1
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Saintomé C, Monfret O, Doisneau G, Guianvarc'h D. Oligonucleotide-Based Photoaffinity Probes: Chemical Tools and Applications for Protein Labeling. Chembiochem 2024:e202400097. [PMID: 38703401 DOI: 10.1002/cbic.202400097] [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] [Received: 01/31/2024] [Revised: 04/30/2024] [Accepted: 05/03/2024] [Indexed: 05/06/2024]
Abstract
A variety of proteins interact with DNA and RNA, including polymerases, histones, ribosomes, transcription factors, and repair enzymes. However, the transient non-covalent nature of these interactions poses challenges for analysis. Introducing a covalent bond between proteins and DNA via photochemical activation of a photosensitive functional group introduced onto nucleic acids offers a means to stabilize these often weak interactions without significantly altering the binding interface. Consequently, photoactivatable oligonucleotides are powerful tools for investigating nucleic acid-protein interactions involved in numerous biological and pathological processes. In this review, we provide a comprehensive overview of the chemical tools developed so far and the different strategies used for incorporating the most commonly used photoreactive reagents into oligonucleotide probes or nucleic acids. Furthermore, we illustrate their application with several examples including protein binding site mapping, identification of protein binding partners, and in cell studies.
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Affiliation(s)
- Carole Saintomé
- Sorbonne Université, UFR 927, MNHN CNRS UMR 7196, INSERM U1154, 43 rue Cuvier, 75005, Paris, France
| | - Océane Monfret
- Université Paris-Saclay, CNRS, Institut de Chimie Moléculaire et des Matériaux d'Orsay, UMR CNRS 8182, 91405, Orsay, France
| | - Gilles Doisneau
- Université Paris-Saclay, CNRS, Institut de Chimie Moléculaire et des Matériaux d'Orsay, UMR CNRS 8182, 91405, Orsay, France
| | - Dominique Guianvarc'h
- Université Paris-Saclay, CNRS, Institut de Chimie Moléculaire et des Matériaux d'Orsay, UMR CNRS 8182, 91405, Orsay, France
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2
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Abstract
Herein, we described an efficient method for the construction of highly functionalized diazirines from the carbohydrazide and diazo-substituted hypervalent iodine reagents. Unambiguous transformation has been designed with user applicable and easy practicable conditions. Remarkably, d-glucose, menthol, aspirin, proline, and lithocholic acid were efficiently diazirinated. Furthermore, the method is mild, robust, and highly selective, which successfully converted a variety of aryl, alkyl, benzyl, and heterocyclic hydrazides into the corresponding diazirine derivatives.
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Affiliation(s)
- Monish Arbaz Ansari
- Department of Chemistry, Institute of Science, Banaras Hindu University, Varanasi 221 005, India
| | - Ganesh Kumar
- Department of Chemistry, Institute of Science, Banaras Hindu University, Varanasi 221 005, India
| | - Maya Shankar Singh
- Department of Chemistry, Institute of Science, Banaras Hindu University, Varanasi 221 005, India
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3
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Elskens J, Madder A. Crosslinker-modified nucleic acid probes for improved target identification and biomarker detection. RSC Chem Biol 2021; 2:410-422. [PMID: 34458792 PMCID: PMC8341421 DOI: 10.1039/d0cb00236d] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2020] [Accepted: 02/11/2021] [Indexed: 01/02/2023] Open
Abstract
Understanding the intricate interaction pattern of nucleic acids with other molecules is essential to gain further insight in biological processes and disease mechanisms. To this end, a multitude of hybridization-based assays have been designed that rely on the non-covalent recognition between complementary nucleic acid sequences. However, the ephemeral nature of these interactions complicates straightforward analysis as low efficiency and specificity are rule rather than exception. By covalently locking nucleic acid interactions by means of a crosslinking agent, the overall efficiency, specificity and selectivity of hybridization-based assays could be increased. In this mini-review we highlight methodologies that exploit the use of crosslinker-modified nucleic acid probes for interstrand nucleic acid crosslinking with the objective to study, detect and identify important targets as well as nucleic acid sequences that can be considered relevant biomarkers. We emphasize on the usefulness and advantages of crosslinking agents and elaborate on the chemistry behind the crosslinking reactions they induce.
