Hydrophilic interaction liquid chromatography based method for simultaneous determination of purines and their derivatives in food spices

This work presents method for separation and quantification of adenine, guanine, xanthine, hypoxanthine, uric acid, and creatinine in food spices using hydrophilic interaction liquid chromatography with UV detection. Optimized conditions allowed separation with mobile phases containing acetonitrile and additives ammonium acetate (90:10, v/v, pH 6.1) or formate (90:10, v/v, pH 3.2). In food spices no uric acid was detected, creatinine (16 ± 2 μg g-1) was found only in instant dried yeast. The highest content of purines was determined in dried yeast (xanthine 110 ± 8 μg g-1, hypoxanthine 441 ± 24 μg g-1, adenine 84 ± 16 μg g-1, guanine 163 ± 12 μg g-1), high in curry, herbal pepper, and chicken seasoning, the lowest concentration was in black pepper (hypoxanthine 12 ± 2 μg g-1, adenine 27 ± 3 μg g-1). To best of our knowledge, no such complementary method and obtained data have been reported so far.

Exposure of children to brominated flame retardants and heavy metals in Morocco: Urine and blood levels in association with global cytosine and adenine methylation

Persistent pollutants, namely brominated flame retardants (BFRs) and heavy metals, are compounds that are added to a wide range of products and materials for preventing ignition, increasing the functionality of materials or improving their performance, e.g. electric conductivity. The exposure of children might consequently be inferred, through indoor dust and hand-to-mouth or toy-chewing behaviors. The current study is aimed at assessing the exposure of Moroccan children to BFRs and heavy metal elements, and evaluating their associations with global DNA methylation. First, parents responded to a questionnaire pertaining to children's lifestyle, then blood and urine samples were collected from (n = 93) children aged between 5 and 11 years for biomonitoring and DNA methylation analysis. BFRs were detected in 54.84% of samples with a median concentration of 0.01 nmol/mL (range: 0.004-0.051 nmol/mL) while metal elements were detected in more than 90% of samples. BFRs showed no variations with global DNA methylation, unlike metal elements, which revealed significant associations with global DNA methylation markers, namely 5-mC, 5-hmC and N⁶-mA levels. Moroccan children may be exposed to flame retardants and heavy metals through several routes. Further research is required to assess the exposure and the health impacts of environmental pollutants and ultimately protect the Moroccan population by the prevention of adverse health effects.

Exploiting Purine as an Internal Standard for SERS Quantification of Purine Derivative Molecules Released by Bacteria

Surface-enhanced Raman scattering (SERS) is a highly sensitive technique used in diverse biomedical applications including rapid antibiotic susceptibility testing (AST). However, signal fluctuation in SERS, particularly the widespread of signals measured from different batches of SERS substrates, compromises its reliability and introduces potential errors in SERS-AST. In this study, we investigate the use of purine as an internal standard (IS) to recalibrate SERS signals and quantify the concentrations of two important purine derivatives, adenine and hypoxanthine, which are the most important biomarkers used in SERS-AST. Our findings demonstrate that purine IS effectively mitigates SERS signal fluctuations and enables accurate prediction of adenine and hypoxanthine concentrations across a wide range (5 orders of magnitude). Calibrations with purine as an IS outperform those without, exhibiting a 10-fold increase in predictive accuracy. Additionally, the calibration curve obtained from the first batch of SERS substrates remains effective for 64 additional substrates fabricated over a half-year period. Measurements of adenine and hypoxanthine concentrations in bacterial supernatants using SERS with purine IS closely align with the liquid chromatography-mass spectrometry results. The use of purine as an IS offers a simple and robust platform to enhance the speed and accuracy of SERS-AST, while also paving the way for in situ SERS quantification of purine derivatives released by bacteria under various stress conditions.

Genome-wide DNA N6-adenine methylation in sea buckthorn (Hippophae rhamnoides L.) fruit development

As a new epigenetic mark, DNA N6-adenine (6mA) methylation plays an important role in various biological processes and has been reported in many prokaryotic organisms in recent years. However, the distribution patterns and functions of DNA 6mA modification have been poorly studied in non-model crops. In this study, we observed that the methylation ratio of 6mA was about 0.016% in the sea buckthorn (Hippophae rhamnoides L.) genome using mass spectrometry. We first constructed a comprehensive 6mA landscape in sea buckthorn genome using nanopore sequencing at single-base resolution. Distribution analysis suggested that 6mA methylated sites were widely distributed in the sea buckthorn chromosomes, which were similar to those in Arabidopsis and rice. Furthermore, reduced 6mA DNA methylation is associated with different expression of genes related to the fruit-ripening process in sea buckthorn. Our results revealed that 6mA DNA modification could be considered an important epigenomic mark and contributes to the fruit ripening process in plants.

