- 5-Oxyacetic Acid Modification Destabilizes Double Helical Stem Structures and Favors Anionic Watson–Crick like cmo5U-G Base Pairs
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Watson–Crick like G-U mismatches with tautomeric Genol or Uenol bases can evade fidelity checkpoints and thereby contribute to translational errors. The 5-oxyacetic acid uridine (cmo5U) modification is a base modification at the wobble position on tRNAs and is presumed to expand the decoding capability of tRNA at this position by forming Watson–Crick like cmo5Uenol-G mismatches. A detailed investigation on the influence of the cmo5U modification on structural and dynamic features of RNA was carried out by using solution NMR spectroscopy and UV melting curve analysis. The introduction of a stable isotope labeled variant of the cmo5U modifier allowed the application of relaxation dispersion NMR to probe the potentially formed Watson–Crick like cmo5Uenol-G base pair. Surprisingly, we find that at neutral pH, the modification promotes transient formation of anionic Watson–Crick like cmo5U?-G, and not enolic base pairs. Our results suggest that recoding is mediated by an anionic Watson–Crick like species, as well as bring an interesting aspect of naturally occurring RNA modifications into focus—the fine tuning of nucleobase properties leading to modulation of the RNA structural landscape by adoption of alternative base pairing patterns.
- Strebitzer, Elisabeth,Rangadurai, Atul,Plangger, Raphael,Kremser, Johannes,Juen, Michael Andreas,Tollinger, Martin,Al-Hashimi, Hashim M.,Kreutz, Christoph
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supporting information
p. 18903 - 18906
(2018/11/25)
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- Mechanism and stem-cell activity of 5-carboxycytosine decarboxylation determined by isotope tracing
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Eraserhead: Stem cells seem to erase epigenetic information by decarboxylation of the newly discovered epigenetic base 5-carboxycytosine (caC; see picture). This reaction is likely to involve a nucleophilic attack of the C5-C6 double bond. Copyright
- Schiesser, Stefan,Hackner, Benjamin,Pfaffeneder, Toni,Müller, Markus,Hagemeier, Christian,Truss, Matthias,Carell, Thomas
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supporting information; experimental part
p. 6516 - 6520
(2012/08/14)
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- The economical synthesis of [2'-(13)C, 1,3-(15)N2]uridine; preliminary conformational studies by solid state NMR.
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The synthesis of [2'-(13)C, 1,3-(15)N2]uridine 11 was achieved as follows. An epimeric mixture of D-[1-(13)C]ribose 3 and D-[1-(13)C]arabinose 4 was obtained in excellent yield by condensation of K13CN with D-erythrose 2 using a modification of the Kiliani-Fischer synthesis. Efficient separation of the two aldose epimers was pivotally achieved by a novel ion-exchange (Sm3+) chromatography method. D-[2-(13)C]Ribose 5 was obtained from D-[1-(13)C]arabinose 4 using a Ni(II) diamine complex (nickel chloride plus TEMED). Combination of these procedures in a general cycling manner can lead to the very efficient preparation of specifically labelled 13C-monosaccharides of particular chirality. 15N-labelling was introduced in the preparation of [2'-(13)C, 1,3-(15)N2]uridine 11 via [15N2]urea. Cross polarisation magic angle spinning (CP-MAS) solid-state NMR experiments using rotational echo double resonance (REDOR) were carried out on crystals of the labelled uridine to show that the inter-atomic distance between C-2' and N-1 is closely similar to that calculated from X-ray crystallographic data. The REDOR method will be used now to determine the conformation of bound substrates in the bacterial nucleoside transporters NupC and NupG.
- Patching, Simon G,Middleton, David A,Henderson, Peter J F,Herbert, Richard B
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p. 2057 - 2062
(2007/10/03)
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- Synthesis and characterization of isotopically enriched pyrimidine deoxynucleoside oxidation damage products
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Oxidative damage to DNA is an established source of genomic instability. In this paper, we describe the synthesis and characterization of several pyrimidine deoxynucleoside oxidation damage products, enriched with stable isotopes. These products include the 2'-deoxynucleoside derivatives of 5- (hydroxymethyl)uracil, 5-formyluracil, 5-hydroxyuracil, 5-(hydroxymethyl)- cytosine, 5-formylcytosine, and 5-hydroxycytosine. The common precursor is 2'-deoxy-2''-deutero[1,3-15N]uridine. Additional stable isotopes are added during functional group conversions. Characterization of these derivatives includes mass spectrometry and 1H and 15N NMR spectroscopy. Proton and nitrogen NMR studies reported here allow an examination of the influence of the modification on sugar conformation and tautomeric equilibrium, properties likely to be important in understanding the biological consequences of these DNA damage products.
- LaFrancois, Christopher J.,Fujimoto, June,Sowers, Lawrence C.
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