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Affiliation(s)
- Joke Elskens
- Department of Organic and Macromolecular Chemistry, Faculty of Sciences, Ghent University Krijgslaan 281 Building S4 9000 Ghent Belgium +32-9-264-49-98 +32-9-264-44-72
| | - Annemieke Madder
- Department of Organic and Macromolecular Chemistry, Faculty of Sciences, Ghent University Krijgslaan 281 Building S4 9000 Ghent Belgium +32-9-264-49-98 +32-9-264-44-72
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4
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Krell K, Harijan D, Ganz D, Doll L, Wagenknecht HA. Postsynthetic Modifications of DNA and RNA by Means of Copper-Free Cycloadditions as Bioorthogonal Reactions. Bioconjug Chem 2020; 31:990-1011. [DOI: 10.1021/acs.bioconjchem.0c00072] [Citation(s) in RCA: 29] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Affiliation(s)
- Katja Krell
- Karlsruhe Institute of Technology (KIT), Institute for Organic Chemistry, Fritz-Haber-Weg 6, 76131 Karlsruhe, Germany
| | - Dennis Harijan
- Karlsruhe Institute of Technology (KIT), Institute for Organic Chemistry, Fritz-Haber-Weg 6, 76131 Karlsruhe, Germany
| | - Dorothée Ganz
- Karlsruhe Institute of Technology (KIT), Institute for Organic Chemistry, Fritz-Haber-Weg 6, 76131 Karlsruhe, Germany
| | - Larissa Doll
- Karlsruhe Institute of Technology (KIT), Institute for Organic Chemistry, Fritz-Haber-Weg 6, 76131 Karlsruhe, Germany
| | - Hans-Achim Wagenknecht
- Karlsruhe Institute of Technology (KIT), Institute for Organic Chemistry, Fritz-Haber-Weg 6, 76131 Karlsruhe, Germany
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5
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Procacci B, Roy SS, Norcott P, Turner N, Duckett SB. Unlocking a Diazirine Long-Lived Nuclear Singlet State via Photochemistry: NMR Detection and Lifetime of an Unstabilized Diazo-Compound. J Am Chem Soc 2018; 140:16855-16864. [PMID: 30407809 PMCID: PMC6300312 DOI: 10.1021/jacs.8b10923] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
![]()
Diazirines
are important for photoaffinity labeling, and their
photoisomerization is relatively well-known. This work shows how hyperpolarized
NMR spectroscopy can be used to characterize an unstable diazo-compound
formed via photoisomerization of a 15N2-labeled
silyl-ether-substituted diazirine. This diazirine is prepared in a
nuclear spin singlet state via catalytic transfer of spin order from para-hydrogen. The active hyperpolarization catalyst is
characterized to provide insight into the mechanism. The photochemical
isomerization of the diazirine into the diazo-analogue allows the
NMR invisible nuclear singlet state of the parent compound to be probed.
The identity of the diazo-species is confirmed by trapping with N-phenyl maleimide via a cycloaddition reaction to afford
bicyclic pyrazolines that also show singlet state character. The presence
of singlet states in the diazirine and the diazo-compound is validated
by comparison of experimental nutation behavior with theoretical simulation.
The magnetic state lifetime of the diazo-compound is determined as
12 ± 1 s in CD3OD solution at room temperature, whereas
its chemical lifetime is measured as 100 ± 5 s by related hyperpolarized
NMR studies. Indirect evidence for the generation of the photoproduct para-N2 is presented.
