Beyond Chelation: EDTA Tightly Binds Taq DNA Polymerase, MutT and dUTPase and Directly Inhibits dNTPase Activity

Spectroscopic characterization of europium binding to a calmodulin-EF4 hand peptide-polymer conjugate

The emergence of biological ligand as an alternative to chemical ligands enables a sustainable lanthanide extraction route. In this study, a peptide originating from the loop of domain 4 calmodulin (EF4) was synthesized and the interaction with europium ions was monitored using time resolved laser fluorescence spectroscopy (TRLFS). Despite being retracted from its full protein structure, the twelve amino acids of calmodulin-EF4 showed binding to europium. Europium-peptide complex formation was evident by an increase in decay time from 110 to 187 μs. The spectra of europium bound to peptide can be easily distinguished from the free europium ion as the 5D0 → 7F2 peak intensifies. When europium bound to the peptide-polymer conjugate, the decay time was further increased to 259 μs. This suggests that lanthanide binding can be enhanced by immobilizing the short peptide into a polymer matrix. The europium-peptide/conjugate bond was reversible, triggered by pH, promoting peptide reusability. Due to the fact that the study was conducted exclusively in water, it suggests minimal use of chemicals is possible while maintaining peptide affinity. This makes the calmodulin-EF4 peptide an ideal candidate as biological ligand. This study lays the groundwork for developing a peptide-based filter material for lanthanide separation.

Highly Efficient Gel Electrophoresis for Accurate Quantification of Nucleic Acid Modifications via in-Gel Digestion with UHPLC-MS/MS

Gel electrophoresis is a powerful technique for the characterization of sequences, sizes and conformations of nucleic acids due to its remarkable separation efficiency. In parallel, liquid chromatography-mass spectrometry (LC-MS) has established itself as a staple tool for the meticulous characterization and accurate quantification of a multitude of DNA modifications. In this study, we devised an in-gel digestion method for coupling gel electrophoresis with LC-MS/MS. This process involves the enzymatic digestion of DNA within the gel by nucleases and release single nucleosides, which subsequently serve as a preprocessing step for (LC-MS/MS) analysis. We demonstrated that ethylenediaminetetraacetic acid (EDTA) in the routine gel electrophoresis buffer reduced the enzymatic digestion efficiency, while Mg2+ could mitigate this inhibition. We further showed EDTA-free gel electrophoresis and the process of digestion of genomic DNA and plasmid DNA within a gel was fluorescently imaged, proving the efficient digestion of DNA. By this improvement, the efficiency of an in-gel digestion could reach 60% or more of the control, compared with direct in-solution digestion. The measured abundances of DNA modifications (5-methylcytosine and N6-methyladenine) via in-gel digestion are consistent with that measured by in-solution digestion. Collectively, we showed an in-gel digestion method, which is a very useful pretreatment technique for the precise quantification of epigenetic modifications in diverse DNA molecules.

Analysis of mono-, di-, and triphosphates of thioguanosine and methylthioinosine in children with acute lymphoblastic leukemia by LC-MS/MS

Mercaptopurine (6-MP) is an indispensable, first-line, drug in the treatment of pediatric acute lymphoblastic leukemia (ALL). However, 6-MP has several intrinsic drawbacks, such as large individual variability in the drug response, undesirable adverse reactions, and drug resistance in patients with release ALL, which requires therapeutic drug monitoring (TDM). Several studies analyzed the total concentration of thiopurine nucleotides in red blood cells (RBCs) after hydrolysis, and two studies detected them separately and accurately by liquid chromatography-tandem mass spectrometry (LC-MS/MS). In this study, we developed a rapid and robust LC-MS/MS method for simultaneous quantitation of mono-, di-, and triphosphates of thioguanosine and methylthioinosine. Not only EDTA and DTT were added, but also EHT1864, a new Rac family small GTPases inhibitor, was innovatively added to ensure the stability of the analytes. Commercial availability and relatively low cost compound methotrexate-D3 was selected as internal standards. The linearity, accuracy, precision, recovery, matrix effect and stability of the method were all in line with the guidelines. This method provide an accurate and robust new solution for the determination of 6 metabolites of MP in RBCs from ALL patients with maintenance therapy.