Incorporation of a FRET Pair into a Riboswitch RNA to Measure Mg2+ Concentration and RNA Conformational Change in Cell

Riboswitches are natural biosensors that can regulate gene expression by sensing small molecules. Knowledge of the structural dynamics of riboswitches is crucial to elucidate their regulatory mechanism and develop RNA biosensors. In this work, we incorporated the fluorophore, Cy3, and its quencher, TQ3, into a full-length adenine riboswitch RNA and its isolated aptamer domain to monitor the dynamics of the RNAs in vitro and in cell. The adenine riboswitch was sensitive to Mg²⁺ concentrations and could be used as a biosensor to measure cellular Mg²⁺ concentrations. Additionally, the TQ3/Cy3-labeled adenine riboswitch yielded a Mg²⁺ concentration that was similar to that measured using a commercial assay kit. Furthermore, the fluorescence response to the adenine of the TQ3/Cy3-labeled riboswitch RNA was applied to determine the proportions of multiple RNA conformational changes in cells. The strategy developed in this work can be used to probe the dynamics of other RNAs in cells and may facilitate the developments of RNA biosensors, drugs and engineering.

Surface-enhanced Raman scattering of DNA bases using frozen silver nanoparticle dispersion as a platform

Raman spectroscopy is a powerful method to characterize molecules in various media. Although surface-enhanced Raman scattering (SERS) is often employed to compensate for the intrinsically poor sensitivity of Raman spectroscopy, there remain serious tasks, such as simple preparations of SERS substrates, sensitivity control, and reproducible measurements. Here, we propose freezing as an efficient way to overcome these problems in SERS measurements using DNA bases as model targets. Solutes are expelled from ice crystals and concentrated in the liquid phase upon freezing. Silver nanoparticles (AgNPs) are also concentrated in the liquid phase to aggregate with Raman target analytes. The SERS signal intensity is maximized when the AgNP concentration exceeds the critical aggregation value. Freezing allows up to 5000 times enhancements of the SERS signal. Thus, an efficient SERS platform is prepared by simple freezing. The simultaneous detection of four DNA bases effectively eliminates variations of signal intensities and allows the reliable determination of concentration ratios.

Quantitative analysis of m6A RNA modification by LC-MS

N6-adenosine methylation (m6A) of messenger RNA (mRNA) plays key regulatory roles in gene expression. Accurate measurement of m6A levels is thus critical to understand its dynamic changes in various biological settings. Here, we provide a protocol to quantitate the levels of adenosine and m6A in cellular mRNAs. Using nuclease and phosphatase, we digest mRNA into nucleosides, which are subsequently quantified using liquid chromatography mass spectrometry. For complete details on the use and execution of this protocol, please refer to Cho et al. (2021).

Tenofovir and emtricitabine concentrations in hair are comparable between individuals on tenofovir disoproxil fumarate versus tenofovir alafenamide-based ART

Tenofovir disoproxil fumarate (TDF) in combination with emtricitabine (FTC) is the backbone for both human immunodeficiency virus (HIV) treatment and pre-exposure prophylaxis (PrEP) worldwide. Tenofovir alafenamide (TAF) with FTC is increasingly used in HIV treatment and was recently approved for PrEP among men-who-have-sex-with-men. TDF and TAF are both metabolized into tenofovir (TFV). Antiretrovirals in plasma are taken up into hair over time, with hair levels providing a long-term measure of adherence. Here, we report a simple, robust, highly sensitive, and validated high-performance liquid chromatography coupled with tandem mass spectrometry (LC/MS/MS)-based analytical method for analyzing TFV and FTC from individuals on either TDF/FTC or TAF/FTC in small hair samples. TFV/FTC are extracted from ~5 mg hair and separated on a column using a gradient elution. The lower quantification limits are 0.00200 (TFV) and 0.0200 (FTC) ng/mg hair; the assay is linear up to 0.400 (TFV) and 4.00 (FTC) ng/mg hair. The intra-day and inter-day coefficients of variance (CVs) are 5.39-12.6% and 6.40-13.5% for TFV and 0.571-2.45% and 2.45-5.16% for FTC. TFV concentrations from participants on TDF/FTC-based regimens with undetectable plasma HIV RNA were 0.0525 ± 0.0295 ng/mg, whereas those from individuals on TAF/FTC-based regimens were 0.0426 ± 0.0246 ng/mg. Despite the dose of TFV in TDF being 10 times that of TAF, hair concentrations of TFV were not significantly different for those on TDF versus TAF regimens. Pharmacological enhancers (ritonavir and cobicistat) did not boost TFV concentrations in hair. In summary, we developed and validated a sensitive analytical method to analyze TFV and FTC in hair and found that hair concentrations of TFV were essentially equivalent among those on TDF and TAF.

