G-Quadruplexes as Sensors of Intracellular Na+/K+ Ratio: Potential Role in Regulation of Transcription and Translation.

Data on the structure of G-quadruplexes, noncanonical nucleic acid forms, supporting an idea of their potential participation in regulation of gene expression in response to the change in intracellular Na+i/K+i ratio are considered in the review. Structural variety of G-quadruplexes, role of monovalent cations in formation of this structure, and thermodynamic stability of G-quadruplexes are described. Data on the methods of their identification in the cells and biological functions of these structures are presented. Analysis of information about specific interactions of G-quadruplexes with some proteins was conducted, and their potential participation in the development of some pathological conditions, in particular, cancer and neurodegenerative diseases, is considered. Special attention is given to the plausible role of G-quadruplexes as sensors of intracellular Na+i/K+i ratio, because alteration of this parameter affects folding of G-quadruplexes changing their stability and, thereby, organization of the regulatory elements of nucleic acids. The data presented in the conclusion section demonstrate significant change in the expression of some early response genes under certain physiological conditions of cells and tissues depending on the intracellular Na+i/K+i ratio.

Converted paddy to upland in saline-sodic land could improve soil ecosystem multifunctionality by enhancing soil quality and alleviating microbial metabolism limitation.

Soil salinization is one of the major soil degradation threats worldwide, and parameters related to soil quality and ecosystem multifunctionality (EMF) are crucial for evaluating the success of reclamation efforts in saline-sodic wasteland (WL). Microbial metabolic limitation is also one of the main factors that influences EMF in agricultural cropping systems. A ten-year localization experiment was conducted to reveal the key predictors of soil quality index (SQI) values, microbial metabolic characteristics, and EMF in different farmland cropping systems. A random forest model showed that the ß-glucosidase (BG), cellobiosidase (CBH) and saturated hydraulic conductivity (SHC) of the SQI factors were the main driving forces of soil EMF. Compared to monoculture models, such as paddy field (PF) or upland field (UF), the converted paddy field to upland field (CF) cropping system was most effective at improving EMF in reclaimed saline-sodic WL, increasing this metric by 275.35 %. CF integrates practices from both PF and UF planting systems, improved soil quality and relieves microbial metabolic limitation. Specifically, both CF and PF significantly reduced soil pH (by 16-23 %) and sodium adsorption ration (SAR) (by 65-83 %) and significantly reduced the abundance of large macroaggregates. Moreover, CF significantly improved soil saturated hydraulic conductivity relative to PF and UF (p < 0.05), indicating an improvement in soil physical properties. Overall, although reclamation improved SQI compared to WL (0.25), the EMF of CF (0.56) was significantly higher than that of other treatments (p < 0.05). Thus, while increasing SQI can improve soil EMF, it was not as effective alone as it was when combined with more comprehensive efforts that focus on improving various soil properties and alleviating microbial metabolic limitations. Therefore, our results suggested that future saline-sodic wasteland reclamation efforts should avoid monoculture systems to enhance soil EMF.

Exploring the Effect of V2O5 and Nb2O5 Content on the Structural, Thermal, and Electrical Characteristics of Sodium Phosphate Glasses and Glass-Ceramics.

Na-V-P-Nb-based materials have gained substantial recognition as cathode materials in high-rate sodium-ion batteries due to their unique properties and compositions, comprising both alkali and transition metal ions, which allow them to exhibit a mixed ionic-polaronic conduction mechanism. In this study, the impact of introducing two transition metal oxides, V2O5 and Nb2O5, on the thermal, (micro)structural, and electrical properties of the 35Na2O-25V2O5-(40 - x)P2O5 - xNb2O5 system is examined. The starting glass shows the highest values of DC conductivity, σDC, reaching 1.45 × 10-8 Ω-1 cm-1 at 303 K, along with a glass transition temperature, Tg, of 371 °C. The incorporation of Nb2O5 influences both σDC and Tg, resulting in non-linear trends, with the lowest values observed for the glass with x = 20 mol%. Electron paramagnetic resonance measurements and vibrational spectroscopy results suggest that the observed non-monotonic trend in σDC arises from a diminishing contribution of polaronic conductivity due to the decrease in the relative number of V4+ ions and the introduction of Nb2O5, which disrupts the predominantly mixed vanadate-phosphate network within the starting glasses, consequently impeding polaronic transport. The mechanism of electrical transport is investigated using the model-free Summerfield scaling procedure, revealing the presence of mixed ionic-polaronic conductivity in glasses where x < 10 mol%, whereas for x ≥ 10 mol%, the ionic conductivity mechanism becomes prominent. To assess the impact of the V2O5 content on the electrical transport mechanism, a comparative analysis of two analogue series with varying V2O5 content (10 and 25 mol%) is conducted to evaluate the extent of its polaronic contribution.

