Polyphosphate attachment to lysine repeats is a non-covalent protein modification.

Polyphosphate (polyP) is a chain of inorganic phosphate that is present in all domains of life and affects diverse cellular phenomena, ranging from blood clotting to cancer. A study by Azevedo et al. described a protein modification whereby polyP is attached to lysine residues within polyacidic serine and lysine (PASK) motifs via what the authors claimed to be covalent phosphoramidate bonding. This was based largely on the remarkable ability of the modification to survive extreme denaturing conditions. Our study demonstrates that lysine polyphosphorylation is non-covalent, based on its sensitivity to ionic strength and lysine protonation and absence of phosphoramidate bond formation, as analyzed via 31P NMR. Ionic interaction with lysine residues alone is sufficient for polyP modification, and we present a new list of non-PASK lysine repeat proteins that undergo polyP modification. This work clarifies the biochemistry of polyP-lysine modification, with important implications for both studying and modulating this phenomenon. This Matters Arising paper is in response to Azevedo et al. (2015), published in Molecular Cell. See also the Matters Arising Response by Azevedo et al. (2024), published in this issue.

Effects of different primers and colouring solutions on orthodontic bonding: shear bond strength and colour change.

OBJECTIVES: This in vitro study evaluated the effect of different colouring solutions and primer systems used in the bonding of brackets on enamel colour change and bond strength. MATERIALS AND METHODS: 120 premolar teeth were divided into four main groups; brackets were bonded with 37% orthophosphoric acid + Transbond XT Primer in Group 1, 3 M Single Bond Universal in Group 2, Transbond Plus SEP in Group 3, and G-Premio Bond in Group 4. Each group was divided into three subgroups, and the teeth were placed in a cup containing coffee and tea mixture, in a cup containing cola and in distilled water. A bond strength test was applied to all teeth. Colour measurements of all teeth were performed at 2 different times: before bonding and after the bond strength test. RESULTS: The average bond strength of the 37% orthophosphoric acid group was higher than that of the other groups. The effect of primer and solution groups on colour change was statistically significant (p = 0.001 and p = 0.023, respectively). CONCLUSIONS: In this study, the bond strength was clinically sufficient in all primer groups. The highest colour change was observed when the tea-coffee solution and Transbond Plus SEP primer were used. CLINICAL RELEVANCE: This study has identified enamel discoloration and bond strength from different colouring solutions and primer systems used for bonding braces, which can be used to inform clinicians and patients to achieve better treatment results.

Separation of inorganic anions on reversed-phase C18 columns with a phosphomolybdate mobile phase.

Reversed-phase high performance liquid chromatography (RP-HPLC) is the most widely used chromatographic method. In addition to hydrophobic interactions, additional interactions such as electrostatic interactions may participate in the retention behaviour of an analyte. This makes it possible to use RP-HPLC for many types of analyte. We describe a simple method for separating inorganic anions on a C18 column, in which retention of inorganic anions is almost entirely due to electrostatic interactions. This leads to rapid separations as well as higher theoretical plate numbers. We used 2 mM phosphoric acid containing a low concentration of disodium molybdate as the mobile phase, which allows UV detection of non-UV-absorbing anions. With this method, we determined eight inorganic anions including several non-UV-absorbing anions photometrically at 220 nm. The detection limits of the examined eight inorganic anions calculated at a signal-to-noise ratio of 3 were between 0.3 and 10 µM. The detector response was linear over three orders of magnitude of inorganic anion concentration. The proposed RP-HPLC/UV method was successfully applied to determine inorganic anions in some water samples.

Dietary contribution of iron from limestone and dicalcium phosphate for broiler chickens.

