Selective regulation of human TRAAK channels by biologically active phospholipids.

TRAAK is an ion channel from the two-pore domain potassium (K2P) channel family with roles in maintaining the resting membrane potential and fast action potential conduction. Regulated by a wide range of physical and chemical stimuli, the affinity and selectivity of K2P4.1 toward lipids remains poorly understood. Here we show the two isoforms of K2P4.1 have distinct binding preferences for lipids dependent on acyl chain length and position on the glycerol backbone. The channel can also discriminate the fatty acid linkage at the SN1 position. Of the 33 lipids interrogated using native mass spectrometry, phosphatidic acid had the lowest equilibrium dissociation constants for both isoforms of K2P4.1. Liposome potassium flux assays with K2P4.1 reconstituted in defined lipid environments show that those containing phosphatidic acid activate the channel in a dose-dependent fashion. Our results begin to define the molecular requirements for the specific binding of lipids to K2P4.1.

Synthesis of Nucleoside-like Molecules from a Pyrolysis Product of Cellulose and Their Computational Prediction as Potential SARS-CoV-2 RNA-Dependent RNA Polymerase Inhibitors.

(1R,5S)-1-Hydroxy-3,6-dioxa-bicyclo[3.2.1]octan-2-one, available by an efficient catalytic pyrolysis of cellulose, has been applied as a chiral building block in the synthesis of seven new nucleoside analogues, with structural modifications on the nucleobase moiety and on the carboxyl- derived unit. The inverted configuration by Mitsunobu reaction used in their synthesis was verified by 2D-NOESY correlations, supported by the optimized structure employing the DFT methods. An in silico screening of these compounds as inhibitors of SARS-CoV-2 RNA-dependent RNA polymerase has been carried out in comparison with both remdesivir, a mono-phosphoramidate prodrug recently approved for COVID-19 treatment, and its ribonucleoside metabolite GS-441524. Drug-likeness prediction and data by docking calculation indicated compound 6 [=(3S,5S)-methyl 5-(hydroxymethyl)-3-(6-(4-methylpiperazin-1-yl)-9H-purin-9-yl)tetrahydrofuran-3-carboxylate] as the best candidate. Furthermore, molecular dynamics simulation showed a stable interaction of structure 6 in RNA-dependent RNA polymerase (RdRp) complex and a lower average atomic fluctuation than GS-441524, suggesting a well accommodation in the RdRp binding pocket.

m6A regulator-mediated RNA methylation modification patterns are involved in immune microenvironment regulation of periodontitis.

The role of epigenetic regulation in immunity is emerging, especially for RNA N6-methyladenosine (m6A) modification. However, little is known about the role of m6A in the regulation of the immune microenvironment of periodontitis. Thus, we aim to investigate the impact of m6A modification in periodontitis immune microenvironment. The RNA modification patterns mediated by 23 m6A-regulators were systematically evaluated in 310 periodontitis samples. The impact of m6A modification on immune microenvironment characteristics was explored, including infiltrating immunocytes, immune reaction gene-sets and HLAs (human leukocyte antigen) gene. m6A phenotype-related immune genes were also identified. 17 m6A regulators were dysregulated and a 15-m6A regulator signature can well distinguish periodontitis and control samples. ALKBH5 and FMR1 are closely related to infiltrating monocyte abundance. ELAVL1 and CBLL1 are significant regulators in immune reaction of TNF_Family_Members_Receptors and Cytokine. The expression of HLA-B and HLA-DOA is affected by ALKBH5 and LRPPRC. 3 distinct RNA modification patterns mediated by 23 m6A regulators were identified. They differ from immunocyte abundance, immune reaction and HLA gene. 1631 m6A phenotype-related genes and 70 m6A-mediated immune genes were identified, and the biological functions of these were explored. Our finding demonstrated the m6A modification plays a crucial role in the diversity and complexity of the immune microenvironment of periodontitis.

In situ label-free and sensitive detection assay for cell apoptosis via polyadenosine-coralyne fluorescence enhancement strategy.

Cell apoptosis detection is vital for biological analysis and clinical application; some detection assays are already commercially available. However, it is still far from perfect and needs further improvement for less cost, time-consuming and operation demanding. TUNEL, a high market share cell apoptosis assay, depends on adulteration fluorescent labelling dUTP by terminal deoxynucleotidyl transferase(TdT) which randomly adds deoxyribonucleoside triphosphates (dNTPs) at the 3'-OH terminal of ssDNA with a template-free manner. Based on our previous work, we adopted a label-free strategy to reduce the cost and operation maintenance of TUNEL and developed a facile, rapid, convenient and in-situ assay for cell apoptosis.