Decoding the epitranscriptional landscape from native RNA sequences

Traditional epitranscriptomics relies on capturing a single RNA modification by antibody or chemical treatment, combined with short-read sequencing to identify its transcriptomic location. This approach is labor-intensive and may introduce experimental artifacts. Direct sequencing of native RNA using Oxford Nanopore Technologies (ONT) can allow for directly detecting the RNA base modifications, although these modifications might appear as sequencing errors. The percent Error of Specific Bases (%ESB) was higher for native RNA than unmodified RNA, which enabled the detection of ribonucleotide modification sites. Based on the %ESB differences, we developed a bioinformatic tool, epitranscriptional landscape inferring from glitches of ONT signals (ELIGOS), that is based on various types of synthetic modified RNA and applied to rRNA and mRNA. ELIGOS is able to accurately predict known classes of RNA methylation sites (AUC > 0.93) in rRNAs from Escherichiacoli, yeast, and human cells, using either unmodified in vitro transcription RNA or a background error model, which mimics the systematic error of direct RNA sequencing as the reference. The well-known DRACH/RRACH motif was localized and identified, consistent with previous studies, using differential analysis of ELIGOS to study the impact of RNA m6A methyltransferase by comparing wild type and knockouts in yeast and mouse cells. Lastly, the DRACH motif could also be identified in the mRNA of three human cell lines. The mRNA modification identified by ELIGOS is at the level of individual base resolution. In summary, we have developed a bioinformatic software package to uncover native RNA modifications.

Silver-Based SERS Pico-Molar Adenine Sensor

Adenine is an important molecule for biomedical and agricultural research and applications. The detection of low concentration adenine molecules is thus desirable. Surface-enhanced Raman scattering (SERS) is a promising label-free detection and fingerprinting technique for molecules of significance. A novel SERS sensor made of clusters of silver nanostructures deposited on copper bumps in valleys of an etched silicon substrate was previously reported to exhibit a low and reproducible detection limit for a 10⁻¹¹ M neutral adenine aqueous solution. Reflection of laser illumination from the silicon surface surrounding a valley provides additional directions of laser excitation to adenine molecules adsorbing on a silver surface for the generation of enhanced SERS signal strength leading to a low detection limit. This paper further reports a concentration dependent shift of the ring-breathing mode SERS adenine peak towards 760 cm⁻¹ with decreasing concentration and its pH-dependent SERS signal strength. For applications, where the pH value can vary, reproducible detection of 10⁻¹² M adenine in a pH 9 aqueous solution is feasible, making the novel SERS structure a desirable pico-molar adenine sensor.

Ground and Excited States of Gas-Phase DNA Nucleobase Cation-Radicals. A UV-vis Photodisociation Action Spectroscopy and Computational Study of Adenine and 9-Methyladenine