Iron is routinely supplemented in broiler feeds aiming to prevent dietary deficiencies. Limestone and phosphates are very rich in Fe; however, its contribution from these sources have not been thoroughly investigated with chickens. The present research was conducted to evaluate live performance and blood parameters of broilers when using limestone and dicalcium phosphate as sources of Fe. A total of 576 one-day-old male Cobb x Cobb 500 were allocated into a total of 72 battery cages, 6 treatments with 12 replication cages of 8 chicks at placement. Chicks were fed diets formulated with corn, soybean meal (SBM) with laboratory grade calcium carbonate and phosphoric acid (having traces of Fe). All chicks were fed a common prestarter without Fe supplementation (analyzed total 58.2 ± 2.4 mg/kg Fe) from placement to 7 d. Allocation of birds to dietary treatments was completely randomized on day 8. Treatments had increasing Fe derived from commercial limestone and dicalcium phosphate (analyzed Fe 7,218 and 4,783 mg/kg, respectively) progressively replacing calcium carbonate and phosphoric acid to provide graded increases in total Fe (analyzed Fe in the feeds were 57.6 ± 2.1, 92.0 ± 2.3, 124.1 ± 2.7, 159.3 ± 3.1, 187.2 ± 3.2, 223.7 ± 3.6 mg/kg, respectively). There were no effects of dietary Fe on live performance, hematocrit, and hemoglobin the end of the study on day 28 (P > 0.05). Increasing dietary Fe from commercial limestone and dicalcium phosphate led to a linear reduction in the percent ileal digestible Fe. However, linear increments in Fe retention, serum ferritin and liver Fe occurred when compared to feeds without Fe derived from limestone and phosphate dicalcium. It is concluded that Fe from limestone and dicalcium phosphate can be partially utilized by broiler chickens. It was estimated that the Fe retained from limestone and dicalcium phosphate is of 1.9%. Broilers fed corn-soy feeds (58.2 mg/kg Fe) do not require supplemental Fe.

75 Years Ago: Discovery of Resin Adhesion to Acid-etched Enamel - A Comparison of the 1949 and 1955 Methods.

PURPOSE: This paper describes previously unknown details about the discovery of resin adhesion to acid-etched human enamel. MATERIALS AND METHODS: A literature review was performed through manual assessments. Primary sources revealing the discovery of resin curing on etched enamel were analyzed considering the research objectives and methodological procedure during that era, including the type of teeth used, preparatory measures, acid-etching process, type of resin and its application, and follow-up observations. Additionally, the political and economic contexts were examined. RESULTS: In 1949, acid etching was found to promote adhesion with acrylic resin, a finding described again in 1955. The 1949 studies utilized nitric acid for enamel etching and the acrylate resin Paladon from the Kulzer company (Germany). Conversely, the 1955 investigations employed phosphoric acid and an unnamed acrylate, likely a self-curing resin supported by Kulzer in the late 1930s. Disparities in the 1949 and 1955 findings can be ascribed to varying objectives and test conditions amidst a turbulent political backdrop, significantly impacting the Kulzer company. CONCLUSION: The discovery of resin adhesion to acid-etched enamel, approaching its 75th anniversary in 2024, is a landmark in 20th-century adhesive dentistry. Paladon represents a pioneering compound, exemplifying the influence of political, ideological, and economic factors on scientific advancements during that period.

Analytical quality by design approach for the development of high-performance liquid chromatography method for simultaneous analysis of metformin and sitagliptin in the presence of major degradation products.

An analytical quality by design-based high-performance liquid chromatography method for determining metformin (MET) and sitagliptin (SIT) in stress-degraded samples was developed and validated. The analytical target profile and risk assessment-driven critical method variables, for example, pH, % aqueous, and buffer concentration, were studied for their effect on method responses of retention time and resolution using a central composite design. The correlation regression coefficient was more than 0.8, and variables interaction was significant on method responses with curvature effect. The method operable design region afforded an aqueous range of 55%-70% and an ortho-phosphoric acid buffer of 0.1% with a pH of 3.0-4.0 as a robust region for the suitable method performance characteristics. The separation of MET and SIT from their degradants (m/z 85.0509; m/z 193.0694) on the C8 column was achieved using a mobile phase consisting of 0.1% ortho-phosphoric acid and methanol (60:40% v/v; pH 3.0). The optimized method eluted MET and SIT at 4.3 ± 0.2 and 7.1 ± 0.2 min, respectively, with acceptable specificity and resolution. The linearity ranges of 25-250 µg/mL (r2 : 0.9982) and 5-50 µg/mL (r2 : 0.9989) was established for MET and SIT, respectively. The % recovery (98.81%-102.17%), precision (0.55%-1.65%), and robustness study for method variables were acceptable.

