76
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Schiffers S, Wildenhof TM, Iwan K, Stadlmeier M, Müller M, Carell T. Label‐Free Quantification of 5‐Azacytidines Directly in the Genome. Helv Chim Acta 2019. [DOI: 10.1002/hlca.201800229] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
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77
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Dialer CR, Stazzoni S, Drexler DJ, Müller FM, Veth S, Pichler A, Okamura H, Witte G, Hopfner KP, Carell T. A Click-Chemistry Linked 2'3'-cGAMP Analogue. Chemistry 2019; 25:2089-2095. [PMID: 30536650 DOI: 10.1002/chem.201805409] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2018] [Indexed: 11/09/2022]
Abstract
2'3'-cGAMP is an uncanonical cyclic dinucleotide where one A and one G base are connected via a 3'-5' and a unique 2'-5' linkage. The molecule is produced by the cyclase cGAS in response to cytosolic DNA binding. cGAMP activates STING and hence one of the most powerful pathways of innate immunity. cGAMP analogues with uncharged linkages that feature better cellular penetrability are currently highly desired. Here, the synthesis of a cGAMP analogue with one amide and one triazole linkage is reported. The molecule is best prepared via a first CuI -catalyzed click reaction, which establishes the triazole, while the cyclization is achieved by macrolactamization.
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78
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Becker S, Schneider C, Crisp A, Carell T. Publisher Correction: Non-canonical nucleosides and chemistry of the emergence of life. Nat Commun 2019; 10:325. [PMID: 30644395 PMCID: PMC6333768 DOI: 10.1038/s41467-019-08340-9] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
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79
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Okamura H, Becker S, Tiede N, Wiedemann S, Feldmann J, Carell T. A one-pot, water compatible synthesis of pyrimidine nucleobases under plausible prebiotic conditions. Chem Commun (Camb) 2019; 55:1939-1942. [DOI: 10.1039/c8cc09435g] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/30/2023]
Abstract
A prebiotically plausible one-pot formation pathway of 4-substituted pyrimidine nucleobases in water, starting from cyanoacetylene.
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80
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Abstract
An artificially evolved ribozyme can catalyse the synthesis of RNA by using trinucleotide triphosphates as building blocks.
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81
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Schneider C, Becker S, Okamura H, Crisp A, Amatov T, Stadlmeier M, Carell T. Noncanonical RNA Nucleosides as Molecular Fossils of an Early Earth-Generation by Prebiotic Methylations and Carbamoylations. Angew Chem Int Ed Engl 2018. [PMID: 29533524 DOI: 10.1002/anie.201801919] [Citation(s) in RCA: 27] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Abstract
The RNA-world hypothesis assumes that life on Earth started with small RNA molecules that catalyzed their own formation. Vital to this hypothesis is the need for prebiotic routes towards RNA. Contemporary RNA, however, is not only constructed from the four canonical nucleobases (A, C, G, and U), it also contains many chemically modified (noncanonical) bases. A still open question is whether these noncanonical bases were formed in parallel to the canonical bases (chemical origin) or later, when life demanded higher functional diversity (biological origin). Here we show that isocyanates in combination with sodium nitrite establish methylating and carbamoylating reactivity compatible with early Earth conditions. These reactions lead to the formation of methylated and amino acid modified nucleosides that are still extant. Our data provide a plausible scenario for the chemical origin of certain noncanonical bases, which suggests that they are fossils of an early Earth.
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82
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Schneider C, Becker S, Okamura H, Crisp A, Amatov T, Stadlmeier M, Carell T. Nicht-kanonische RNA-Nukleoside als molekulare Fossilien einer frühen Erde - Generierung durch präbiotische Methylierungen und Carbamoylierungen. Angew Chem Int Ed Engl 2018. [DOI: 10.1002/ange.201801919] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
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83
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Carell T, Kurz MQ, Müller M, Rossa M, Spada F. Non-canonical Bases in the Genome: The Regulatory Information Layer in DNA. Angew Chem Int Ed Engl 2018; 57:4296-4312. [DOI: 10.1002/anie.201708228] [Citation(s) in RCA: 69] [Impact Index Per Article: 11.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2017] [Indexed: 01/06/2023]
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84
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Stadlmeier M, Bogena J, Wallner M, Wühr M, Carell T. Ein auf Sulfoxid basierendes, isobares Derivatisierungsreagens für die präzise quantitative Massenspektrometrie. Angew Chem Int Ed Engl 2018. [DOI: 10.1002/ange.201708867] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
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85
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Stadlmeier M, Bogena J, Wallner M, Wühr M, Carell T. A Sulfoxide-Based Isobaric Labelling Reagent for Accurate Quantitative Mass Spectrometry. Angew Chem Int Ed Engl 2018; 57:2958-2962. [PMID: 29316131 DOI: 10.1002/anie.201708867] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2017] [Indexed: 01/21/2023]
Abstract
Modern proteomics requires reagents for exact quantification of peptides in complex mixtures. Peptide labelling is most typically achieved with isobaric tags that consist of a balancer and a reporter part that separate in the gas phase. An ingenious distribution of stable isotopes provides multiple reagents with identical molecular weight but a different mass of the reporter groups, allowing relative quantification of multiple samples in one measurement. Here we report a new isobaric labelling reagent, where the balancer and the reporter are linked by a sulfoxide group, which, based on the sulfoxide pyrolysis, leads to easy and asymmetric cleavage at low fragmentation energy. The fragmentation of our new design is significantly improved, yielding more intense complementary ion signals, allowing complementary ion cluster analysis as well.