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Affiliation(s)
- Barbara Procacci
- Centre for Hyperpolarisation in Magnetic Resonance, Department of Chemistry, York Science Park , University of York , York YO10 5NY , United Kingdom
| | - Soumya S Roy
- Centre for Hyperpolarisation in Magnetic Resonance, Department of Chemistry, York Science Park , University of York , York YO10 5NY , United Kingdom
| | - Philip Norcott
- Centre for Hyperpolarisation in Magnetic Resonance, Department of Chemistry, York Science Park , University of York , York YO10 5NY , United Kingdom
| | - Norman Turner
- Accelerator Research Group, University of Huddersfield , Queensgate, Huddersfield HD1 3DH , United Kingdom
| | - Simon B Duckett
- Centre for Hyperpolarisation in Magnetic Resonance, Department of Chemistry, York Science Park , University of York , York YO10 5NY , United Kingdom
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6
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Gérard-Hirne T, Thiebaut F, Sachon E, Désert A, Drujon T, Guérineau V, Michel BY, Benhida R, Coulon S, Saintomé C, Guianvarc'h D. Photoactivatable oligonucleotide probes to trap single-stranded DNA binding proteins: Updating the potential of 4-thiothymidine from a comparative study. Biochimie 2018; 154:164-175. [PMID: 30171884 DOI: 10.1016/j.biochi.2018.08.007] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2018] [Accepted: 08/27/2018] [Indexed: 02/07/2023]
Abstract
Photoaffinity labeling (PAL) in combination with recent developments in mass spectrometry is a powerful tool for studying nucleic acid-protein interactions, enabling crosslinking of both partners through covalent bond formation. Such a strategy requires a preliminary study of the most judicious photoreactive group to crosslink efficiently with the target protein. In this study, we report a survey of three different photoreactive nucleobases (including a guanine functionalized with a benzophenone or a diazirine and the zero-length agent 4-thiothymine) incorporated in 30-mer oligonucleotides (ODN) containing a biotin moiety for selective trapping and enrichment of single-stranded DNA binding proteins (SSB). First, the conditions and efficiency of the photochemical reaction with a purified protein using human replication protein A as the relevant model was studied. Secondly, the ability of the probe as bait to photocrosslink and enrich SSB in cell lysate was addressed. Among the different ODN probes studied, we showed that 4-thiothymine was the most relevant: i) it allows efficient and specific trapping of SSB in whole cell extracts in a similar extent as the widely used diazirine, ii) it features the advantages of a zero-length agent thus retaining the physicochemical properties of the ODN bait; iii) ODN including this photochemical agent are easily accessible. In combination with mass spectrometry, the probes incorporating this nucleobase are powerful tools for PAL strategies and can be added in the toolbox of the traditional photocrosslinkers for studying DNA-protein interactions.
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Affiliation(s)
- Tom Gérard-Hirne
- Sorbonne Université, École normale supérieure, PSL University, CNRS, Laboratoire des biomolécules, LBM, 75005 Paris, France
| | - Frédéric Thiebaut
- Sorbonne Université, École normale supérieure, PSL University, CNRS, Laboratoire des biomolécules, LBM, 75005 Paris, France; MNHN CNRS UMR 7196, INSERM U1154, 43 Rue Cuvier, 75005, Paris, France
| | - Emmanuelle Sachon
- Sorbonne Université, École normale supérieure, PSL University, CNRS, Laboratoire des biomolécules, LBM, 75005 Paris, France; Plateforme de spectrométrie de masse et protéomique, IBPS, FR3631, UPMC, 4 Place Jussieu, 75005, Paris, France
| | - Alexandre Désert
- Sorbonne Université, École normale supérieure, PSL University, CNRS, Laboratoire des biomolécules, LBM, 75005 Paris, France
| | - Thierry Drujon
- Sorbonne Université, École normale supérieure, PSL University, CNRS, Laboratoire des biomolécules, LBM, 75005 Paris, France
| | - Vincent Guérineau
- Institut de Chimie des Substances Naturelles, CNRS UPR2301, Université Paris-Sud, Université Paris-Saclay, Avenue de la Terrasse, 91198, Gif-sur-Yvette Cedex, France
| | - Benoît Y Michel
- Université Côte d'Azur, CNRS, Institut de Chimie de Nice UMR 7272, 06108 Nice, France
| | - Rachid Benhida
- Université Côte d'Azur, CNRS, Institut de Chimie de Nice UMR 7272, 06108 Nice, France
| | - Stéphane Coulon
- CRCM, CNRS, Inserm, Aix-Marseille Univ, Institut Paoli-Calmettes, Equipe Labellisée Ligue, Marseille, France
| | - Carole Saintomé
- MNHN CNRS UMR 7196, INSERM U1154, 43 Rue Cuvier, 75005, Paris, France; Sorbonne Université, UFR927, 4, Place Jussieu, F-75005, Paris, France.
