Colorimetric inorganic pyrophosphate assay using a double cycling enzymatic method

Screening the Thermotoga maritima genome for new wide-spectrum nucleoside and nucleotide kinases

Enzymes from thermophilic organisms are interesting biocatalysts for a wide variety of applications in organic synthesis, biotechnology and molecular biology. Next to an increased stability at elevated temperatures, they were described to show a wider substrate spectrum than their mesophilic counterparts. To identify thermostable biocatalysts for the synthesis of nucleotide analogs, we performed a database search on the carbohydrate and nucleotide metabolism of T. maritima. After expression and purification of 13 enzyme candidates involved in nucleotide synthesis, these enzymes were screened for their substrate scope. We found that the synthesis of 2'-deoxynucleoside 5'-monophosphates (dNMPs) and uridine 5'-monophosphate from nucleosides was catalyzed by the already known wide-spectrum thymidine kinase (TK) and the ribokinase. In contrast, no NMP-forming activity was detected for adenosine-specific kinase, uridine kinase or nucleotidase. The NMP kinases (NMPKs) and the pyruvate-phosphate-dikinase of T. maritima exhibited a rather specific substrate spectrum for the phosphorylation of NMPs, while pyruvate kinase, acetate kinase and three of the NMPKs showed a broad substrate scope with (2'-deoxy)nucleoside 5'-diphosphates as substrates. Based on these promising results, TmNMPKs were applied in enzymatic cascade reactions for nucleoside 5'-triphosphate synthesis using four modified pyrimidine nucleosides and four purine NMPs as substrates, and we determined that base- and sugar-modified substrates were accepted. In summary, besides the already reported TmTK, NMPKs of T. maritima were identified to be interesting enzyme candidates for the enzymatic production of modified nucleotides.

Spectrophotometric, fluorimetric and electrochemical selective pyrophosphate/ATP sensing based on the dimethyltin(IV)-tiron system

Sensing of pyrophosphate anion (PPi) in the presence of nucleotide triphosphates allows the real time monitoring of the polymerase chain reaction. To get a deeper understanding of the factors involved in PPi/nucleotide triphosphate discrimination, a detailed study on the performance of a dimethyltin (IV)-catecholate complex capable of both separate fluorimetric or electrochemical detection of PPi in the presence of adenosine triphosphate (ATP) has been undertaken. Dimethyltin (IV) tightly binds PPi or ATP, and forms a stable 1:1 complex with tiron (4,5-dihydroxy-1,3-benzenedisulfonic acid) in water. The complexation equilibria with all components are characterized quantitatively by potentiometric and spectroscopic titrations. Pyrophosphate anion can be detected owing to its ability to release free tiron from the complex by measuring either a fluorimetric or an electrochemical signal. On the contrary, ATP does not displace tiron but causes an interference with PPi in the fluorimetric detection method due to the formation of a ternary Me₂Sn(IV)-tiron-ATP complex with optical properties intermediate between those of free and bound tiron. In the electrochemical (square wave voltammetry) method, the ternary ATP complex shows a separate peak which does not coincide with the peaks of neither free nor bound tiron, thus making possible the simultaneous detection of ATP in addition to PPi.

Color-Coded Single-Particle Pyrophosphate Assay with Dark-Field Optical Microscopy

In this work, we demonstrate a convenient yet sensitive color-coded single-particle detection method for the quantification of pyrophosphate (PPi) by using single gold nanoparticle (GNP) as the probe. The design is based on GNP-dependent catalytic deposition of Cu onto the surface of GNPs with reduced nicotinamide adenine dinucleotide (NADH). Without PPi, Cu²⁺ can be directly reduced to Cu⁰ through the gold-catalyzed oxidization of NADH. In the presence of PPi, the coating process is impeded due to the strong coordination capability of PPi with Cu²⁺. The selective coating of Cu shell onto the GNPs surface results in the extraordinary red-shift of localized surface plasmon resonance from individual GNPs. By quantitatively counting the fraction of yellow particles with color-coded dark-field optical microscopy, the trace amounts of PPi in solution can be accurately quantified. The limit-of-detection is as low as 1.49 nM with a linear dynamic range of 0-4.29 μM, which is much lower than the spectroscopic measurements in bulk solution. In artificial urine sample, good recovery efficiency was achieved. As a consequence, the method demonstrated herein will find promising applications for the ultrasensitive detection of target biomolecules under biological milieu in the future.

Characterization and application of a novel nicotinamide mononucleotide adenylyltransferase from Thermus thermophilus HB8

Herein, we describe a novel enzymatic cycling method to measure nicotinamide mononucleotide (NMN) or nicotinic acid mononucleotide (NaMN), which are precursors of NAD biosynthesis. A gene encoding an NMN adenylyltransferase (NMNAT, EC 2.7.7.1) homologue was identified in Thermus thermophilus HB8. The gene from T. thermophilus (TtNMNAT) was engineered for expression in Escherichia coli and the recombinant enzyme found to be stable, retaining full activity after incubation for 45 min at 70°C. The K_m values for NMN and ATP were calculated to be 0.263 and 1.27 mM, respectively, with a V_max value of 60.3 μmoL/min/mg. TtNMNAT was successfully applied to the colorimetric NMN or NaMN assays, which employed (i) adenylation of NMN to NAD by TtNMNAT or adenylation of NaMN to deamido-NAD (NaAD) by TtNMNAT followed by amidation of NaAD to NAD by NAD synthetase (NADS, EC 6.3.1.5) and (ii) an NAD cycling reaction using 12α-hydroxysteroid dehydrogenase (12α-HSD, EC 1.1.1.176) and diaphorase (DI, EC 1.6.99.3) to accumulate reduced WST-8. This enzymatic cycling method enabled detection of 0.5 μM (12.2 nM in the reaction mixture) NMN or NaMN in an automatic clinical analyzer.