. Here we have employed a classical reaction, reductive amination, to selectively functionalize the N2-amine of guanosine and 2'-deoxyguanosine monophosphate (GMP/dGMP). This method specifically modifies guanine in DNA and RNA oligonucleotides, while leaving the other nucleobases unaffected. Using this approach, we have successfully incorporated a reactive handle chemoselectively into nucleic acids for further functionalization and downstream applications.
Collapse
Affiliation(s)
- Bapurao A Bhoge
- Department of Chemistry, Indian Institute of Science Education and Research Bhopal, Bhopal Bypass Road, Bhauri, Bhopal 462066, MP, India.
| | | | | | | | | |
Collapse
|
8
|
Matyašovský J, Hocek M. 2-Substituted 2'-deoxyinosine 5'-triphosphates as substrates for polymerase synthesis of minor-groove-modified DNA and effects on restriction endonuclease cleavage. Org Biomol Chem 2020; 18:255-262. [PMID: 31815989 DOI: 10.1039/c9ob02502b] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
Five 2-substituted 2'-deoxyinosine triphosphates (dRITP) were synthesized and tested as substrates in enzymatic synthesis of minor-groove base-modified DNA. Only 2-methyl and 2-vinyl derivatives proved to be good substrates for Therminator DNA polymerase, whilst all other dRITPs and other tested DNA polymerases did not give full length products in primer extension. The DNA containing 2-vinylhypoxanthine was then further modified through thiol-ene reactions with thiols. Cross-linking reaction between cysteine-containing minor-groove binding dodecapeptide and DNA proceeded thanks to the proximity effect between thiol and vinyl groups inside the minor groove. 2-Substituted dIRTPs and also previously prepared 2-substituted 2'-deoxyadenosine triphosphates (dRATP) were then used for enzymatic synthesis of minor-groove modified DNA to study the effect of minor-groove modifications on cleavage of DNA by type II restriction endonucleases (REs). Although the REs should recognize the sequence through H-bonds in the major groove, some minor-groove modifications also had an inhibiting effect on the cleavage.
Collapse
Affiliation(s)
- Ján Matyašovský
- Institute of Organic Chemistry and Biochemistry, Czech Academy of Sciences, Flemingovo namesti 2, CZ-16610 Prague 6, Czech Republic.
| | | |
Collapse
|
9
|
Rodríguez J, Martínez-Calvo M. Transition-Metal-Mediated Modification of Biomolecules. Chemistry 2020; 26:9792-9813. [PMID: 32602145 DOI: 10.1002/chem.202001287] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2020] [Revised: 06/25/2020] [Indexed: 01/15/2023]
Abstract
The site-selective modification of biomolecules has grown spectacularly in recent years. The presence of a large number of functional groups in a biomolecule makes its chemo- and regioselective modification a challenging goal. In this context, transition-metal-mediated reactions are emerging as a powerful tool owing to their unique reactivity and good functional group compatibility, allowing highly efficient and selective bioconjugation reactions that operate under mild conditions. This Minireview focuses on the current state of organometallic chemistry for bioconjugation, highlighting the potential of transition metals for the development of chemoselective and site-specific methods for functionalization of peptides, proteins and nucleic acids. The importance of the selection of ligands attached to the transition metal for conferring the desired chemoselectivity will be highlighted.
Collapse
Affiliation(s)
- Jessica Rodríguez
- Laboratoire Hétérochimie Fondamentale et Appliquée, Université Paul Sabatier/CNRS UMR 5069, 118 Route de Narbonne, 31062, Toulouse Cedex 09, France
| | - Miguel Martínez-Calvo
- Centro de Investigaciones Científicas Avanzadas (CICA), AE CICA-INIBIC, Departamento de Química, Facultade de Ciencias, Universidade da Coruña, Campus de Elviña, 15071 A, Coruña, Galicia, Spain
| |
Collapse
|
10
|
Ivancová I, Leone DL, Hocek M. Reactive modifications of DNA nucleobases for labelling, bioconjugations, and cross-linking. Curr Opin Chem Biol 2019; 52:136-144. [DOI: 10.1016/j.cbpa.2019.07.007] [Citation(s) in RCA: 27] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2019] [Revised: 06/26/2019] [Accepted: 07/18/2019] [Indexed: 12/20/2022]
|
11
|
Escudier JM, Payrastre C, Gerland B, Tarrat N. Convertible and conformationally constrained nucleic acids (C 2NAs). Org Biomol Chem 2019; 17:6386-6397. [PMID: 31210235 DOI: 10.1039/c9ob01150a] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Abstract
We introduce the concept of Convertible and Constrained Nucleic Acids (C2NAs). By means of the synthesis of a stereocontrolled N-propargyl dioxo-1,3,2-oxaza-phosphorinane as an internucleotidic linkage, the torsional angles α and β can adopt either the canonical (g-, t) set of values able to increase DNA duplex stability or the non-canonical (g+, t) set that stabilized the hairpin structure when installed within the loop moiety. With an appended propargyl function on the nitrogen atom of the six-membered ring, the copper catalysed Huisgen's cycloaddition (CuAAC click chemistry) allows for the introduction of new functionalities at any location on the nucleic acid chain while maintaining the properties brought by the geometrical constraint and the neutral internucleotidic linkage.