Configurational Changes of Retinal Schiff Base during Membrane Na+ Transport by a Sodium Pumping Rhodopsin.

Microbial rhodopsins are photoreceptors containing the retinal Schiff base chromophore and are ubiquitous among microorganisms. The Schiff base configuration of the chromophore, 15-anti (C═N trans) or 15-syn (C═N cis), is structurally important for their functions, such as membrane ion transport, because this configuration dictates the orientation of the positively charged NH group that interacts with substrate ions. The 15-anti/syn configuration is thus essential for elucidating the ion-transport mechanisms in microbial rhodopsins. Here, we identified the Schiff base configuration during the photoreaction of a sodium pumping rhodopsin from Indibacter alkaliphilus using Raman spectroscopy. We found that the unique configurational change from the 13-cis, 15-anti to all-trans, 15-syn form occurs between the photointermediates termed O1 and O2, which accomplish the Na+ uptake and release, respectively. This isomerization is considered to give rise to the highly irreversible O1 → O2 step that is crucial for unidirectional Na+ transport.

Understanding the Electrochemical Extraction of Lithium from Ultradilute Solutions.

The electrochemical extraction of lithium (Li) from aqueous sources using electrochemical means is a promising direct Li extraction technology. However, to this date, most electrochemical Li extraction studies are confined to Li-rich brine, neglecting the practical and existing Li-lean resources, with their overall extraction behaviors currently not fully understood. More still, the effect of elevated sodium (Na) concentrations typically found in most Li-lean water sources on Li extraction is unclear. Hence, in this work, we first understand the electrochemical Li extraction behaviors from ultradilute solutions using spinel lithium manganese oxide as the model electrode. We discovered that Li extraction depends highly on the Li concentration and cell operation current density. Then, we switched our focus on low Li to Na ratio solutions, revealing that Na can dominate the electrostatic screening layer, reducing Li ion concentration. Based on these understandings, we rationally employed pulsed electrochemical operation to restructure the electrode surface and distribute the surface-adsorbed species, which efficiently achieves a high Li selectivity even in extremely low initial Li/Na concentrations of up to 1:20,000.

Ion-Selective Micropipette Sensor for In Vivo Monitoring of Sodium Ion with Crown Ether-Encapsulated Metal-Organic Framework Subnanopores.

In vivo sensing of the dynamics of ions with high selectivity is essential for gaining molecular insights into numerous physiological and pathological processes. In this work, we report an ion-selective micropipette sensor (ISMS) through the integration of functional crown ether-encapsulated metal-organic frameworks (MOFs) synthesized in situ within the micropipette tip. The ISMS features distinctive sodium ion (Na+) conduction and high selectivity toward Na+ sensing. The selectivity is attributed to the synergistic effects of subnanoconfined space and the specific coordination of 18-crown-6 toward potassium ions (K+), which largely increase the steric hindrance and transport resistance for K+ to pass through the ISMS. Furthermore, the ISMS exhibits high stability and sensitivity, facilitating real-time monitoring of Na+ dynamics in the living rat brain during spreading of the depression events process. In light of the diversity of crown ethers and MOFs, we believe this study paves the way for a nanofluidic platform for in vivo sensing and neuromorphic electrochemical sensing.

Functional and structural asymmetry suggest a unifying principle for catalysis in membrane-bound pyrophosphatases.