Cation radicals of adenine (A^•+) and 9-methyladenine (MA^•+) were generated in the gas phase by collision-induced intramolecular electron transfer in copper-terpyridine-nucleobase ternary complexes and characterized by collision-induced dissociation (CID) mass spectra and UV-vis photodissociation action spectroscopy in the 210-700 nm wavelength region. The action spectra of both A^•+ and MA^•+ displayed characteristic absorption bands in the near-UV and visible regions. Another tautomer of A^•+ was generated as a minor product by multistep CID of protonated 9-(2-bromoethyl)adenine. Structure analysis by density functional theory and coupled-clusters ab initio calculations pointed to the canonical 9-H-tautomer Ad1^•+ as the global energy minimum of adenine cation radicals. The canonical tautomer MA1^•+ was also calculated to be a low-energy structure among methyladenine cation radicals. However, two new noncanonical tautomers were found to be energetically comparable to MA1^•+. Vibronic absorption spectra were calculated for several tautomers of A^•+ and MA^•+ and benchmarked on equation-of-motion coupled-clusters excited-state calculations. Analysis of the vibronic absorption spectra of A^•+ tautomers pointed to the canonical tautomer Ad1^•+ as providing the best match with the action spectrum. Likewise, the canonical tautomer MA1^•+ was the unequivocal best match for the MA^•+ ion generated in the gas phase. According to potential-energy mapping, MA1^•+ was separated from energetically favorable noncanonical cation radicals by a high-energy barrier that was calculated to be above the dissociation threshold for loss of a methyl hydrogen atom, thus preventing isomerization. Structures and energetics of all four DNA nucleobase cation radicals are compared and discussed.

Silver SERS Adenine Sensors with a Very Low Detection Limit

The detection of adenine molecules at very low concentrations is important for biological and medical research and applications. This paper reports a silver-based surface-enhanced Raman scattering (SERS) sensor with a very low detection limit for adenine molecules. Clusters of closely packed silver nanoparticles on surfaces of discrete ball-like copper bumps partially covered with graphene are deposited by immersion in silver nitrate. These clusters of silver nanoparticles exhibit abundant nanogaps between nanoparticles, where plasmonic coupling induces very high local electromagnetic fields. Silver nanoparticles growing perpendicularly on ball-like copper bumps exhibit surfaces of large curvature, where electromagnetic field enhancement is high. Between discrete ball-like copper bumps, the local electromagnetic field is low. Silver is not deposited on the low-field surface area. Adenine molecules interact with silver by both electrostatic and functional groups and exhibit low surface diffusivity on silver surface. Adenine molecules are less likely to adsorb on low-field sensor surface without silver. Therefore, adenine molecules have a high probability of adsorbing on silver surface of high local electric fields and contribute to the measured Raman scattering signal strength. We demonstrated SERS sensors made of clusters of silver nanoparticles deposited on discrete ball-like copper bumps with very a low detection limit for detecting adenine water solution of a concentration as low as 10⁻¹¹ M.

DNA N6-methyladenine increased in human esophageal squamous cell carcinoma

Esophageal cancer is one of the most common malignancies worldwide. DNA N6-methyladenine (6mA) has been well-studied in prokaryotes, while the distribution and biological functions of DNA 6mA in eukaryotic cells remain to be elucidated. Recently, DNA 6mA epigenetic modification was found in human gastric and liver cancers. To explore the status of DNA 6mA epigenetic modification in esophageal cancer, 101 cases of human esophageal squamous cell carcinoma (ESCC) and matched adjacent normal tissue samples were analyzed by dot blot assay. The levels of genomic DNA 6mA were significantly higher in ESCC tissue samples than in matched adjacent normal tissue samples (P<0.001). Increased DNA 6mA was associated with poor tumor differentiation (P<0.05), while no association was found between 6mA modification and gender, age, tumor size, TNM stage, lymph node metastasis, smoking, alcohol intake, or family history (all P>0.05). In conclusion, DNA 6mA epigenetic modification increased in human ESCC and may serve as a prognostic marker.

Voltammetric determination of adefovir dipivoxil by using a nanocomposite prepared from molecularly imprinted poly(o-phenylenediamine), multi-walled carbon nanotubes and carbon nitride

An electrochemical sensor for adefovir dipivoxil (ADV) detection was prepared by electropolymerization of o-phenylenediamine in the presence of ADV on a glassy carbon electrode modified with multi-walled carbon nanotubes and carbon nitride. The electrode was characterized by field emission scanning electron microscopy and differential pulse voltammetry. The performance was optimized by response surface methodology. The changes in differential pulse voltammetric peak currents of the redox probe, ferricyanide, were linear to ADV concentrations in the range from 0.1 to 9.9 μmol L^-1, with the detection limit of 0.05 μmol L^-1 (S/N = 3). The sensor was applied to the determination of ADV in drug formulations, human serum and urine samples. It is selective due to the use of an imprinted material, well reproducible, long-term stable, and regenerable. Graphical abstract By merging the unique properties of carbon nitride with intrinsic properties of MWCNTs, and molecularly imprinted polymers, a novel electrochemical sensor with selective binding sites was prepared for determination of adefovir dipivoxil in pharmaceutical and biological samples.