Applying EDTA in Chelating Excess Metal Ions to Improve Downstream DNA Recovery from Mine Tailings for Long-Read Amplicon Sequencing of Acidophilic Fungi Communities

The hostile environment of mine tailings contains unique microbial life capable of bioleaching. The metagenomic analysis of such an environment provides an in-depth understanding of the microbial life and its potential, especially in biomining operations. However, DNA recovery from samples collected in those environments is challenging due to the presence of metal ions that interfere with the DNA analysis. A varied concentration of EDTA (4–13 µg/µL) to chelate the metal ions of enriched tailing samples prior to DNA extraction was performed. The results show that 9 µg/µL of EDTA was effective in most samples. However, the increasing concentration of EDTA negatively affected the DNA recovery. The sequencing of the successfully extracted DNA revealed a diverse range of fungal genera, some of which have not been previously reported in tailing or bioleaching applications. The dominant genera include Fodinomyces, Penicillium, Recurvomuces, Trichoderma, and Xenoacremonium; their traits were determined using the FungalTraits database. This study demonstrates the need to include a preliminary metal-chelating step using EDTA before DNA extractions for samples collected from metal-rich environments. It further showed the need for optimization but provided a benchmark range, particularly for tailings. However, we caution that a further EDTA removal step from the extracted DNA should be included to avoid its interferences in downstream applications.

Lyophilized Ready-to-Use Mix for the Real-Time Polymerase Chain Reaction Diagnosis

Real-time polymerase chain reaction (real-time PCR) brings a more efficient and accurate method for detecting and analyzing nucleic acids in hospitals and laboratories. To solve the inconvenience of PCR reagent delivery and storage via cold-chain transportation, a solid-state reagent with robust characteristics should be employed. In this report, a lyophilized mix containing all necessary components for real-time PCR and its production method was designed, and its stability was tested at different temperatures. Some cryoprotectants and carriers are required to protect the function of the enzyme and primer as much as possible and provide the cake structure. Formulations with polyhydroxy compounds were considered to have the potential for protecting the enzymatic microstructure and functionality of dried mixes during the whole manufacturing and cold-free storage. The final products with the most superior protective formulation containing trehalose, Ficoll 400, and gelatin were able to provide the totally same testing result and sensitivity as the freshly made mix after 300 days of storage at 45 °C and can be deduced to maintain the function at room temperature (22.5-25.5 °C) for about 2 years.

Toward the Development of Ultrasensitive Detectors for Environmental Applications: A Kinetic Study of Cr(III) Monitoring in Water Using EDTA and SERS Techniques

We report for the first time kinetic studies on chromium(III) detection in aqueous solution using citrate-capped silver nanoparticles (AgNPs) and the surface-enhanced Raman spectroscopy (SERS) technique. Moreover, we have shown an important effect of adding ethylenediaminetetraacetic acid (EDTA) on the enhancement and the stability of the Raman signal. The origin of the SERS signal was attributed to the coordination of Cr(III) by citrate/EDTA molecules and the formation of hot spots on aggregated AgNPs. Depending on the mixing method of Cr(III) and EDTA with AgNPs, the temporal SERS spectral features reveal a Prout-Tompkins or a Langmuir kinetic detection model. The UV-visible data, the temporal response of the Raman signal, and the scanning electron microscopy analysis have allowed us to elucidate the mechanism of Cr(III) detection. We observed that mixing simultaneously Cr(III), AgNPs, and EDTA leads to the most stable and intense time-dependent SERS signal. The obtained results should open the way to perform kinetic studies on different host-guest interactions in solution using the SERS technique.