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86
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Beckwitt EC, Simon N, Carnaval I, Kisker C, Carell T, Van Houten B. Peakforce Tapping AFM Reveals that Human XPA Binds to DNA Damage as a Monomer Producing a 60° Bend. Biophys J 2018. [DOI: 10.1016/j.bpj.2017.11.549] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022] Open
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87
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Schröder AS, Parsa E, Iwan K, Traube FR, Wallner M, Serdjukow S, Carell T. 2'-(R)-Fluorinated mC, hmC, fC and caC triphosphates are substrates for DNA polymerases and TET-enzymes. Chem Commun (Camb) 2018; 52:14361-14364. [PMID: 27905578 DOI: 10.1039/c6cc07517g] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
A deeper investigation of the chemistry that occurs on the newly discovered epigenetic DNA bases 5-hydroxymethyl-(hmdC), 5-formyl-(fdC), and 5-carboxy-deoxycytidine (cadC) requires chemical tool compounds, which are able to dissect the different potential reaction pathways in cells. Here we report that the 2'-(R)-fluorinated derivatives F-hmdC, F-fdC, and F-cadC, which are resistant to removal by base excision repair, are good substrates for DNA polymerases and TET enzymes. This result shows that the fluorinated compounds are ideal tool substances to investigate potential C-C-bond cleaving reactions in the context of active demethylation.
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88
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Becker S, Schneider C, Okamura H, Crisp A, Amatov T, Dejmek M, Carell T. Wet-dry cycles enable the parallel origin of canonical and non-canonical nucleosides by continuous synthesis. Nat Commun 2018; 9:163. [PMID: 29323115 PMCID: PMC5765019 DOI: 10.1038/s41467-017-02639-1] [Citation(s) in RCA: 76] [Impact Index Per Article: 12.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2017] [Accepted: 12/14/2017] [Indexed: 12/28/2022] Open
Abstract
The molecules of life were created by a continuous physicochemical process on an early Earth. In this hadean environment, chemical transformations were driven by fluctuations of the naturally given physical parameters established for example by wet-dry cycles. These conditions might have allowed for the formation of (self)-replicating RNA as the fundamental biopolymer during chemical evolution. The question of how a complex multistep chemical synthesis of RNA building blocks was possible in such an environment remains unanswered. Here we report that geothermal fields could provide the right setup for establishing wet-dry cycles that allow for the synthesis of RNA nucleosides by continuous synthesis. Our model provides both the canonical and many ubiquitous non-canonical purine nucleosides in parallel by simple changes of physical parameters such as temperature, pH and concentration. The data show that modified nucleosides were potentially formed as competitor molecules. They could in this sense be considered as molecular fossils.
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89
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Ensfelder TT, Kurz MQ, Iwan K, Geiger S, Matheisl S, Müller M, Beckmann R, Carell T. ALKBH5-induced demethylation of mono- and dimethylated adenosine. Chem Commun (Camb) 2018; 54:8591-8593. [DOI: 10.1039/c8cc03980a] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
ALKBH5 is able to accept m62A as a substrate and demethylates it to m6A and A.