| | - Dominique Guianvarc'h
- Sorbonne Université, École normale supérieure, PSL University, CNRS, Laboratoire des biomolécules, LBM, 75005 Paris, France; Institut de Chimie Moléculaire et des Matériaux d'Orsay, Univ. Paris-Sud, CNRS, Université Paris-Saclay, F-91405, Orsay, France.
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7
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Ge SS, Chen B, Wu YY, Long QS, Zhao YL, Wang PY, Yang S. Current advances of carbene-mediated photoaffinity labeling in medicinal chemistry. RSC Adv 2018; 8:29428-29454. [PMID: 35547988 PMCID: PMC9084484 DOI: 10.1039/c8ra03538e] [Citation(s) in RCA: 47] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2018] [Accepted: 07/07/2018] [Indexed: 12/21/2022] Open
Abstract
Photoaffinity labeling (PAL) in combination with a chemical probe to covalently bind its target upon UV irradiation has demonstrated considerable promise in drug discovery for identifying new drug targets and binding sites. In particular, carbene-mediated photoaffinity labeling (cmPAL) has been widely used in drug target identification owing to its excellent photolabeling efficiency, minimal steric interference and longer excitation wavelength. Specifically, diazirines, which are among the precursors of carbenes and have higher carbene yields and greater chemical stability than diazo compounds, have proved to be valuable photolabile reagents in a diverse range of biological systems. This review highlights current advances of cmPAL in medicinal chemistry, with a focus on structures and applications for identifying small molecule–protein and macromolecule–protein interactions and ligand-gated ion channels, coupled with advances in the discovery of targets and inhibitors using carbene precursor-based biological probes developed in recent decades. Photoaffinity labeling (PAL) in combination with a chemical probe to covalently bind its target upon UV irradiation has demonstrated considerable promise in drug discovery for identifying new drug targets and binding sites.![]()
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Affiliation(s)
- Sha-Sha Ge
- State Key Laboratory Breeding Base of Green Pesticide and Agricultural Bioengineering
- Key Laboratory of Green Pesticide and Agricultural Bioengineering
- Ministry of Education
- Center for R&D of Fine Chemicals of Guizhou University
- Guiyang 550025
| | - Biao Chen
- State Key Laboratory Breeding Base of Green Pesticide and Agricultural Bioengineering
- Key Laboratory of Green Pesticide and Agricultural Bioengineering
- Ministry of Education
- Center for R&D of Fine Chemicals of Guizhou University
- Guiyang 550025
| | - Yuan-Yuan Wu
- State Key Laboratory Breeding Base of Green Pesticide and Agricultural Bioengineering
- Key Laboratory of Green Pesticide and Agricultural Bioengineering
- Ministry of Education
- Center for R&D of Fine Chemicals of Guizhou University
- Guiyang 550025
| | - Qing-Su Long
- State Key Laboratory Breeding Base of Green Pesticide and Agricultural Bioengineering
- Key Laboratory of Green Pesticide and Agricultural Bioengineering
- Ministry of Education
- Center for R&D of Fine Chemicals of Guizhou University
- Guiyang 550025
| | - Yong-Liang Zhao
- State Key Laboratory Breeding Base of Green Pesticide and Agricultural Bioengineering
- Key Laboratory of Green Pesticide and Agricultural Bioengineering
- Ministry of Education
- Center for R&D of Fine Chemicals of Guizhou University
- Guiyang 550025
| | - Pei-Yi Wang