Anomalous Reverse Transcription through Chemical Modifications in Polyadenosine Stretches.

Thermostable reverse transcriptases are workhorse enzymes underlying nearly all modern techniques for RNA structure mapping and for the transcriptome-wide discovery of RNA chemical modifications. Despite their wide use, these enzymes' behaviors at chemical modified nucleotides remain poorly understood. Wellington-Oguri et al. recently reported an apparent loss of chemical modification within putatively unstructured polyadenosine stretches modified by dimethyl sulfate or 2' hydroxyl acylation, as probed by reverse transcription. Here, reanalysis of these and other publicly available data, capillary electrophoresis experiments on chemically modified RNAs, and nuclear magnetic resonance spectroscopy on (A)12 and variants show that this effect is unlikely to arise from an unusual structure of polyadenosine. Instead, tests of different reverse transcriptases on chemically modified RNAs and molecules synthesized with single 1-methyladenosines implicate a previously uncharacterized reverse transcriptase behavior: near-quantitative bypass through chemical modifications within polyadenosine stretches. All tested natural and engineered reverse transcriptases (MMLV; SuperScript II, III, and IV; TGIRT-III; and MarathonRT) exhibit this anomalous bypass behavior. Accurate DMS-guided structure modeling of the polyadenylated HIV-1 3' untranslated region requires taking into account this anomaly. Our results suggest that poly(rA-dT) hybrid duplexes can trigger an unexpectedly effective reverse transcriptase bypass and that chemical modifications in mRNA poly(A) tails may be generally undercounted.

Head-to-head comparative pharmacokinetic and biodistribution (PK/BD) study of two dexamethasone prodrug nanomedicines on lupus-prone NZB/WF1 mice.

HPMA copolymer-based dexamethasone prodrug (P-Dex) and PEG-based dexamethasone prodrug (PEG-Dex, ZSJ-0228) were previously found to passively target the inflamed kidney and provide potent and sustained resolution of nephritis in NZB/WF1 lupus-prone mice. While both prodrug nanomedicines effectively ameliorate lupus nephritis, they have demonstrated distinctively different safety profiles. To explore the underlining mechanisms of these differences, we conducted a head-to-head comparative PK/BD study of P-Dex and PEG-Dex on NZB/WF1 mice. Overall, the systemic organ/tissue exposures to P-Dex and Dex released from P-Dex were found to be significantly higher than those of PEG-Dex. The high prodrug concentrations were sustained in kidney for only 24 h, which cannot explain their lasting therapeutic efficacy (>1 month). P-Dex showed sustained presence in liver, spleen and adrenal gland, while the presence of PEG-Dex in these organs was transient. This difference in PK/BD profiles may explain PEG-Dex' superior safety than P-Dex.

Label-free and sensitive detection assay for terminal deoxynucleotidyl transferase via polyadenosine-coralyne fluorescence enhancement strategy.

Terminal deoxynucleotidyl transferase (TdT) is a unique template-free polymerase that randomly adds multiple deoxyribonucleoside triphosphates (dNTPs) to the 3'-OH terminus of ssDNA. This characteristic makes TdT a versatile enzymatic tool in many fields. Moreover, aberrant TdT expression is a well-recognized biomarker of several leukemic diseases and is related to carcinogenesis. In this study, we developed a facile, rapid, label-free, and convenient assay for TdT detection. TdT-generated poly A tails formed a fluorescent enhancement complex in the presence of coralyne. To achieve a better signal-to-noise ratio, we used potassium thiocyanate (KSCN), instead of other halogen anions (KCl, KBr, KI, NaI) as the quenching agent of dissociate coralyne. Our results demonstrate that this assay is extremely facile, rapid, and label-free; at levels as low as 0.025 U/mL, TdT was distinctly detected within 55 min. And the determination of TdT activity in RBL-2H3 and Reh cells lysates exhibited a good sensing performance, demonstrating its potential applications in biochemical research and clinical diagnosis.

Effect of the Structure of Therapeutic Adenosine Analogues on Stability and Surface Electrostatic Potential of their Complexes with Poly(propyleneimine) Dendrimers.

