Waste DNA from the lab bench converted toward dGTP in a crude-enzyme cascade

Researchers have reported a proof-of-concept route that turns laboratory waste DNA into guanine deoxynucleotides, using a simplified enzymatic cascade built around a crude bacterial lysate rather than purified reagents.

The team, Zehra Özdemir and Ercan Arıcan, first hydrolysed waste DNA with S1 nuclease, an enzyme that cleaves DNA into its constituent deoxynucleotide monophosphates. This produced a mixed nucleotide pool containing deoxyguanosine monophosphate (dGMP), the starting point for the downstream phosphorylation steps. The hydrolysis itself was verified analytically: ion-pair HPLC showed that the dGMP signal in the reaction was about 1.4-fold higher than in a DNA-free control, a difference the authors report as statistically significant (p = 0.023), confirming that the nucleotide pool genuinely derived from the waste-DNA feedstock.

From that monophosphate pool, the researchers ran a one-pot phosphorylation cascade. Its centrepiece was recombinant guanylate kinase (GUK1) from the yeast Saccharomyces cerevisiae, expressed in Escherichia coli BL21(DE3) and used without purification, directly in the crude lysate. Guanylate kinase phosphorylates dGMP to dGDP, and the lysate’s endogenous nucleoside diphosphate kinase activity was relied upon to carry the phosphorylation one step further to dGTP. To keep the cascade running, the authors included a pyruvate kinase/phosphoenolpyruvate ATP-regeneration system, which continuously resupplies the ATP that the phosphorylation reactions consume. Recombinant GUK1 expression was confirmed by SDS-PAGE.

Identifying the final product required high-resolution mass spectrometry. Q-TOF LC-MS/MS detected dGTP through its accurate mass ([M − H]⁻ m/z 505.98, C10H16N5O13P3), its isotope pattern, an acetate adduct, and diagnostic product ions at m/z 158.93, 408.01 and 78.96.

However, the dGTP finding comes with important caveats that the authors state explicitly. dGTP was present only at trace level, and neither full-scan LC-MS nor ion-pair HPLC could distinguish the reaction’s dGTP signal from that of a DNA-free control. The crude lysate evidently carries a substantial background of endogenous guanine nucleotides, so the detected dGTP could not be attributed to the waste-DNA substrate.

To disentangle the enzyme’s contribution from this background, the team ran an empty-vector cascade control lacking recombinant GUK1. At the diphosphate level the attribution became clear: the lysate containing recombinant GUK1 produced roughly 2.3-fold more dGDP, the direct product of guanylate kinase, than the empty-vector lysate across three replicates (Welch’s t-test, p = 0.007). This indicates a specific contribution of the recombinant enzyme above the endogenous background of the crude lysate.

The conclusions the authors draw are deliberately modest. They establish that waste DNA can be depolymerized to a dGMP-containing nucleotide pool, and that dGTP can be identified analytically in the cascade’s output. What they could not demonstrate is DNA-dependent formation of dGTP itself, and the triphosphate was not quantified. The findings therefore provide a basis for further development rather than a quantified conversion process, and no yield figure for dGTP can be stated from this work.

Even so, the study sketches a direction that fits circular-biotechnology thinking. The appeal of the crude-lysate approach tested here is that it avoids enzyme purification, but the same crudeness that simplifies the workflow also introduces the endogenous nucleotide background that complicated the dGTP attribution.

For now, the reported results stand as an early analytical demonstration: waste DNA can be enzymatically depolymerized to dGMP, recombinant GUK1 demonstrably boosts dGDP formation in a crude cascade, and dGTP is identifiable at trace level by high-resolution mass spectrometry.

Subject of Research: Enzymatic conversion of laboratory waste DNA into guanine deoxynucleotides using a crude-lysate guanylate kinase cascade

Article Title: Enzymatic depolymerization of laboratory waste DNA to a dGMP-containing pool and analytical assessment of dGTP in a crude-lysate guanylate kinase system

Article References: Özdemir, Z., & Arıcan, E. (2026). Enzymatic depolymerization of laboratory waste DNA to a dGMP-containing pool and analytical assessment of dGTP in a crude-lysate guanylate kinase system. Molecular Biology Reports, 53(1), Article 1503. https://doi.org/10.1007/s11033-026-12693-y

Image Credits: AI Generated

DOI: 10.1007/s11033-026-12693-y

Keywords: waste DNA, dGTP, dGMP, guanylate kinase, GUK1, S1 nuclease, nucleotide recycling, circular biotechnology, LC-MS/MS, enzyme cascade, deoxynucleotides, proof of concept