- State Key Laboratory Breeding Base of Green Pesticide and Agricultural Bioengineering
- Key Laboratory of Green Pesticide and Agricultural Bioengineering
- Ministry of Education
- Center for R&D of Fine Chemicals of Guizhou University
- Guiyang 550025
| | - Song Yang
- State Key Laboratory Breeding Base of Green Pesticide and Agricultural Bioengineering
- Key Laboratory of Green Pesticide and Agricultural Bioengineering
- Ministry of Education
- Center for R&D of Fine Chemicals of Guizhou University
- Guiyang 550025
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8
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Sugihara Y, Tatsumi S, Kobori A. Development of Novel Photoresponsive Oligodeoxyribonucleotides with a 2′-O-Diazirine-conjugated Adenosine for DNA Interstrand Crosslinking. CHEM LETT 2017. [DOI: 10.1246/cl.160998] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
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9
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Theis T, Ortiz GX, Logan AWJ, Claytor KE, Feng Y, Huhn WP, Blum V, Malcolmson SJ, Chekmenev EY, Wang Q, Warren WS. Direct and cost-efficient hyperpolarization of long-lived nuclear spin states on universal (15)N2-diazirine molecular tags. SCIENCE ADVANCES 2016; 2:e1501438. [PMID: 27051867 PMCID: PMC4820385 DOI: 10.1126/sciadv.1501438] [Citation(s) in RCA: 181] [Impact Index Per Article: 22.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/12/2015] [Accepted: 02/05/2016] [Indexed: 05/17/2023]
Abstract
Conventional magnetic resonance (MR) faces serious sensitivity limitations which can be overcome by hyperpolarization methods, but the most common method (dynamic nuclear polarization) is complex and expensive, and applications are limited by short spin lifetimes (typically seconds) of biologically relevant molecules. We use a recently developed method, SABRE-SHEATH, to directly hyperpolarize (15)N2 magnetization and long-lived (15)N2 singlet spin order, with signal decay time constants of 5.8 and 23 minutes, respectively. We find >10,000-fold enhancements generating detectable nuclear MR signals that last for over an hour. (15)N2-diazirines represent a class of particularly promising and versatile molecular tags, and can be incorporated into a wide range of biomolecules without significantly altering molecular function.
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Affiliation(s)
- Thomas Theis
- Department of Chemistry, Duke University, Durham, NC 27708, USA
- Corresponding author. E-mail: (W.S.W.); (Q.W.); (T.T.)
| | | | | | | | - Yesu Feng
- Department of Chemistry, Duke University, Durham, NC 27708, USA
| | - William P. Huhn
- Department of Mechanical Engineering and Materials Science, Duke University, Durham, NC 27708, USA
| | - Volker Blum
- Department of Mechanical Engineering and Materials Science, Duke University, Durham, NC 27708, USA
| | | | - Eduard Y. Chekmenev
- Departments of Radiology and Biomedical Engineering, Vanderbilt University, Institute of Imaging Science, Nashville, TN 37232, USA
| | - Qiu Wang
- Department of Chemistry, Duke University, Durham, NC 27708, USA
- Corresponding author. E-mail: (W.S.W.); (Q.W.); (T.T.)
| | - Warren S. Warren
- Department of Chemistry, Duke University, Durham, NC 27708, USA
- Department of Physics, Duke University, Durham, NC 27708, USA
- Departments of Radiology and Biomedical Engineering, Duke University, Durham, NC 27708, USA
- Corresponding author. E-mail: (W.S.W.); (Q.W.); (T.T.)