Longitudinal bond strength of a universal adhesive and chemical dentin characterization under different acid etching protocols.

OBJECTIVE: This study aimed to analyze the longitudinal bond strength of a universal adhesive and chemically characterize the dentin substrate under different acid etching protocols. METHODOLOGY: Dentin samples were etched with polyacrylic acid 25% (PAA) for 10 seconds (n=3) and phosphoric acid 32% (PA) for 15 seconds (n=3) and analyzed by Fourier transform infrared spectroscopy - attenuated total reflectance (FTIR-ATR) before and after treatment. For collagen degradation, samples (n=12) were divided into 3 groups: PAA, PA, and Deionized water (control), and analyzed by the quantity of solubilized type I collagen C-terminal cross-linked telopeptides and solubilized C-terminal peptide in relation to total protein concentration (ICTPtp and CTXtp) and by their ultimate tensile strength (UTS). For the adhesive interface analysis, dentin samples (n=72) were divided into 3 groups: PAA, PA, and Self-etch (SE), and subdivided into 2 groups: 24 h (baseline) and 1 year. The following tests were performed: microtensile bond strength (µTBS) (n=48), scanning electron microscopy (SEM) (n=12), and nanoleakage (n=12). RESULTS: The FTIR of PAA showed lower reduction of the peaks in the phosphate group when compared to PA. For ICTPtp, PA showed a significantly higher value. For CTXtp, PA and PAA groups failed to statically differ from each other. UTS was significantly lower for PA. For µTBS, storage time significantly affected bond strength. The results were unaffected by the etching protocol. For SEM, after 1 year, PA had little evidence of degradation in the upper third of the adhesive interface in comparison to the other groups. Nanoleakage showed no considerable silver impregnation after 1 year in the SE group. CONCLUSION: The use of PAA prior to a universal adhesive (when compared to PA) represents a less aggressive type of etching to dentin. However, self-etching still seems to be the best option for universal adhesive systems that have functional monomers in their composition.

Optimizing Typha biochar with phosphoric acid modification and ferric chloride impregnation for hexavalent chromium remediation in water and soil.

Considering the persistent and covert nature of heavy metal soil contamination, the sustainable development of ecological environments and food safety is at significant risk. Our study focuses on remediating soils contaminated with chromium (Cr); we introduce an advanced remediation material, iron oxide phosphoric acid-loaded activated biochar (HFBC), synthesized through pyrolysis. This HFBC displays greater microporosity, fewer impurities, and enhanced efficiency for the remediation process. Our research utilized a comprehensive set of analytical techniques, including Scanning Electron Microscopy (SEM), Fourier Transform Infrared Spectroscopy (FTIR), and X-ray Photoelectron Spectroscopy (XPS), alongside adsorption studies to elucidate the Cr removal mechanism. The effectiveness of HFBC in remediation was influenced by several factors: the pH level, dosage of HFBC, the initial concentration of Cr, and the ambient temperature. Our results indicated an optimal chromium (VI) adsorption capacity of 55.5 mg/g by HFBC at a pH of 6.0 and a temperature of 25 °C, with the process adhering to the pseudo-second-order kinetic model and the Langmuir adsorption isotherm, thus suggesting spontaneity in the uptake method. Moreover, this mechanism encompasses both adsorption and reduction reactions. Using HFBC in pot experiments with cabbage indicated not only an increase in soil pH and cation exchange capacity (CEC), but also a surge in bacterial community abundance. Significant reductions in bioavailable chromium were also recorded. Interestingly, HFBC addition bolstered the growth of cabbage, while concurrently diminishing chromium accumulation within the plant, particularly notable as the HFBC application rate increased. In summation, the HFBC produced in our study has demonstrated convincing efficacy in removing chromium from aqueous solutions and soil. Moreover, the positive agronomic implications of its use, such as enhanced plant growth and reduced heavy metal uptake by plants, indicate its high potential for operational value in the domain of environmental remediation of heavy metals.