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90
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Kitsera N, Allgayer J, Parsa E, Geier N, Rossa M, Carell T, Khobta A. Functional impacts of 5-hydroxymethylcytosine, 5-formylcytosine, and 5-carboxycytosine at a single hemi-modified CpG dinucleotide in a gene promoter. Nucleic Acids Res 2017; 45:11033-11042. [PMID: 28977475 PMCID: PMC5737506 DOI: 10.1093/nar/gkx718] [Citation(s) in RCA: 30] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2017] [Accepted: 08/08/2017] [Indexed: 12/19/2022] Open
Abstract
Enzymatic oxidation of 5-methylcytosine (5-mC) in the CpG dinucleotides to 5-hydroxymethylcytosine (5-hmC), 5-formylcytosine (5-fC) and 5-carboxycytosine (5-caC) has central role in the process of active DNA demethylation and epigenetic reprogramming in mammals. However, it is not known whether the 5-mC oxidation products have autonomous epigenetic or regulatory functions in the genome. We used an artificial upstream promoter constituted of one cAMP response element (CRE) to measure the impact of 5-mC in a hemi-methylated CpG on the promoter activity and further explored the consequences of 5-hmC, 5-fC, and 5-caC in the same system. All modifications induced mild impairment of the CREB transcription factor binding to the consensus 5'-TGACGTCA-3' CRE sequence. The decrease of the gene expression by 5-mC or 5-hmC was proportional to the impairment of CREB binding and had a steady character over at least 48 h. In contrast, promoters containing single 5-fC or 5-caC underwent further progressive loss of activity, up to an almost complete repression. This decline was dependent on the thymine-DNA glycosylase (TDG). The results thus indicate that 5-fC and 5-caC can provide a signal for perpetuation and enhancement of the repressed transcriptional state by a mechanism that requires base excision repair.
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91
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Iwan K, Rahimoff R, Kirchner A, Spada F, Schröder AS, Kosmatchev O, Ferizaj S, Steinbacher J, Parsa E, Müller M, Carell T. 5-Formylcytosine to cytosine conversion by C–C bond cleavage in vivo. Nat Chem Biol 2017; 14:72-78. [DOI: 10.1038/nchembio.2531] [Citation(s) in RCA: 58] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2017] [Accepted: 10/31/2017] [Indexed: 12/17/2022]
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92
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Michaelides IN, Tago N, Viverge B, Carell T. Synthesis of RNA Containing 5-Hydroxymethyl-, 5-Formyl-, and 5-Carboxycytidine. Chemistry 2017; 23:15894-15898. [PMID: 28906048 DOI: 10.1002/chem.201704216] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2017] [Indexed: 12/17/2022]
Abstract
5-Hydroxymethyl-, 5-formyl-, and 5-carboxy-2'-deoxycytidine are new epigenetic bases (hmdC, fdC, cadC) that were recently discovered in the DNA of higher eukaryotes. The same bases (5-hydroxymethyl-, 5-formyl-, and 5-carboxycytidine; hmC, fC, and caC) have now also been detected in mammalian RNA with a high abundance in mRNA. While DNA phosphoramidites (PAs) that allow the synthesis of xdC-containing oligonucleotides for deeper biological studies are available, the corresponding silyl-protected RNA PAs for fC and caC have not yet been disclosed. Here, we report novel RNA PAs for hmC, fC, and caC that can be used in routine RNA synthesis. The new building blocks are compatible with the canonical PAs and also with themselves, which enables even the synthesis of RNA strands containing all three of these bases. The study will pave the way for detailed physical, biochemical, and biological studies to unravel the function of these non-canonical modifications in RNA.
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93
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Raddaoui N, Stazzoni S, Möckl L, Viverge B, Geiger F, Engelke H, Bräuchle C, Carell T. Dendrimer-Based Signal Amplification of Click-Labelled DNA in Situ. Chembiochem 2017. [DOI: 10.1002/cbic.201700209] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/14/2023]
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94
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Rahimoff R, Kosmatchev O, Kirchner A, Pfaffeneder T, Spada F, Brantl V, Müller M, Carell T. 5-Formyl- and 5-Carboxydeoxycytidines Do Not Cause Accumulation of Harmful Repair Intermediates in Stem Cells. J Am Chem Soc 2017; 139:10359-10364. [PMID: 28715893 DOI: 10.1021/jacs.7b04131] [Citation(s) in RCA: 46] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
5-Formyl-dC (fdC) and 5-carboxy-dC (cadC) are newly discovered bases in the mammalian genome that are supposed to be substrates for base excision repair (BER) in the framework of active demethylation. The bases are recognized by the monofunctional thymine DNA glycosylase (Tdg), which cleaves the glycosidic bond of the bases to give potentially harmful abasic sites (AP-sites). Because of the turnover of fdC and cadC during cell state transitions, it is an open question to what extent such harmful AP-sites may accumulate during these processes. Here, we report the development of a new reagent that in combination with mass spectrometry (MS) allows us to quantify the levels of AP-sites. This combination also allowed the quantification of β-elimination (βE) products, which are repair intermediates of bifunctional DNA glycosylases. In combination with feeding of isotopically labeled nucleosides, we were able to trace the intermediates back to their original nucleobases. We show that, while the steady-state levels of fdC and cadC are substantially increased in Tdg-deficient cells, those of both AP- and βE-sites are unaltered. The levels of the detected BER intermediates are 1 and 2 orders of magnitude lower than those of cadC and fdC, respectively. Thus, neither the presence of fdC nor that of cadC in stem cells leads to the accumulation of harmful AP- and βE-site intermediates.