Poly(propyleneimine) glycodendrimers are proposed as nanocarriers for triphosphate forms of anticancer adenosine analogues to improve the efficiency of chemotherapy and to overcome drug resistance mechanisms. This approach has proven successful for fludarabine administration-an autonomous way of cellular entry of a nucleotide-dendrimer noncovalent complex enables an increase in the intracellular accumulation and cytotoxic activity of the active metabolite of the drug. However, the attempt to apply an analogous strategy for clofarabine results in the inhibition of drug activity. To better understand this phenomenon, characterization and comparison of drug-dendrimer complexes were needed to indicate the differences in their surface properties and the strengths of fludarabine-dendrimer and clofarabine-dendrimer interactions. Here, zeta potential measurements, ultrafiltration, and asymmetric flow field-flow fractionation are applied to determine the surface electrostatic potential and stability of nucleotide-dendrimer formulations. This approach significantly extends the authors' research on the complexation potential of perfectly branched macromolecules, ultimately explaining previously observed differences and their consequences.

Electrochemical competitive immunodetection of messenger RNA modified with N6-methyladenosine by using DNA-modified mesoporous PtCo nanospheres.

N6-Methyladenosine (m6A) is the most abundant RNA modification in eukaryotic messenger RNA (mRNA). A highly sensitive electrochemical immunosensor is described for the determination of m6A-RNA. The method is based on the use of antibody (anti-m6A) and PtCo mesoporous nanospheres (MPNs). The analogously modified probe of type m6A-DNA-PtCo competes with m6A-RNA for antibodies on the gold electrode as an electrical signal probe. The electrical signal, best acquired at a working potential of -0.37 V (vs. Ag/AgCl) reflects the concentration of m6A. The PtCo MPNs catalyze the reduction of H2O2, and this amplifies the current and enhances sensitivity. The detection time of the assay is <1.5 h. Under optimal conditions, response is linear in the 0.005 to 100 nM m6A RNA concentration range, and the detection limit is 2.1 pM. The results obtained by this immunoassay with human cell lines are comparable to those obtained with a commercial kit. Graphical abstractSchematic representation of a method for electrochemical determination of m6A-modified mRNA. Anti-m6A Ab: antibody against m6A; BSA: bovine serum albumin; PtCo: PtCo mesoporous nanospheres; SH-m6A-DNA: DNA modified with both m6A and thiol groups; DPV: differential pulse voltammetry.

Response-Retaliation Behavior in Synthetic Protocell Communities.

Two different artificial predation strategies are spatially and temporally coupled to generate a simple tit-for-tat mechanism in a ternary protocell network capable of antagonistic enzyme-mediated interactions. The consortium initially consists of protease-sensitive glucose-oxidase-containing proteinosomes (1), non-interacting pH-sensitive polypeptide/mononucleotide coacervate droplets containing proteinase K (2), and proteinosome-adhered pH-resistant polymer/polysaccharide coacervate droplets (3). On receiving a glucose signal, secretion of protons from 1 triggers the disassembly of 2 and the released protease is transferred to 3 to initiate a delayed contact-dependent killing of the proteinosomes and cessation of glucose oxidase activity. Our results provide a step towards complex mesoscale dynamics based on programmable response-retaliation behavior in artificial protocell consortia.

The Optimal PEG for Kidney Preservation: A Preclinical Porcine Study.

University of Wisconsin (UW) solution is not optimal for preservation of marginal organs. Polyethylene glycol (PEG) could improve protection. Similarly formulated solutions containing either 15 or 20 g/L PEG 20 kDa or 5, 15 and 30 g/L PEG 35 kDa were tested in vitro on kidney endothelial cells, ex vivo on preserved kidneys, and in vivo in a pig kidney autograft model. In vitro, all PEGs provided superior preservation than UW in terms of cell survival, adenosine triphosphate (ATP) production, and activation of survival pathways. Ex vivo, tissue injury was lower with PEG 20 kDa compared to UW or PEG 35 kDa. In vivo, function recovery was identical between UW and PEG 35 kDa groups, while PEG 20 kDa displayed swifter recovery. At three months, PEG 35 kDa 15 and 30 g/L animals had worse outcomes than UW, while 5 g/L PEG 35 kDa was similar. PEG 20 kDa was superior to both UW and PEG 35 kDa in terms of function and fibrosis development, with low activation of damage pathways. PEG 20 kDa at 15 g/L was superior to 20 g/L. While in vitro models did not discriminate between PEGs, in large animal models of transplantation we showed that PEG 20 kDa offers a higher level of protection than UW and that longer chains such as PEG 35 kDa must be used at low doses, such as found in Institut George Lopez (IGL1, 1g/L).