Effects of different surface treatments on surface topography and bond strength in the repair of fiber-reinforced dentin composite.

OBJECTIVE: This study aimed to evaluate the effects of different surface treatments on the repair bond strength between a fiber-reinforced dentin composite and a posterior composite. METHODS: Forty fiber-reinforced dentin composite resin blocks (4 mm × 4 mm × 4 mm) were separated into eight groups (n = 5) according to the surface preparation methods: (G1) negative control group, (G2) adhesive application, (G3) 50% dimethylsulfoxide (DMSO) application, (G4) 50% DMSO + adhesive application, (G5) 37% phosphoric acid etch + adhesive application, (G6) air abrasion + adhesive application, (G7) 37% phosphoric acid etch + 50% DMSO application + adhesive application, and (G8) air abrasion +50% DMSO application + adhesive application group. The composite surfaces were repaired in two layers with a posterior composite. Composite sticks were subjected to a micro tensile bond strength (µTBS) test. Fractured surfaces were evaluated using a stereomicroscope (×25). Short fiber-reinforced composite samples' surfaces were investigated by scanning electron microscope (SEM). Shapiro Wilk, one-way ANOVA, and Tukey HSD tests were used for statistical evaluation. RESULTS: The highest average (µTBS) values were observed in G8, whereas the lowest mean µTBS values were evident in the G1 group. Statistically significant µTBS values were found in all adhesive-applied groups when compared with the negative control group. Notably, the application of 50% DMSO without adhesive did not lead to a statistically significant increase in µTBS values. SEM images demonstrated that acid etching partially eliminated residues on the composite surface, while air abrasion had a detrimental effect on the integrity of fiber structures. CONCLUSION: In the repair of fiber-reinforced dentin composite with a posterior composite, adhesive application is an effective approach. The treatment of 50% DMSO without adhesive did not confer a statistically significant advantage, and the supplemental use of acid etch or air abrasion did not show an additional benefit compared to adhesive-only repairs. CLINICAL SIGNIFICANCE: Adhesive application emerges as a potent and effective strategy for the repair of bur-roughened fiber-reinforced dentin composites. With its limitations, the study highlights the efficacy of adhesive-only repairs without the necessity for additional surface treatments.

Modulating the properties and structure of lignins produced by alkaline delignification of sugarcane bagasse pretreated with two different mineral acids at pilot-scale.

Sugarcane bagasse was pretreated with dilute phosphoric acid or sulfuric acid to facilitate cellulose hydrolysis and lignin extraction. With phosphoric acid, only 8 % of the initial cellulose was lost after delignification, whereas pretreatment with sulfuric acid resulted in the solubilization of 38 % of the initial cellulose. After enzymatic hydrolysis, the process using phosphoric acid produced approximately 35 % more glucose than that using sulfuric acid. In general, the lignins showed 95-97 % purity (total lignin, w/w), an average molar mass of 9500-10,200 g mol-1, a glass transition temperature of 140-160 °C, and a calorific value of 25 MJ kg-1. Phosphoric acid lignin (PAL) was slightly more polar than sulfuric acid lignin (SAL). PAL had 13 % more oxidized units and 20 % more OH groups than SAL. Regardless of the acid used, the lignins shared similar properties, but differed slightly in the characteristics of their functional groups and chemical bonds. These findings show that pretreatment catalyzed with either of the two acids resulted in lignin with sufficiently good characteristics for use in industrial processes.

Preparation and structural characterization of epoxidized soybean oils-based pressure sensitive adhesive grafted with tea polyphenol palmitate.