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10
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Merkel M, Peewasan K, Arndt S, Ploschik D, Wagenknecht HA. Copper-Free Postsynthetic Labeling of Nucleic Acids by Means of Bioorthogonal Reactions. Chembiochem 2015; 16:1541-53. [DOI: 10.1002/cbic.201500199] [Citation(s) in RCA: 64] [Impact Index Per Article: 7.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2015] [Indexed: 12/25/2022]
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11
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Liu Y, Zheng W, Zhang W, Chen N, Liu Y, Chen L, Zhou X, Chen X, Zheng H, Li X. Photoaffinity labeling of transcription factors by DNA-templated crosslinking. Chem Sci 2015; 6:745-751. [PMID: 28706637 PMCID: PMC5494549 DOI: 10.1039/c4sc01953a] [Citation(s) in RCA: 29] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2014] [Accepted: 09/30/2014] [Indexed: 12/24/2022] Open
Abstract
Characterization of transcription factor-DNA interaction is of high importance in elucidating the molecular mechanisms of gene transcriptions. DNA-based affinity probes were developed to capture and identify transcription factors by covalent crosslinking; however, the requirement of a crosslinker on the affinity probe remains a disadvantage, as the crosslinker itself often interferes with the protein-DNA interactions. We report a dual-probe method able to capture DNA-binding transcription factors with unmodified protein-binding sites in scenarios where conventional probes have failed. We have also shown the method's converse application in selecting specific transcription factor-binding DNA sequences from a probe library and its extension to studying proteins recognizing epigenetic marks. This study may provide a new tool for exploring DNA-binding proteins in biology.
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Affiliation(s)
- Ying Liu
- Key Laboratory of Bioorganic Chemistry and Molecular Engineering of the Ministry of Education , Beijing National Laboratory of Molecular Sciences , College of Chemistry and Molecular Engineering , Peking University , Beijing , China 100871 .
| | - Wenlu Zheng
- Key Laboratory of Chemical Genomics , School of Chemical Biology and Biotechnology , Peking University Shenzhen Graduate School , Shenzhen , China 518055
| | - Wan Zhang
- Key Laboratory of Chemical Genomics , School of Chemical Biology and Biotechnology , Peking University Shenzhen Graduate School , Shenzhen , China 518055
| | - Nan Chen
- Key Laboratory of Bioorganic Chemistry and Molecular Engineering of the Ministry of Education , Beijing National Laboratory of Molecular Sciences , College of Chemistry and Molecular Engineering , Peking University , Beijing , China 100871 .
| | - Yang Liu
- Key Laboratory of Bioorganic Chemistry and Molecular Engineering of the Ministry of Education , Beijing National Laboratory of Molecular Sciences , College of Chemistry and Molecular Engineering , Peking University , Beijing , China 100871 .
| | - Li Chen
- Key Laboratory of Bioorganic Chemistry and Molecular Engineering of the Ministry of Education , Beijing National Laboratory of Molecular Sciences , College of Chemistry and Molecular Engineering , Peking University , Beijing , China 100871 .
| | - Xiaozhou Zhou
- Key Laboratory of Bioorganic Chemistry and Molecular Engineering of the Ministry of Education , Beijing National Laboratory of Molecular Sciences , College of Chemistry and Molecular Engineering , Peking University , Beijing , China 100871 .
| | - Xingshuo Chen
- Key Laboratory of Bioorganic Chemistry and Molecular Engineering of the Ministry of Education , Beijing National Laboratory of Molecular Sciences , College of Chemistry and Molecular Engineering , Peking University , Beijing , China 100871 .
| | - Haifeng Zheng
- Key Laboratory of Bioorganic Chemistry and Molecular Engineering of the Ministry of Education , Beijing National Laboratory of Molecular Sciences , College of Chemistry and Molecular Engineering , Peking University , Beijing , China 100871 .
| | - Xiaoyu Li
- Key Laboratory of Bioorganic Chemistry and Molecular Engineering of the Ministry of Education , Beijing National Laboratory of Molecular Sciences , College of Chemistry and Molecular Engineering , Peking University , Beijing , China 100871 .