Using artificial neural network and multivariate calibration methods for simultaneous spectrophotometric analysis of Emtricitabine and Tenofovir alafenamide fumarate in pharmaceutical formulation of HIV drug

Spectrophotometric analysis method based on artificial neural network (ANN), partial least squares regression (PLS) and principal component regression (PCR) models was proposed for the simultaneous determination of Emtricitabine (ETB) and Tenofovir alafenamide fumarate (TAF) in human immunodeficiency virus (HIV) drug. An artificial neural network consisting of two, five, and seven layers with 2,3,5,7, and 9 neurons was trained by applying a feed forward back-propagation learning. In this method, Levenberg-Marquardt (LM) and gradient descent with momentum and adaptive learning rate back propagation (GDX) algorithms were used. Statistical parameters indicated that the ability of LM was better than GDX algorithm. Also, root mean square error (RMSE) and recovery (%) of the PLS and PCR methods showed that PLS has worked better than PCR. The proposed models were compared to the high- performance liquid chromatography (HPLC) as a reference method. Furthermore, the obtained results of the one-way analysis of variance (ANOVA) test at the 95% confidence level represented that there was no significant difference between the proposed and reference methods.

Real Time Normalization of Fast Photochemical Oxidation of Proteins Experiments by Inline Adenine Radical Dosimetry

Hydroxyl radical protein footprinting (HRPF) is a powerful method for measuring protein topography, allowing researchers to monitor events that alter the solvent accessible surface of a protein (e.g., ligand binding, aggregation, conformational changes, etc.) by measuring changes in the apparent rate of reaction of portions of the protein to hydroxyl radicals diffusing in solution. Fast Photochemical Oxidation of Proteins (FPOP) offers an ultrafast benchtop method for radical generation for HRPF, photolyzing hydrogen peroxide using a UV laser to generate high concentrations of hydroxyl radicals that are consumed on roughly a microsecond time scale. The broad reactivity of hydroxyl radicals means that almost anything added to the solution (e.g., ligands, buffers, excipients, etc.) will scavenge hydroxyl radicals, altering their half-life and changing the effective radical concentration experienced by the protein. Similarly, minute changes in peroxide concentration, laser fluence, and buffer composition can alter the effective radical concentration, making reproduction of data challenging. Here, we present a simple method for radical dosimetry that can be carried out as part of the FPOP workflow, allowing for measurement of effective radical concentration in real time. Additionally, by modulating the amount of radical generated, we demonstrate that effective hydroxyl radical yields in FPOP HRPF experiments carried out in buffers with widely differing levels of hydroxyl radical scavenging capacity can be compensated on the fly, yielding statistically indistinguishable results for the same conformer. This method represents a major step in transforming FPOP into a robust and reproducible technology capable of probing protein structure in a wide variety of contexts.

Recurrence rates of urinary calculi according to stone composition and morphology

Few studies have examined the relative risk of recurrence of different stone types. The object of the present study was to evaluate the tendency for stone recurrence as a function of major mineral composition of the stones and morphological characteristics of the stones. This study was carried out using 38,274 stones for which we had data available to specify if the stone was from the first or a subsequent urinary stone episode. Stones were analyzed for morphology by stereomicroscope and for composition by infrared spectroscopy. Overall, 42.7% of stones were from patients who had had a previous stone event, with these being more frequent in men (44.4%) than in women (38.9%, p < 0.0001). Age of first stone occurrence was lowest for dihydroxyadenine (15.7 ± 16.6 years) and highest for anhydrous uric acid (62.5 ± 14.9 years), with the average age of first stones of calcium oxalate falling in the middle (40.7 ± 14.6 years for calcium oxalate dihydrate, and 48.4 ± 15.1 years for calcium oxalate monohydrate, COM). By composition alone, COM was among the least recurrent of stones, with only 38.0% of COM stones coming from patients who had had a previous episode; however, when the different morphological types of COM were considered, type Ic-which displays a light color, budding surface and unorganized section-had a significantly greater rate of recurrence, at 82.4% (p < 0.0001), than did other morphologies of COM. Similarly, for stones composed of apatite, morphological type IVa2-a unique form with cracks visible beneath a glossy surface-had a higher rate of recurrence than other apatite morphologies (78.8 vs. 39-42%, p < 0.0001). Stone mineral type alone is insufficient for identifying the potential of recurrence of the stones. Instead, the addition of stone morphology may allow the diagnosis of highly recurrent stones, even among common mineral types (e.g., COM) that in general are less recurrent.