Linear Chain Formation of Split-Aptamer Dimers on Surfaces Triggered by Adenosine.

The detection of small molecules impacts various fields; however, their small size and low concentration are usually the cause of limitations in their detection. Thus, the need for biosensors with appropriate probes and signal amplification strategies is required. Aptamers are appropriate probes selected specifically against small targets such as adenosine. The possibility to split aptamers in parts led to original amplification strategies based on sandwich assays. By combining the self-assembling of oligonucleotide dimers with split-aptamer dangling ends and a surface plasmon resonance imaging technique, we developed an original amplification approach based on linear chain formation in the presence of the adenosine target. In this article, on the basis of sequence engineering, we analyzed its performance and the effect of the probe grafting density on the length of the chains formed at the surface of the biosensor.

Label-free fluorescence detection of microRNA based on target induced adenosine2-coralyne-adenosine2 formation.

This study develops a simple and label-free biosensor for sensitive and selective detection of microRNA (miRNA) based on the formation of the adenosine2-coralyne-adenosine2 complex mediated by miRNA-specific polyadenosine extension.

Selective adsorption of modified nucleoside cancer biomarkers by hybrid molecularly imprinted adsorbents.

Modified adenosine nucleosides have been proposed to be potential DNA-based biomarkers for early diagnosis of tumor and a promising tool for the development of noninvasive prediction systems. However, the low concentration of modified adenosine nucleosides in physiological fluids makes them challenging for both quantitative and qualitative determination. Therefore, materials, which are potentially useful for selective adsorption of nucleobase-containing compounds, were obtained. To obtain the adsorbents, the silica gel particles were coated layer-by-layer with films of the polymers with different combinations of polymers containing thymine groups. Next, the microspheres were irradiated with UV light in the presence of 2'-deoxyadenosine or 5'-deoxy-5'-(methylthio)adenosine, as template molecules, which resulted in the photodimerization of thymine moieties and molecular imprinting of adsorbed modified adenosine compounds. The selectivity of the adsorption was significantly enhanced by the photoimprinting process. Eventually, the imprinted particles have shown an improved ability to recognize mainly 2'-deoxyadenosine and 5'-deoxy-5'-(methylthio)adenosine molecules. The best performing adsorbent was obtained using modified natural polysaccharides. The studied materials could serve as promising adsorbents of biomarkers for tumor diagnostics.

Structural basis for the molecular recognition of polyadenosine RNA by Nab2 Zn fingers.

The yeast poly(A) RNA binding protein, Nab2, facilitates poly(A) tail length regulation together with targeting transcripts to nuclear pores and their export to the cytoplasm. Nab2 binds polyadenosine RNA primarily through a tandem repeat of CCCH Zn fingers. We report here the 2.15 Å resolution crystal structure of Zn fingers 3-5 of Chaetomium thermophilum Nab2 bound to polyadenosine RNA and establish the structural basis for the molecular recognition of adenosine ribonucleotides. Zn fingers 3 and 5 each bind two adenines, whereas finger 4 binds only one. In each case, the purine ring binds in a surface groove, where it stacks against an aromatic side chain, with specificity being provided by a novel pattern of H-bonds, most commonly between purine N6 and a Zn-coordinated cysteine supplemented by H-bonds between purine N7 and backbone amides. Residues critical for adenine binding are conserved between species and provide a code that allows prediction of finger-binding stoichiometry based on their sequence. Moreover, these results indicate that, in addition to poly(A) tails, Nab2 can also recognize sequence motifs elsewhere in transcripts in which adenosines are placed at key positions, consistent with its function in mRNP organization and compaction as well as poly(A) tail length regulation.

Synthesis and complementary self-association of novel lipophilic π-conjugated nucleoside oligomers.

A series of lipophilic nucleosides comprising natural and non-natural bases that are π-conjugated to a short oligophenylene-ethynylene fragment has been synthesized. These bases comprise guanosine, isoguanosine, and 2-aminoadenosine as purine heterocycles, and cytidine, isocytosine and uridine as complementary pyrimidine bases. The hydrogen-bonding dimerization and association processes between complementary bases were also studied by (1)H NMR and absorption spectroscopy in order to obtain the relevant association constants.

