Uracil

Technical Specifications

Product Description & Scientific Applications

Uracil (pyrimidine-2,4(1H,3H)-dione) is a canonical RNA nucleobase, pairing with adenine through two hydrogen bonds (N3-H···N1 and C4=O···H-N6). It differs from thymine only in lacking the C5-methyl group; the free C5-H position is a handle for C5 halogenation and electrophilic derivatisation. UV absorption peaks at 258.3 nm (ε ≈ 8,200 M⁻¹cm⁻¹), with very low fluorescence quantum yield.

Nucleoside synthesis. Parent nucleobase for uridine, 2′-deoxyuridine, and modified uridine analogues by Vorbrüggen / silyl-Hilbert-Johnson glycosylation: uracil is silylated (HMDS, BSA, or TMSCl/HMDS), then coupled with a peracylated sugar donor under TMSOTf or SnCl4. N3-benzoyluracil masks N3 for N1 regiocontrol. Products are elaborated to uridine 5′-phosphates and oligoribonucleotide phosphoramidite building blocks. Uracil also gives uracil-PNA monomers, which need no nucleobase amine protection.

Yeast URA3 selection. Standard supplement for synthetic defined media culturing Saccharomyces cerevisiae ura3 strains, which cannot generate UMP and depend on exogenous uracil. URA3 (orotidine-5′-phosphate decarboxylase) is a widely used selectable marker on SC−Ura media and enables 5-fluoroorotic acid counter-selection.

Watson–Crick model. Benchmark nucleobase for the uracil·adenine pair in RNA duplex thermodynamics, base-pair kinetics, and mismatch discrimination, and a hydrogen-bonding handle in synthetic receptors that recognise adenine, AMP, and ATP.

Pyrimidine catabolism. Uracil and its metabolite dihydrouracil are the analyte pair for dihydropyrimidine dehydrogenase (DPD) activity; the plasma uracil:dihydrouracil ratio is a surrogate readout of DPD status by HPLC and LC-MS/MS.

Analytical reference standard. Standard void-volume / dead-time marker for reversed-phase C18 method development, combining weak retention with a strong UV chromophore at 260 nm; included in NIST SRM 870. Also a calibration standard for HPLC and LC-MS quantification of free pyrimidine bases and genomic-uracil incorporation.

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