Collapse
Affiliation(s)
- Jean-Marc Escudier
- Laboratoire de Synthèse et Physico-Chimie de Molécules d'Intérêt Biologique, UMR CNRS 5068, Université Paul Sabatier, 118 route de Narbonne, 31062 Toulouse, France.
| | - Corinne Payrastre
- Laboratoire de Synthèse et Physico-Chimie de Molécules d'Intérêt Biologique, UMR CNRS 5068, Université Paul Sabatier, 118 route de Narbonne, 31062 Toulouse, France.
| | - Béatrice Gerland
- Laboratoire de Synthèse et Physico-Chimie de Molécules d'Intérêt Biologique, UMR CNRS 5068, Université Paul Sabatier, 118 route de Narbonne, 31062 Toulouse, France.
| | - Nathalie Tarrat
- CEMES, Université de Toulouse, CNRS, 29 rue Jeanne Marvig, Toulouse 31055, France
| |
Collapse
|
12
|
Hocek M. Enzymatic Synthesis of Base-Functionalized Nucleic Acids for Sensing, Cross-linking, and Modulation of Protein-DNA Binding and Transcription. Acc Chem Res 2019; 52:1730-1737. [PMID: 31181911 DOI: 10.1021/acs.accounts.9b00195] [Citation(s) in RCA: 62] [Impact Index Per Article: 12.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
Protein-DNA interactions are important in replication, transcription, repair, as well as epigenetic modifications of DNA, which involve methylation and demethylation of DNA resulting in regulation of gene expression. Understanding of these processes and chemical tools for studying and perhaps even modulating them could be of great relevance and importance not only in chemical biology but also in real diagnostics and treatment of diseases. In the past decade, we have been working on development of synthesis of base-modified 2'-deoxyribo- or ribonucleoside triphosphates (dNTPs or NTPs) and their use in enzymatic synthesis of modified nucleic acids using DNA or RNA polymerases. These synthetic and enzymatic methods are briefly summarized with focus on recent development and outlining of scope, limitations, and further challenges. The main focus of this Account is on applications of base-modified nucleic acids in sensing of protein-DNA interactions, in covalent cross-linking to DNA-binding proteins ,and in modulation of protein-DNA binding and transcription. Several environment-sensitive fluorescent nucleotides were incorporated to DNA probes which responded to protein binding by light-up, changing of color, or lifetime of fluorescence. Using a cyclodextrin-peptide transporter, fluorescent nucleotides can be transported through the cell membrane and incorporated to genomic DNA. Several dNTPs bearing reactive groups (i.e., vinylsulfonamide or chloroacetamide) were used for polymerase synthesis of DNA reactive probes which cross-link to Cys, His, or Lys in peptides or proteins. An attractive challenge is to use DNA modifications and bioorthogonal reactions in the major groove of DNA for modulation and switching of protein-DNA interactions. We have systematically explored the influence of major-groove modifications on recognition and cleavage of DNA by restriction endonucleases and constructed simple chemical switches of DNA cleavage. Systematic study of the influence of major-groove modifications on transcription with bacterial RNA polymerases revealed not only that some modified bases are tolerated, but also that the presence of 5-hydroxymethyluracil or -cytosine can even enhance the transcription (350 or 250% compared to native DNA). Based on these results, we have constructed the first chemical switch of transcription based on photocaging of hydroxymethylpyrimidines in DNA by 2-nitrobenzyl protection (transcription off), photochemical deprotection of the DNA (transcription on), and enzymatic phosphorylation (only for 5-hydroxymethyluracil, transcription off). Although it has been so far demonstrated only in vitro, it is the proof-of-principle first step toward chemical epigenetics.