- Key Laboratory of Chemical Genomics , School of Chemical Biology and Biotechnology , Peking University Shenzhen Graduate School , Shenzhen , China 518055
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12
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Nakamoto K, Ueno Y. Diazirine-Containing RNA Photo-Cross-Linking Probes for Capturing microRNA Targets. J Org Chem 2014; 79:2463-72. [DOI: 10.1021/jo402738t] [Citation(s) in RCA: 32] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Affiliation(s)
- Kosuke Nakamoto
- Course of Applied Life Science, Faculty of
Applied Biological Sciences and ‡United Graduate
School of Agricultural Science, Gifu University, 1-1 Yanagido, Gifu 501-1193, Japan
| | - Yoshihito Ueno
- Course of Applied Life Science, Faculty of
Applied Biological Sciences and ‡United Graduate
School of Agricultural Science, Gifu University, 1-1 Yanagido, Gifu 501-1193, Japan
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13
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Smith CC, Hollenstein M, Leumann CJ. The synthesis and application of a diazirine-modified uridine analogue for investigating RNA–protein interactions. RSC Adv 2014. [DOI: 10.1039/c4ra08682a] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022] Open
Abstract
A uridine analogue equipped with a photoactive diazirine unit was generated and incorporated into RNA either syntheticallyviaphosphoramidite chemistry or by enzymatic polymerization. The new analogue was developed to identify and investigate RNA–protein interactions.
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Affiliation(s)
- Christine C. Smith
- Department of Chemistry and Biochemistry
- University of Bern
- 3012 Bern, Switzerland
| | - Marcel Hollenstein
- Department of Chemistry and Biochemistry
- University of Bern
- 3012 Bern, Switzerland
| | - Christian J. Leumann
- Department of Chemistry and Biochemistry
- University of Bern
- 3012 Bern, Switzerland
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14
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Affiliation(s)
- Ofer I. Wilner
- Institute of Chemistry, Center for Nanoscience and Nanotechnology, The Hebrew University of Jerusalem, Jerusalem 91904, Israel
| | - Itamar Willner
- Institute of Chemistry, Center for Nanoscience and Nanotechnology, The Hebrew University of Jerusalem, Jerusalem 91904, Israel
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15
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Song CX, He C. Bioorthogonal labeling of 5-hydroxymethylcytosine in genomic DNA and diazirine-based DNA photo-cross-linking probes. Acc Chem Res 2011; 44:709-17. [PMID: 21539303 DOI: 10.1021/ar2000502] [Citation(s) in RCA: 40] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
Abstract
DNA is not merely a combination of four genetic codes, namely A, T, C, and G. It also contains minor modifications that play crucial roles throughout biology. For example, the fifth DNA base, 5-methylcytosine (5-mC), which accounts for ∼1% of all the nucleotides in mammalian genomic DNA, is a vital epigenetic mark. It impacts a broad range of biological functions, from development to cancer. Recently, an oxidized form of 5-methylcytosine, 5-hydroxymethylcytosine (5-hmC), was found to constitute the sixth base in the mammalian genome; it was believed to be another crucial epigenetic mark. Unfortunately, further study of this newly discovered DNA base modification has been hampered by inadequate detection and sequencing methods, because current techniques fail to differentiate 5-hmC from 5-mC. The immediate challenge, therefore, is to develop robust methods for ascertaining the positions of 5-hmC within the mammalian genome. In this Account, we describe our development of the first bioorthogonal, selective labeling of 5-hmC to specifically address this challenge. We utilize β-glucosyltransferase (βGT) to transfer an azide-modified glucose onto 5-hmC in genomic DNA. The azide moiety enables further bioorthogonal click chemistry to install a biotin group, which allows for detection, affinity enrichment, and, most importantly, deep sequencing of the 5-hmC-containing DNA. With this highly effective and selective method, we revealed the first genome-wide distribution of 5-hmC in the mouse genome and began to shed further light on the biology of 5-hmC. The strategy lays the foundation for developing high-throughput, single-base-resolution sequencing methods for 5-hmC in mammalian genomes in the future. DNA and RNA are not static inside cells. They interact with protein and other DNA and RNA in fundamental biological processes such as replication, transcription, translation, and DNA and RNA modification and repair. The ability to investigate these interactions will also be enhanced by developing and utilizing bioorthogonal probes. We have chosen the photoreactive diazirine photophore as a bioorthogonal moiety to develop nucleic acid probes. The small size and unique photo-cross-linking activity of diazirine enabled us to develop a series of novel cross-linking probes to streamline the study of protein-nucleic acid and nucleic acid-nucleic acid interactions. In the second half of this Account, we highlight a few examples of these probes.