Influence of nanopore surface charge and magnesium ion on polyadenosine translocation.

We investigate the influence of a nanopore surface state and the addition of Mg(2+) on poly-adenosine translocation. To do so, two kinds of nanopores with a low aspect ratio (diameter ∼3-5 nm, length 30 nm) were tailored: the first one with a negative charge surface and the second one uncharged. It was shown that the velocity and the energy barrier strongly depend on the nanopore surface. Typically if the nanopore and polyA exhibit a similar charge, the macromolecule velocity increases and its global energy barrier of entrance in the nanopore decreases, as opposed to the non-charged nanopore. Moreover, the addition of a divalent chelating cation induces an increase of energy barrier of entrance, as expected. However, for a negative nanopore, this effect is counterbalanced by the inversion of the surface charge induced by the adsorption of divalent cations.

Enrichment of adenosine using thermally responsive chromatographic materials under friendly pH conditions.

A thermally responsive boronate affinity chromatographic material, which showed thermal sensitivity, had been successfully applied for the enrichment and separation of cis-diol-containing compounds, and the capture and release process could be facilitated by adjusting the temperature. However, in this system, the pH of the mobile phase must be higher than 9.8, and alkaline media can lead to the degradation of labile compounds; the use of silica beads also limits its use. In this study, thermally responsive boronate affinity chromatographic material, namely poly(N-isopropylacrylamide-co-N-acryloyl-3-aminophenylboronic acid) grafted silica, was successfully prepared by atom transfer radical polymerization. Its structure was confirmed by IR spectroscopy and the graft ratio was 20.8%, determined by thermogravimetric analysis. Furthermore, the capture/release of adenosine, a cis-diol, was performed from pH 5.0-9.0 and 10-50°C. The elution of adenosine was remarkably retarded at decreased temperatures and adenosine could be captured completely at 10°C at pH values of 5.0-9.0. The enrichment of adenosine could be achieved by simply changing the temperature from 10 to 50°C. Therefore, this material not only improved the stability of the silica, but was also suitable for the capture of oxidation-sensitive biological analytes. Moreover, it could be used for the enrichment of cis-diol-containing compounds in LC with MS.

Evaluation of systemic exposure of nanoparticle suspensions subcutaneously administered to mice regarding stabilization, volume, location, concentration and size.

Different routes of administration are likely to result in very different outcomes due to different availability or plasma profile. The objective of the present study was to evaluate the pharmacokinetic profile after different subcutaneous (s.c.) administration of nanoparticle suspensions of a lipophilic compound to mice. Pharmacokinetics of the selected test compound and the effect of drug concentration, particle size, location of administration, volume given and particle stabilizers were studied. Adding PEGylated lipids or pluronic F-127 to the negatively charged surface of the nanoparticles increased the stability of the particles and the bioavailability. The in vivo studies demonstrated linear absorption kinetics for the selected model compound up to at least 500 µmol/kg. Absorption from upper-neck resulted in different systemic exposure compared to administration in the hip. The former was preferred if a prolonged Cmax was desired while the latter ensured a flat profile for approximately 24 hours. Administering the double volume (but the same dose) had no effect on the pharmacokinetics, whereas smaller particle size significantly increased the exposure.

[Energy of interaction in actinomycin-nucleotide complexes].

Variety of different compounds has been used for delivery of antibiotics to the tumor cells. In this work, using the highly sensitive spectrophotometry, the natural complexes of heterocyclic antibiotic actinomycin D (AMD) with such possible curriers like purine and pyrimidine nucleotides as well as fragmented DNA and phospholipid liposomes were studied. The antibiotic is not only adsorbed on the surface of purine clusters, but also is embedded in them. The antibiotic is especially well integrated into the unwound DNA regions. Embedding is accompanied by a long-wavelength shift in the absorption spectrum. The magnitude of the shift was used for calculation of the interaction energy. In the case of AMD with caffeine and adenosine, the value of energy is 2.4 and 2.7 kcal/mol and in the case of guanosine and fragmented DNA--considerably higher: 3.3 and 3.7 kcal/mol. It can be assumed that guanosine, adenosine, caffeine, and the fragmented DNA could serve as carriers of antibiotic.