A highly sensitive and rapid enzymatic method using a biochemical automated analyzer to detect inorganic pyrophosphate generated by nucleic acid sequence-based amplification

Abstract

Background and aims: Polymerase chain reaction-based techniques require expensive equipment for fluorescence detection of the products. However, the measurement of inorganic pyrophosphate (PPi) released during DNA synthesis can be used to quantify target genes without such equipment. Here, we devised a high-sensitivity enzymatic assay for detection of PPi.

Materials and methods: In our assay method, PPi was converted to hypoxanthine by hypoxanthine phosphoribosyl transferase. Xanthine dehydrogenase converted the hypoxanthine to uric acid and yielded two molecules of NADH, which in turn reduced Fe³⁺ to Fe²⁺ (mediated by 1-methoxy-5-ethylphenazinium ethylsulfate). 2-Nitroso-5-(N-propyl-N-sulfopropylamino) phenol chelated the Fe²⁺, which resulted in an intensely colored product that could be measured using a biochemical automated analyzer.

Results: The assay was able to detect PPi within 10 min. It was linear between 0 and 10 µmol/L PPi, and intra-run and inter-run coefficients of variation were 1%-2%. Other validation tests with a biochemical automated analyzer were satisfactory. The assay could potentially be used to directly quantify samples after isothermal nucleic acid sequence-based amplification of a target gene.

Conclusion: The method developed here for detection of PPi can be used to measure nucleic acid biomarkers in biological samples in clinical practice using a high-throughput biochemical automated analyzer.

Keywords: Biochemical automated analyzer; Enzymatic method; Inorganic pyrophosphate; Nitroso-PSAP; Nucleic acid sequence-based amplification.