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95
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Ebert C, Simon N, Schneider S, Carell T. Structural Insights into the Recognition of N 2 -Aryl- and C8-Aryl DNA Lesions by the Repair Protein XPA/Rad14. Chembiochem 2017. [PMID: 28444956 DOI: 10.3760/cma.j.issn.2095-428x.2017.18.005] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/25/2023]
Abstract
Aromatic amines are strongly carcinogenic. They are activated in the liver to give reactive nitrenium ions that react with nucleobases within the DNA duplex. The reaction occurs predominantly at the C8 position of the dG base, thereby giving C8-acetyl-aryl- or C8-aryl-dG adducts in an electrophilic aromatic substitution reaction. Alternatively, reaction with the exocyclic 2-NH2 group is observed. Although the C8 adducts retain base-pairing properties, base pairing is strongly compromised in the case of the N2 adducts. Here we show crystal structures of two DNA lesions, N2 -acetylnaphthyl-dG and C8-fluorenyl-dG, within a DNA duplex recognized by the repair protein Rad14. The structures confirm that two molecules of the repair protein recognize the lesion and induce a 72 or 78° kink at the site of the damage. Importantly, the same overall kinked structure is induced by binding of the repair proteins, although the structurally different lesions result in distinct stacking interactions of the lesions within the duplex. The results suggest that the repair protein XPA/Rad14 is a sensor that recognizes flexibility. The protein converts the information that structurally different lesions are present in the duplex into a unifying sharply kinked recognition motif.
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96
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Ebert C, Simon N, Schneider S, Carell T. Structural Insights into the Recognition of N
2
-Aryl- and C8-Aryl DNA Lesions by the Repair Protein XPA/Rad14. Chembiochem 2017; 18:1379-1382. [DOI: 10.1002/cbic.201700169] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2017] [Indexed: 01/28/2023]
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97
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Abstract
Chemical modification of nucleobases plays an important role for the control of gene expression on different levels. That includes the modulation of translation by modified tRNA-bases or silencing and reactivation of genes by methylation and demethylation of cytosine in promoter regions. Especially dynamic methylation of adenine and cytosine is essential for cells to adapt to their environment or for the development of complex organisms from a single cell. Errors in the cytosine methylation pattern are associated with most types of cancer and bacteria use methylated nucleobases to resist antibiotics. This Point of View wants to shed light on the known and potential chemistry of DNA and RNA methylation and demethylation. Understanding the chemistry of these processes on a molecular level is the first step towards a deeper knowledge about their regulation and function and will help us to find ways how nucleobase methylation can be manipulated to treat diseases.
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98
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Schiffers S, Ebert C, Rahimoff R, Kosmatchev O, Steinbacher J, Bohne AV, Spada F, Michalakis S, Nickelsen J, Müller M, Carell T. Quantitative LC-MS Provides No Evidence for m6dA or m4dC in the Genome of Mouse Embryonic Stem Cells and Tissues. Angew Chem Int Ed Engl 2017; 56:11268-11271. [DOI: 10.1002/anie.201700424] [Citation(s) in RCA: 81] [Impact Index Per Article: 11.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2017] [Revised: 02/15/2017] [Indexed: 12/31/2022]
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99
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Schiffers S, Ebert C, Rahimoff R, Kosmatchev O, Steinbacher J, Bohne AV, Spada F, Michalakis S, Nickelsen J, Müller M, Carell T. Quantitative LC-MS liefert keinen Hinweis auf m6dA oder m4dC im Genom von Mausstammzellen und -geweben. Angew Chem Int Ed Engl 2017. [DOI: 10.1002/ange.201700424] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
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100
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Heidinger L, Kneuttinger AC, Kashiwazaki G, Weber S, Carell T, Schleicher E. Direct observation of a deoxyadenosyl radical in an active enzyme environment. FEBS Lett 2016; 590:4489-4494. [PMID: 27878994 DOI: 10.1002/1873-3468.12498] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2016] [Revised: 11/16/2016] [Accepted: 11/17/2016] [Indexed: 11/11/2022]
Abstract
5'-deoxyadenosyl radicals have been proposed as the first common intermediate in the molecular reaction mechanism of the family of radical S-adenosyl-l-methionine (SAM) enzymes. However, this radical species has not yet been directly observed in a catalytically active enzyme environment. In a reduced and SAM-containing C140A mutant of the spore photoproduct lyase from Geobacillus thermodenitrificans, a mutant with altered catalytic activity, we were able to identify an organic radical with pronounced hyperfine structure using electron paramagnetic resonance spectroscopy. Guided by quantum-chemical computations at the density functional theory level of theory, this radical could be tentatively assigned to a deoxyadenosyl radical, which provides first experimental evidence for this intermediate in the reaction mechanism of radical SAM enzymes.
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