Multiporous molybdenum carbide nanosphere as a new charming electrode material for highly sensitive simultaneous detection of guanine and adenine

By introduction of Mo metal species (molybdenum-based polyoxometalates) into the Cu-MOF as co-precursor, molybdenum carbide nanosphere (Mo_xC@C) was prepared via a simple calcining routine and a further etching the metallic Cu process. The obtained Mo_xC@C showed a unique structure where well-dispersed Mo_xC nanoparticles (NPs) were encapsulated in porous carbon matrix. As-fabricated novel 3D porous architecture Mo_xC@C nanosphere exhibited a potent and persistent electro-oxidation behavior followed by well-separated oxidation peaks (peak to peak voltage is about 350 mV) toward adenine (A) and guanine (G) by differential pulse voltammetry (DPV). This excellent electrochemical performance can be attributed to the unique structure and composition of 3D Mo_xC@C. Furthermore, 3D Mo_xC@C also revealed high selectivity and sensitivity, good reproducibility, excellent stability and anti-interference ability. The calibration curves for quantitive analysis of G and A were obtained: 0.03-122 µM, and 0.02-122 µM, respectively, the detection limits were 0.0085 µM, 0.008 µM, respectively. The proposed procedure was successfully applied to detect G and A in human urine and serum samples with satisfactory recovery, which manifests its viability application for practical analysis.

Continuous Fluorescence Assays for Reactions Involving Adenine

5'-Methylthioadenosine phosphorylase (MTAP) and 5'-methylthioadenosine nucleosidase (MTAN) catalyze the phosphorolysis and hydrolysis of 5'-methylthioadenosine (MTA), respectively. Both enzymes have low KM values for their substrates. Kinetic assays for these enzymes are challenging, as the ultraviolet absorbance spectra for reactant MTA and product adenine are similar. We report a new assay using 2-amino-5'-methylthioadenosine (2AMTA) as an alternative substrate for MTAP and MTAN enzymes. Hydrolysis or phosphorolysis of 2AMTA forms 2,6-diaminopurine, a fluorescent and easily quantitated product. We kinetically characterize 2AMTA with human MTAP, bacterial MTANs and use 2,6-diaminopurine as a fluorescent substrate for yeast adenine phosphoribosyltransferase. 2AMTA was used as the substrate to kinetically characterize the dissociation constants for three-transition-state analogue inhibitors of MTAP and MTAN. Kinetic values obtained from continuous fluorescent assays with MTA were in good agreement with previously measured literature values, but gave smaller experimental errors. Chemical synthesis from ribose and 2,6-dichloropurine provided crystalline 2AMTA as the oxalate salt. Chemo-enzymatic synthesis from ribose and 2,6-diaminopurine produced 2-amino-S-adenosylmethionine for hydrolytic conversion to 2AMTA. Interaction of 2AMTA with human MTAP was also characterized by pre-steady-state kinetics and by analysis of the crystal structure in a complex with sulfate as a catalytically inert analogue of phosphate. This assay is suitable for inhibitor screening by detection of fluorescent product, for quantitative analysis of hits by rapid and accurate measurement of inhibition constants in continuous assays, and pre-steady-state kinetic analysis of the target enzymes.

HPLC-Based Metabolomic Analysis of Normal and Inflamed Gut

The idiopathic inflammatory bowel diseases, which include Crohn's disease and ulcerative colitis, are multifactorial chronic conditions that result in numerous perturbations of metabolism in the gastrointestinal mucosa. Thus, methodologies for the qualitative and quantitative analysis of small molecule metabolites in mucosal tissues are important for further elucidation of mechanisms driving inflammation and the metabolic consequences of inflammation. High-performance liquid chromatography (HPLC) is a ubiquitous analytical technique that can be adapted for both targeted and non-targeted metabolomic analysis. Here, protocols for reversed-phase (RP) HPLC-based methods using two different detection modalities are presented. Ultraviolet detection is used for the analysis of adenine nucleotide metabolites, whereas electrochemical detection is used for the analysis of multiple amino acid metabolites. These methodologies provide platforms for further characterization of the metabolic changes that occur during gastrointestinal inflammation.