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Affiliation(s)
- Chun-Xiao Song
- Department of Chemistry and Institute for Biophysical Dynamics, The University of Chicago, 929 East 57th Street, Chicago, Illinois 60637, United States
| | - Chuan He
- Department of Chemistry and Institute for Biophysical Dynamics, The University of Chicago, 929 East 57th Street, Chicago, Illinois 60637, United States
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Dubinsky L, Krom BP, Meijler MM. Diazirine based photoaffinity labeling. Bioorg Med Chem 2011; 20:554-70. [PMID: 21778062 DOI: 10.1016/j.bmc.2011.06.066] [Citation(s) in RCA: 283] [Impact Index Per Article: 21.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2011] [Revised: 06/19/2011] [Accepted: 06/24/2011] [Indexed: 10/17/2022]
Abstract
Diazirines are among the smallest photoreactive groups that form a reactive carbene upon light irradiation. This feature has been widely utilized in photoaffinity labeling to study ligand-receptor, ligand-enzyme and protein-protein interactions, and in the isolation and identification of unknown proteins. This review summarizes recent advances in the use of diazirines in photoaffinity labeling.
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Affiliation(s)
- Luba Dubinsky
- Department of Chemistry and National Institute for Biotechnology in the Negev, Ben-Gurion University of the Negev, Be'er Sheva, Israel
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17
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Winnacker M, Welzmiller V, Strasser R, Carell T. Development of a DNA Photoaffinity Probe for the Analysis of 8-OxodG-Binding Proteins in a Human Proteome. Chembiochem 2010; 11:1345-9. [DOI: 10.1002/cbic.201000244] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
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18
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Winnacker M, Breeger S, Strasser R, Carell T. Novel diazirine-containing DNA photoaffinity probes for the investigation of DNA-protein-interactions. Chembiochem 2009; 10:109-18. [PMID: 19012292 DOI: 10.1002/cbic.200800397] [Citation(s) in RCA: 45] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
An investigation of the precise interactions between damaged DNA and DNA repair enzymes is required in order to understand the lesion recognition step, which is one of the most fundamental processes in DNA repair. Most recently, photoaffinity labeling approaches have enabled the analysis of even transient protein-DNA interactions. Here we report the synthesis and evaluation of oligonucleotides that contain two photoaffinity "catcher moieties" next to incorporated DNA lesions. With these DNA constructs it is possible to analyze the interactions between DNA lesions and the appropriate repair enzymes. The probes labeled the repair protein efficiently enough to enable subsequent protein analysis by mass spectrometry.
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Affiliation(s)
- Malte Winnacker
- Ludwig-Maximilians University Munich, Center for Integrated Protein Science (CiPSM), Department for Chemistry and Biochemistry, Butenandtstrasse 5-13, Munich, Germany
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Qiu Z, Lu L, Jian X, He C. A diazirine-based nucleoside analogue for efficient DNA interstrand photocross-linking. J Am Chem Soc 2008; 130:14398-9. [PMID: 18842048 DOI: 10.1021/ja805445j] [Citation(s) in RCA: 58] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
A diazirine-based nucleoside analogue (DBN) efficiently forms DNA interstand cross-linking under near-UV irradiation. This new base analogue may find broad applications in biotechnology and phototherapy.
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Affiliation(s)
- Zhihai Qiu
- Department of Chemistry, The University of Chicago, 929 East 57th Street, Chicago, Illinois 60637, USA
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