Collapse
Affiliation(s)
- 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 in Prague, Hlavova 8, CZ-12843 Prague 2, Czech Republic
| |
Collapse
|
13
|
Gardner AF, Jackson KM, Boyle MM, Buss JA, Potapov V, Gehring AM, Zatopek KM, Corrêa IR, Ong JL, Jack WE. Therminator DNA Polymerase: Modified Nucleotides and Unnatural Substrates. Front Mol Biosci 2019; 6:28. [PMID: 31069234 PMCID: PMC6491775 DOI: 10.3389/fmolb.2019.00028] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2018] [Accepted: 04/04/2019] [Indexed: 11/13/2022] Open
Abstract
A variant of 9°N DNA polymerase [Genbank ID (AAA88769.1)] with three mutations (D141A, E143A, A485L) and commercialized under the name "Therminator DNA polymerase" has the ability to incorporate a variety of modified nucleotide classes. This Review focuses on how Therminator DNA Polymerase has enabled new technologies in synthetic biology and DNA sequencing. In addition, we discuss mechanisms for increased modified nucleotide incorporation.
Collapse
Affiliation(s)
| | | | | | | | | | | | | | - Ivan R Corrêa
- New England Biolabs, Inc., Ipswich, MA, United States
| | | | | |
Collapse
|
14
|
Reisacher U, Ploschik D, Rönicke F, Cserép GB, Kele P, Wagenknecht HA. Copper-free dual labeling of DNA by triazines and cyclopropenes as minimal orthogonal and bioorthogonal functions. Chem Sci 2019; 10:4032-4037. [PMID: 31015943 PMCID: PMC6450502 DOI: 10.1039/c8sc05588b] [Citation(s) in RCA: 36] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2018] [Accepted: 03/01/2019] [Indexed: 12/14/2022] Open
Abstract
Two different and small functions for inverse electron demand Diels–Alder reactions were applied for dual labeling of DNA: the 1,2,4-triazine was attached to the 5-position of 2′-deoxyuridine, and the 1-methylcyclopropene to the 7-position of 7-deaza-2′-deoxyadenosine.
Two different and small functions for inverse electron demand Diels–Alder reactions were applied for dual labeling of DNA: the 1,2,4-triazine was attached to the 5-position of 2′-deoxyuridine triphosphate, and the 1-methylcyclopropene to the 7-position of 7-deaza-2′-deoxyadenosine triphosphate. These two modified nucleotides were sequence-selectively incorporated into oligonucleotides by DNA polymerases. These products were labeled by two different fluorescent dyes using postsynthetic reactions that are not only bioorthogonal in general, but also mutually orthogonal.
Collapse
Affiliation(s)
- Ulrike Reisacher
- Institute of Organic Chemistry , Karlsruhe Institute of Technology (KIT) , Fritz-Haber-Weg 6 , 76131 Karlsruhe , Germany .
| | - Damian Ploschik
- Institute of Organic Chemistry , Karlsruhe Institute of Technology (KIT) , Fritz-Haber-Weg 6 , 76131 Karlsruhe , Germany .
| | - Franziska Rönicke
- Institute of Organic Chemistry , Karlsruhe Institute of Technology (KIT) , Fritz-Haber-Weg 6 , 76131 Karlsruhe , Germany .
| | - Gergely B Cserép
- Chemical Biology Research Group , Institute of Organic Chemistry , Research Centre for Natural Sciences , Hungarian Academy of Sciences , Magyar tudósok krt. 2 , H-1117 Budapest , Hungary
| | - Péter Kele
- Chemical Biology Research Group , Institute of Organic Chemistry , Research Centre for Natural Sciences , Hungarian Academy of Sciences , Magyar tudósok krt. 2 , H-1117 Budapest , Hungary
| | - Hans-Achim Wagenknecht
- Institute of Organic Chemistry , Karlsruhe Institute of Technology (KIT) , Fritz-Haber-Weg 6 , 76131 Karlsruhe , Germany .
