5-Fluorouracil (5-FU)

Technical Specifications

Product Description & Scientific Applications

5-Fluorouracil (5-fluoro-2,4(1H,3H)-pyrimidinedione; 5-FU) is the C5-fluorinated analogue of uracil, used as a research probe in pyrimidine biochemistry and ¹⁹F NMR nucleic-acid work. Fluorine replaces the C5 hydrogen, preserving the uracil hydrogen-bonding face while adding a strong C–F bond, an electron-withdrawing substituent, and a spin-active ¹⁹F nucleus. Its van der Waals radius (~1.46 Å) is close to hydrogen (~1.20 Å) and far smaller than methyl, so 5-FU mimics uracil at enzyme active sites with limited steric perturbation.

Thymidylate synthase. The metabolite FdUMP (5-fluoro-2′-deoxyuridine 5′-monophosphate) mimics dUMP at thymidylate synthase (TS, EC 2.1.1.45). With 5,10-methylenetetrahydrofolate and the active-site cysteine it forms a stable covalent ternary complex that traps TS in a catalytic-intermediate-like state — the basis for TS crystallography, active-site mapping, kinetics, and ¹⁹F NMR binding studies.

DPD catabolism. Substrate for dihydropyrimidine dehydrogenase (DPD, EC 1.3.1.2), reduced NADPH-dependently to 5-fluoro-5,6-dihydrouracil and onward to α-fluoro-β-alanine. Used for DPD kinetics and DPYD variant characterisation; the fluorine label distinguishes fluorinated catabolites from endogenous uracil metabolites by LC-MS/MS and NMR.

Bacterial pyrimidine signalling. As a uracil analogue it perturbs uracil-linked regulatory pathways and alters biofilm formation. In Escherichia coli K-12 it reduces biofilm through the global regulator AriR; related work links it to biofilm and quorum-sensing phenotypes in Pseudomonas aeruginosa.

¹⁹F NMR probe. Incorporated as 5-fluorouracil, 5-fluorouridine, or 5-fluoro-2′-deoxyuridine into RNA or DNA, the C5 fluorine reports local base pairing, stacking, and conformational exchange through ¹⁹F shift and linewidth, resolvable in proton-crowded spectra of tRNA and RNA models.

Analytical reference standard. Reference compound for fluorinated-pyrimidine quantification by HPLC-UV, LC-MS/MS, and capillary electrophoresis — calibration, retention-time assignment, and quality control in environmental-water, hospital-effluent, and biological matrices, anchoring identification of 5-fluoro-5,6-dihydrouracil and downstream catabolites.

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