Vegetable oils-based pressure sensitive adhesives (PSAs) are green and sustainable but face unsatisfactory adhesion strengths and are prone to aging during storage and application due to the existence of residual double bonds and massive ester bonds. Nine common antioxidants (tea polyphenol palmitate (TPP), caffeic acid, ferulic acid, gallic acid, butylated hydroxytoluene, tertiary butylhydroquinone, butylated hydroxyanisole, propyl gallate, and tea polyphenols) were grafted into epoxidized soybean oils-PSA (ESO-PSA) system to enhance antiaging properties and adhesion strengths. Results showed ESO-PSAs grafted with caffeic acid, tertiary butylhydroquinone, butylated hydroxyanisole, propyl gallate, tea polyphenols, or TPP didn't occur failure with TPP having best performance. The optimal conditions were ESO reacted with 0.9 % TPP, 70 % rosin ester, and 7.0 % phosphoric acid at 50 °C for 5 min, under which peel strength and loop tack increased to 2.460 N/cm and 1.66 N, respectively, but peel strength residue reduced to 138.09 %, compared with control (0.407 N/cm, 0.43 N, and 1669.99 %). Differential scanning calorimetry and thermogravimetric results showed TPP grafting increased the glass transition temperature of ESO-PSA slightly but improved its thermal stability significantly. Fourier transform infrared spectroscopy and 1H nuclear magnetic resonance results showed TPP, phosphoric acid, and rosin ester all partially participated in the covalently crosslinking polymerization of ESO-PSAs and the rest existed in the network structures in the free form.

Corrosion-induced changes in surface properties and roughness of orthodontic wires.

INTRODUCTION: This study aimed to investigate the surface free energy and surface roughness (SR) of metallic alloys under the influence of acid solutions. METHODS: The experiment involved the use of 270 rectangular wire samples measuring 0.019 × 0.025-in. These samples were sourced from 3 different commercial brands: Dentsply GAC, American Orthodontics, and Orthoclassic. This in vitro study categorized the samples into 3 groups based on the solutions employed: deionized water, citric acid, and phosphoric acid. Each group consisted of 90 samples, with 30 samples representing each type of alloy-stainless steel, nickel-titanium, and titanium molybdenum alloy (TMA). The wire segments were immersed in their respective solutions for 72 hours at a controlled temperature of 37°C, with continuous orbital agitation at 130 rpm. After the immersion period, the study analyzed both surface free energy and SR. The mean values obtained were subjected to an analysis of variance at a significance level of 5%. RESULTS: All alloys displayed hydrophobic behavior, as indicated by interaction free energy values <0. In acidic environments (phosphoric acid and citric acid), significant differences were observed among different brands and alloys, affecting surface energy and interaction free energy. Variations in SR among metallic alloys included steel with the lowest SR variations, followed by nickel-titanium and TMA. Notably, the TMA alloy stood out with significantly higher surface energy compared with that of the other alloys (P <0.001). CONCLUSIONS: In this study, all examined alloys demonstrated a hydrophobic nature, suggesting a limited attraction to water. Notably, TMA exhibited the least hydrophobic behavior among the alloys studied. However, when exposed to citric acid, TMA displayed the most substantial alterations in its surface properties. These results underscored the significance of accounting for the distinctive properties of each alloy and their responses to diverse challenges, such as exposure to acidic solutions, during the selection of orthodontic wires for orthodontics treatment.

Effect of phosphoric acid containing polyvinylpyrrolidone as protective etchant for dentin bonding.

