Prebiotic synthesis of dihydrouridine by photoreduction of uridine in formamide

Abstract

In this report, we show that a very common modification (especially in tRNA), dihydrouridine, was efficiently produced by photoreduction of the canonical pyrimidine ribonucleoside, uridine in formamide. Formamide not only acts as a solvent in this reaction, but also as the reductant. The other three components of the canonical alphabet (C, A, G) remained intact under the same conditions, suggesting that dihydrouridine might have coexisted with all four canonical RNA nucleosides (C, U, A, G) at the dawn of life.

Fig. 1. Photohydration of uridine and cytidine in H₂O.

Fig. 2. Photoreduction of uridine nucleotides to dihydrouridine nucleotides. Yields are based on relative integration of the signals in ¹H NMR spectra compared to an internal standard (sodium succinate).

Fig. 3. Limited UV irradiation of mixtures of canonical ribonucleosides^b (C, U, A, G) leads to a mixture of dihydrouridine (DHU, modified nucleoside in tRNA) with all four RNA canonical nucleosides (C, U, A, G). ^b Thymidine is not reactive under the same conditions.

Fig. 4. The ¹nπ* excited-state potential energy surface (green curve) of the uridine-formamide complex presents an electron-driven proton transfer from formamide to uridine resulting in reactive hydrouridyl and formamide radicals. The results were obtained using the SCS-ADC(2) method and the aug-cc-pVDZ basis set. (a) Quantum-chemical calculations of uridine in formamide upon irradiation. (b) Mechanism of reduction of uridine in formamide inferred from calculations. (c) Reduction of uridine in 1-d-formamide. (i) Proton transfer following electron transfer; (ii) solvent-assisted tautomerization; (iii) hydrogen atom abstraction; (iv) radical recombination. R = β-d-ribofuranosyl.