| |
Collapse
|
15
|
Sarac I, Hollenstein M. Terminal Deoxynucleotidyl Transferase in the Synthesis and Modification of Nucleic Acids. Chembiochem 2019; 20:860-871. [PMID: 30451377 DOI: 10.1002/cbic.201800658] [Citation(s) in RCA: 46] [Impact Index Per Article: 9.2] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2018] [Indexed: 12/26/2022]
Abstract
The terminal deoxynucleotidyl transferase (TdT) belongs to the X family of DNA polymerases. This unusual polymerase catalyzes the template-independent addition of random nucleotides on 3'-overhangs during V(D)J recombination. The biological function and intrinsic biochemical properties of the TdT have spurred the development of numerous oligonucleotide-based tools and methods, especially if combined with modified nucleoside triphosphates. Herein, we summarize the different applications stemming from the incorporation of modified nucleotides by the TdT. The structural, mechanistic, and biochemical properties of this polymerase are also discussed.
Collapse
Affiliation(s)
- Ivo Sarac
- Laboratory for Bioorganic Chemistry of Nucleic Acids, Department of Structural Biology and Chemistry, Institut Pasteur, CNRS UMR3523, 28, rue du Docteur Roux, 75724, Paris Cedex 15, France
| | - Marcel Hollenstein
- Laboratory for Bioorganic Chemistry of Nucleic Acids, Department of Structural Biology and Chemistry, Institut Pasteur, CNRS UMR3523, 28, rue du Docteur Roux, 75724, Paris Cedex 15, France
| |
Collapse
|
16
|
Sinha AK, Equbal D. Thiol−Ene Reaction: Synthetic Aspects and Mechanistic Studies of an Anti-Markovnikov-Selective Hydrothiolation of Olefins. ASIAN J ORG CHEM 2018. [DOI: 10.1002/ajoc.201800639] [Citation(s) in RCA: 60] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Affiliation(s)
- Arun K. Sinha
- Medicinal and Process Chemistry Division; C.S.I.R.-Central Drug Research Institute; Council of Scientific and Industrial Research); Lucknow- 226021 (U.P.) India
- Academy of Scientific and Innovative Research (AcSIR); Postal Staff College Area, Sector 19; Kamla Nehru Nagar; Ghaziabad, Uttar Pradesh- 201002
| | - Danish Equbal
- Medicinal and Process Chemistry Division; C.S.I.R.-Central Drug Research Institute; Council of Scientific and Industrial Research); Lucknow- 226021 (U.P.) India
| |
Collapse
|
17
|
Matyašovský J, Pohl R, Hocek M. 2-Allyl- and Propargylamino-dATPs for Site-Specific Enzymatic Introduction of a Single Modification in the Minor Groove of DNA. Chemistry 2018; 24:14938-14941. [PMID: 30074286 PMCID: PMC6221035 DOI: 10.1002/chem.201803973] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2018] [Indexed: 12/15/2022]
Abstract
A series of 2-alkylamino-2'-deoxyadenosine triphosphates (dATP) was prepared and found to be substrates for the Therminator DNA polymerase, which incorporated only one modified nucleotide into the primer. Using a template encoding for two consecutive adenines, conditions were found for incorporation of either one or two modified nucleotides. In all cases, addition of a mixture of natural dNTPs led to primer extension resulting in site-specific single modification of DNA in the minor groove. The allylamino-substituted DNA was used for the thiol-ene addition, whereas the propargylamino-DNA for the CuAAC click reaction was used to label the DNA with a fluorescent dye in the minor groove. The approach was used to construct FRET probes for detection of oligonucleotides.
Collapse
Affiliation(s)
- Ján Matyašovský
- Institute of Organic Chemistry and BiochemistryCzech Academy of SciencesFlemingovo nam. 216610Prague 6Czech Republic
- Department of Organic ChemistryFaculty of ScienceCharles University in PragueHlavova 812843Prague 2Czech Republic
| | - Radek Pohl
- Institute of Organic Chemistry and BiochemistryCzech Academy of SciencesFlemingovo nam. 216610Prague 6Czech Republic
| | - Michal Hocek
- Institute of Organic Chemistry and BiochemistryCzech Academy of SciencesFlemingovo nam. 216610Prague 6Czech Republic
- Department of Organic ChemistryFaculty of ScienceCharles University in PragueHlavova 812843Prague 2Czech Republic
| |
Collapse
|