STATEMENT OF PROBLEM: Phosphoric acid is commonly used in dentistry as an etchant but can result in excessive demineralization of dentin, a major contributor to the instability of dentin-bonded restorations. Nevertheless, research on the development of etchants that can reduce acid damage is sparse. PURPOSE: The purpose of this in vitro study was to investigate the effects of polyvinylpyrrolidone-modified phosphoric acid on the dentin bonding of an etch-and-rinse adhesive. MATERIAL AND METHODS: Protective etchants were prepared by adding polyvinylpyrrolidone to 35% phosphoric acid aqueous solutions: the 3 concentrations were 0.5% (P0.5% group), 1% (P1% group), and 2% (P2% group) w/v. The treatment agent of the control group (C) was 35% phosphoric acid gel. Scanning electron microscopy (SEM), Fourier transform infrared spectroscopy (FTIR), microhardness, microtensile bonding strength (µTBS), nanoleakage, and in situ zymography were used to evaluate the appearance of the protective etchant on dentin bonding. The results were analyzed with a 1-way ANOVA test (α=.05). RESULTS: SEM showed no obviously exposed collagen fiber in the P1% and P2% groups. FTIR showed less demineralization of the dentin surface, and microhardness was higher after treatment with the protective etchant (P<.05). The µTBS of P1% (70 ±9.2 MPa) was the highest, and group C (44 ±5.8 MPa) was the lowest in all groups (P<.05). Moreover, there was weaker MMP activity in the P1% and P2% groups (P<.05). CONCLUSIONS: This study demonstrated that the protective etchant effectively reduced demineralization, enhanced bond strength, and reduced nanoleakage and enzyme activity within the hybrid layer.

[The method of determination for 2, 3-Butanedione in the air of workplace by high performance liquid chromatography with derivatization].

Objective: To establish a method for the determination of 2, 3-Butanedione (BUT) in the air of workplace, which including the process of collection by absorption in phosphoric acid aqueous solution and the process of analysis and detection by high performance liquid chromatography with derivatization. Methods: In October 2022, a porous glass plate absorption tube containing 10 ml of 0.01% phosphoric acid solution was used to collect BUT in the air of the workplace at a flow rate of 0.2 L/min. The absorption solution was derived by 2, 4-dinitrophenylhydrazine for 75 min and separated on a SB-C18 column (250 mm×4.6 mm, 5 µm) . At the column temperature of 30 ℃, the mixture of acetonitrile-water (V∶V, 1∶1) was eluted at the flow rate of 1.0 ml/min. It was detected by UV detector (λ=365 nm) , qualitatived by retention time and quantitatived by external standard. Results: It showed that BUT in phosphoric acid aqueous solution could be stored for at least 7 d at 4 ℃. There was a linear relationship within the determination range of 0.05-6.00 µg/ml, the linear regression equation was y=89.610x+0.133, r=0.9999. The sampling absorption efficiencies were 98.33%-100.00%, the detection limit of the method was 0.005 µg/ml, the minimum detection concentration was 0.016 mg/m(3) (based on V(0)=3.0 L) . The recovery rates were 95.96%-102.44%, the intra batch precision were 4.36%-7.78%, and the inter batch precision were 4.96%-6.06%. Conclusion: The method has the advantages of simple operation, high sensitivity and good accuracy. It can prevent the loss and degradation of BUT. It can be used for the determination of BUT in the air of workplace.

Influence of etchant type on the shear bond strength of orthodontic brackets to enamel.

The aim of this study was to evaluate the influence of the type of etchant on the shear bond strength (SBS) of metallic brackets to enamel and the Adhesive Remnant Index (ARI) after debonding. A total of 30 mandibular and maxillary premolars were randomly distributed into groups (n = 10) treated with 1 of 3 enamel surface-conditioning agents: 35% phosphoric acid (PA), 35% glycolic acid (GA), or 35% ferulic acid (FA). The designated acid was applied to the buccal enamel surface of the tooth for 20 seconds, and the tooth was then rinsed with distilled water for 20 seconds and air dried for 5 seconds. A metal bracket was bonded to the prepared surface with light-cured orthodontic resin. After 24 hours, the bracket-tooth interface was submitted to SBS testing in a universal testing machine at a speed of 0.5 mm/min. After debonding, the enamel surface was observed under a stereomicroscope (×20 magnification) to determine the ARI. The generalized linear models showed that the PA and GA groups presented significantly higher SBSs than the FA group (P = 0.0003). The ARI was significantly higher in specimens treated with PA than with the other acids (P < 0.05; Kruskal-Wallis and Dunn tests), with a larger quantity of adhesive remaining adhered to the tooth. Both PA and GA are effective for bonding brackets, but GA resulted in a lower percentage of adhesive remnant adhered to the enamel.

