Enzymatic depolymerization of laboratory waste DNA to a dGMP-containing pool and analytical assessment of dGTP in a...

Deoxynucleoside triphosphates (dNTPs) are essential reagents for molecular biology and synthetic biology, yet their conventional chemical synthesis is costly and environmentally burdensome. Enzymatic routes offer a cleaner alternative but typically start from defined, purified precursors. Recovering nucleotides from laboratory waste DNA would align dNTP supply with circular-biotechnology principles, but this route remains largely unexplored, particularly for guanine nucleotides. This proof-of-concept study tests whether waste DNA can be routed toward deoxyguanosine triphosphate (dGTP) using a simplified crude-lysate enzymatic cascade.

Waste DNA was hydrolysed with S1 nuclease into a deoxynucleotide monophosphate pool and subjected to a one-pot phosphorylation cascade combining recombinant Saccharomyces cerevisiae guanylate kinase (GUK1), expressed in Escherichia coli BL21(DE3), with endogenous nucleoside diphosphate kinase activity and a pyruvate kinase/phosphoenolpyruvate ATP-regeneration system. Recombinant GUK1 expression was confirmed by SDS-PAGE. Ion-pair HPLC resolving the monophosphate and triphosphate species showed that S1 hydrolysis reproducibly generated a dGMP-containing nucleotide pool, with the dGMP signal significantly higher in the reaction than in a DNA-free control (~ 1.4-fold; p = 0.023), confirming DNA-dependent depolymerization of the waste-DNA feedstock. High-resolution Q-TOF LC-MS/MS confidently identified dGTP in the reaction through accurate mass ([M - H]⁻ m/z 505.98, C₁₀H₁₆N₅O₁₃P₃), isotope pattern, acetate adduct, and diagnostic product ions (m/z 158.93, 408.01, 78.96), corresponding to Schymanski confidence level 2. dGTP was present at trace level and was not distinguishable from a DNA-free control by either full-scan LC-MS or ion-pair HPLC, indicating a substantial background of endogenous guanine nucleotides in the crude lysate. An empty-vector cascade control resolved the attribution at the diphosphate level: recombinant GUK1 produced ≈ 2.3-fold more dGDP-the direct product of guanylate kinase-than the empty-vector lysate (n = 3; Welch's t-test, p = 0.007), indicating a specific contribution of the recombinant enzyme above the endogenous background.

A crude-lysate GUK1 cascade acting on waste-DNA-derived substrate yields identifiable dGTP. The product was confirmed structurally but its DNA-dependent formation could not be demonstrated and it was not quantified; the findings therefore establish depolymerization of waste DNA to dGMP and the analytical identity of dGTP as a basis for further development, rather than a quantified conversion process.