[Determination of Nucleosides and Nucleobases in Natural, Cultured and Tissue Culture Anoectochilus roxburghii Using LC-MS]

OBJECTIVE

To establish a method for simultaneous determination of nucleosides and nucleobases in natural, cultured and tissue culture Anoectochilus roxburghii by high performance liquid chromatography-electrospray ionization/ion trap mass spectrometry (HPLC-ESI/MS).

METHODS

The separation was performed on a Welch Ultimate XB-C18 column (250 mm x 4.6 mm,5 μm). 20 mmol/L ammonium acetate solution and methanol were adopted as the mobile phase with gradient elution. The flow rate was 1.0 mL/min. The injection volume was 20 μL. The column temperature and UV wavelength were set at 30 degrees C and 260 nm, respectively.

RESULTS

Cytosine, uracil, cytidine, uridine, hypoxanthine, adenine, inosine, guanosine,fl-thymidine and adenosine were identified in natural, cultured and tissue culture Anoectochilus roxburghii. The total content of nucleosides and nucleotides in Anoectochilus roxburghii were 1.6639, 1.8568 and 2.2013 mg/g,respectively.

CONCLUSION

The contents of nucleosides and nucleobases in herb are affected by its growth pattern. The total content of nucleosides and nucleotides was tissue culture herb > cultured herb > natural herb. This investigation would provide the theoretic basis for quality standards and applications of Anoectochilus roxburghii in clinical research.

Nucleobase Recognition by Truncated α-Hemolysin Pores

The α-hemolysin (αHL) protein nanopore has been investigated previously as a base detector for the strand sequencing of DNA and RNA. Recent findings have suggested that shorter pores might provide improved base discrimination. New work has also shown that truncated-barrel mutants (TBM) of αHL form functional pores in lipid bilayers. Therefore, we tested TBM pores for the ability to recognize bases in DNA strands immobilized within them. In the case of TBMΔ6, in which the barrel is shortened by ∼16 Å, one of the three recognition sites found in the wild-type pore, R1, was almost eliminated. With further mutagenesis (Met113 → Gly), R1 was completely removed, demonstrating that TBM pores can mediate sharpened recognition. Remarkably, a second mutant of TBMΔ6 (Met113 → Phe) was able to bind the positively charged β-cyclodextrin, am7βCD, unusually tightly, permitting the continuous recognition of individual nucleoside monophosphates, which would be required for exonuclease sequencing mediated by nanopore base identification.

Synthesis and applications of RNAs with position-selective labelling and mosaic composition

Knowledge of the structure and dynamics of RNA molecules is critical to understanding their many biological functions. Furthermore, synthetic RNAs have applications as therapeutics and molecular sensors. Both research and technological applications of RNA would be dramatically enhanced by methods that enable incorporation of modified or labelled nucleotides into specifically designated positions or regions of RNA. However, the synthesis of tens of milligrams of such RNAs using existing methods has been impossible. Here we develop a hybrid solid-liquid phase transcription method and automated robotic platform for the synthesis of RNAs with position-selective labelling. We demonstrate its use by successfully preparing various isotope- or fluorescently labelled versions of the 71-nucleotide aptamer domain of an adenine riboswitch for nuclear magnetic resonance spectroscopy or single-molecule Förster resonance energy transfer, respectively. Those RNAs include molecules that were selectively isotope-labelled in specific loops, linkers, a helix, several discrete positions, or a single internal position, as well as RNA molecules that were fluorescently labelled in and near kissing loops. These selectively labelled RNAs have the same fold as those transcribed using conventional methods, but they greatly simplify the interpretation of NMR spectra. The single-position isotope- and fluorescently labelled RNA samples reveal multiple conformational states of the adenine riboswitch. Lastly, we describe a robotic platform and the operation that automates this technology. Our selective labelling method may be useful for studying RNA structure and dynamics and for making RNA sensors for a variety of applications including cell-biological studies, substance detection, and disease diagnostics.