Prolinyl Phosphoramidates of Nucleotides with Increased Reactivity.

Nucleoside monophosphates (NMPs) are the subunits of RNA. They are incorporated into growing complementary strands when sequences are copied in enzyme-free reactions using organic leaving groups at the phosphates. Amino acids are rarely considered as leaving groups, but proline can act as a leaving group when N-linked to NMPs, so that prolinyl NMPs hydrolyze in aqueous buffer at 37 °C, with half-life times as short as 2.4 h, and they act as monomers in enzyme-free primer extension. Still, their level of reactivity is insufficient for practical purposes, requiring months for some extensions. Herein we report the synthesis of eight substituted prolinyl AMPs together with seven related compounds and the results of a study of their reactivity. A δ-carboxy prolinyl NMP was found to be converted with a half-life time of just 11 min in magnesium-free buffer, and a δ-isopropyl prolinyl NMP was shown to react sevenfold faster than its prolinyl counterpart in enzyme-free genetic copying of RNA. Our results indicate that both anchimeric and steric effects can be employed to increase the reactivity of aminoacidyl nucleotides, i.e. compounds that combine two fundamental classes of biomolecules in one functional entity.

Protocol for producing phosphoramidate using phosphorus fluoride exchange click chemistry.

Phosphorus fluoride exchange (PFEx) is a catalytic click reaction that involves exchanging high oxidation state P-F bonds with alcohol and amine nucleophiles, reliably yielding P-O- and P-N-linked compounds. Here, we describe steps for preparing a phosphoramidic difluoride and performing two sequential PFEx reactions to yield a phosphoramidate through careful catalyst selection. We then detail procedures for handling and quenching potentially toxic P-F-containing compounds to ensure user safety when conducting PFEx reactions. For complete details on the use and execution of this protocol, please refer to Sun et al.1.

Phosphate Migration versus the Loss of Phosphoric Acid in Protonated Phosphopeptides: A Computational Study.

Residue-specific phosphorylation is a protein post-translational modification that regulates cellular functions. Experimental determination of the exact sites of protein phosphorylation provides an understanding of the signaling and processes at work for a given cellular state. Any experimental artifact that involves migration of the phosphate group during measurement is a concern, as the outcome can lead to erroneous conclusions that may confound studies on cellular signal transduction. Herein, we examine computationally the mechanism by which a phosphate group migrates from one serine residue to another serine in monoprotonated pentapeptides [BA-pSer-Gly-Ser-BB + H]+ → [BA-Ser-Gly-pSer-BB + H]+ (where BA and BB are different combinations of the three basic amino acids, histidine, lysine, and arginine). In addition to moving the phosphate group, the overall mechanism involves transferring a proton from the N-terminal amino acid, BA, to the C-terminal amino acid, BB. This is not a synchronous process, and there is a key high-energy intermediate, structure C, that is zwitterionic with both the basic amino acids protonated and the phosphate group attached to both serine residues and carrying a negative charge. The barriers to moving the phosphate group are calculated to be in the range of 219-274 kJ mol-1 at the B3LYP/6-31G(d) level. These barriers are systematically slightly lower and in good agreement with single-point energy calculations at both M06-2X/6-311++G(d,p) and MP2/6-31++G(d,p) levels. The competitive reaction, loss of phosphoric acid from the protonated pentapeptides, has a barrier in the range of 176-202 kJ mol-1 at the B3LYP/6-31G(d) level. Extension of the theory to M06-2X/6-311++G(d,p)//B3LYP/6-31G(d) and MP2/6-31++G(d,p)// B3LYP/6-31G(d) gives higher values for the loss of phosphoric acid, falling in the range of 196-226 kJ mol-1; these are comparable to the barriers against phosphate migration at the same levels of theory. For larger peptides His-pSer-(Gly)n-Ser-His, where n has values from 2 to 5, the barriers against the loss of phosphoric acid are higher than those against the phosphate group migration. This difference is most pronounced and significant when n = 4 and 5 (the differences are approximately 80 kJ mol-1 under the single-point energy calculations at the M06-2X and MP2 levels). Energy differences using two more recent functionals, M08-HX and MN15, on His-pSer-(Gly)n-Ser-His, where n = 1 and 5, are in good agreement with the M06-2X and MP2 calculations. These results provide the mechanistic rationale for phosphate migration versus other competing reactions in the gas phase under tandem mass spectrometry conditions.

Phosphoramidate Azole Oligonucleotides for Single Nucleotide Polymorphism Detection by PCR.

Detection of the Kirsten rat sarcoma gene (KRAS) mutational status is an important factor for the treatment of various malignancies. The most common KRAS-activating mutations are caused by single-nucleotide mutations, which are usually determined by using PCR, using allele-specific DNA primers. Oligonucleotide primers with uncharged or partially charged internucleotide phosphate modification have proved their ability to increase the sensitivity and specificity of various single nucleotide mutation detection. To enhance the specificity of single nucleotide mutation detection, the novel oligonucleotides with four types of uncharged and partially charged internucleotide phosphates modification, phosphoramide benzoazole (PABA) oligonucleotides (PABAO), was used to prove the concept on the KRAS mutation model. The molecular effects of different types of site-specific PABA modification in a primer or a template on a synthesis of full-length elongation product and PCR efficiency were evaluated. The allele-specific PCR (AS-PCR) on plasmid templates showed a significant increase in analysis specificity without changes in Cq values compared with unmodified primer. PABA modification is a universal mismatch-like disturbance, which can be used for single nucleotide polymorphism discrimination for various applications. The molecular insights of the PABA site-specific modification in a primer and a template affect PCR, structural features of four types of PABAO in connection with AS-PCR results, and improvements of AS-PCR specificity support the further design of novel PCR platforms for various biological targets testing.

The effect of the use of the deproteinization agent hypochlorous acid and two different pit and fissure sealant self-adhesive flowable composites upon its bonding with the enamel.

This study evaluates the effect of the deproteinization agents hypochlorous acid and sodium hypochlorite upon the bonding of the two different pit and fissure sealant, self-adhesive flowable composites with the enamel. Thirty-six third molars were randomly divided into six different groups. The groups were formed as follows: Group 1: 37% phosphoric acid + VertiseTM Flow; Group 2: 200 ppm hypochlorous acid + 37% phosphoric acid VertiseTM Flow; Group 3: 5.25% sodium hypochlorite + 37% phosphoric acid + VertiseTM Flow; Group 4: 37% phosphoric acid + Constic; Group 5: 200 ppm hypochlorous acid + 37% phosphoric acid + Constic; Group 6: 5.25% sodium hypochlorite + 37% phosphoric acid + Constic. In each group, samples were obtained that were rectangular prisms in shape (n = 12). Groups to which a deproteinization agent was applied (Groups 2, 3 and 5, 6) showed statistically higher microtensile bonding strength than Group 1, Group 4. There was no statistically significant difference in terms of microtensile bonding strength values between the Groups 3 and the Group 6. The study found that the groups to which deproteinization agents were applied had statistically higher microtensile bonding strength values compared with those groups to which acid and fissure sealants were applied. In this study, it was concluded that the use of fissure-sealing self-adhesive flowable composites after acid application to permanent tooth enamel provides an acceptable bond strength given the limitations of in vitro studies. In line with the results obtained, it was observed that in addition to the removal of the inorganic structure with the application of acid, the removal of the organic structure with the use of deproteinization agent increased the bond strength to the enamel.