Membrane-bound pyrophosphatases (M-PPases) are homodimeric primary ion pumps that couple the transport of Na+- and/or H+ across membranes to the hydrolysis of pyrophosphate. Their role in the virulence of protist pathogens like Plasmodium falciparum makes them an intriguing target for structural and functional studies. Here, we show the first structure of a K+-independent M-PPase, asymmetric and time-dependent substrate binding in time-resolved structures of a K+-dependent M-PPase and demonstrate pumping-before-hydrolysis by electrometric studies. We suggest how key residues in helix 12, 13, and the exit channel loops affect ion selectivity and K+-activation due to a complex interplay of residues that are involved in subunit-subunit communication. Our findings not only explain ion selectivity in M-PPases but also why they display half-of-the-sites reactivity. Based on this, we propose, for the first time, a unified model for ion-pumping, hydrolysis, and energy coupling in all M-PPases, including those that pump both Na+ and H+.

Acute toxicity of cerium to neonatal Daphnia magna: Responses of antioxidant systems, influence of environmental factors and development of a biotic ligand model.

The bioavailability of cerium (Ce) and its toxic effects on aquatic organisms are still unclear, which limits the toxicity prediction and pollution control for this element. Here, the acute toxicity of Ce to Daphnia magna neonates and the responses of the antioxidant system were investigated, and the quantitative relationships between the toxicity of Ce and environmental factors were determined. The 24 and 48 h EC50Ce-D values based on the dissolved concentration of Ce in Daphnia magna were 60.6 and 10.9 µM, respectively, and the EC50Ce3+ values were 23.4 and 3.73 µM, respectively. After Ce exposure at environmentally relevant concentrations (0.5-3.5 µM), significant increases in superoxide dismutase activity and malondialdehyde content were observed in Daphnia magna, while significant decreases in catalase activity and H2O2 content occurred. Low levels of Ce cause oxidative damage to Daphnia magna and adverse impacts on the antioxidant system; however, further molecular-based studies are needed. The addition of Ca2+ or Na+ reduced the acute toxicity of Ce to Daphnia magna. In contrast, Mg2+ (MgSO4) promoted Ce toxicity, which is a new finding related to the interaction effects between cations and rare earth elements on biological ligands; however, the effects of SO42+ could not be distinguished. Complexation with organic ligands could significantly reduce the toxicity of Ce to Daphnia magna; however, complexes of Ce with citric acid and malic acid might be bioavailable to Daphnia magna. In the absence of organic ligands and competing metals, the binding constant of Ce3+ to Daphnia magna at toxic concentrations was 5.83. The log K values for the competitive effects of Ca2+ and Na+ were 3.73 and 2.59, respectively, while the log K value for the protective effect of fulvic acid was 3.76. These results contribute to understanding the toxicity of Ce and will help predict the toxicity of Ce in freshwater.

Epidermal and dermal cells from adult rat eccrine sweat gland-containing skin can reconstruct the three-dimensional structure of eccrine sweat glands.

BACKGROUND: Previously, we have demonstrated that eccrine sweat gland cells (ESGCs) can reconstruct the three-dimensional (3D) structure of eccrine sweat glands (ESGs). However, there is still a need to explore source cells capable of regenerating ESG to address the issue of ESG regeneration in ESGC-deficient conditions, such as severe burns. METHODS: The epidermal cells and dermal cells in adult rat ventral foot skin (ESG-bearing) were isolated. The isolated single epidermal cells and dermal cells were mixed with Matrigel, and then the mixture was implanted into the axillary/inguinal fat pads of nude mice. Five weeks after implantation, the Matrigel plugs were harvested and the morphology and differentiation of the cells were examined by H&E staining and fluorescent immunohistochemical staining for ESG markers, such as Na+ -K+ -2Cl- cotransporter 1 (NKCC1), Na+ -K+ -ATPase (NKA), Foxa1 and K14. RESULTS: The epidermal cells and dermal cells of adult rat ventral foot skin can reconstruct 3D structure and express specific markers of ESGs in skin, such as NKCC1, NKA and Foxa1, indicating the ESG-phenotypic differentiation of the 3D structures. Double immunofluorescence staining showed that some 3D structures expressed both the myoepithelial cell marker alpha-SMA and the common marker K14 of duct cells and myoepithelial cells, while some 3D structures expressed only K14, indicating that ESG-like 3D structures differentiated into duct-like and secretory coiled cells. CONCLUSION: Epidermal and dermal cells from adult ESG-bearing skin can be used as a cell source for ESG regeneration.

A sodium/potassium switch for G4-prone G/C-rich sequences.

Metal ions are essential components for the survival of living organisms. For most species, intracellular and extracellular ionic conditions differ significantly. As G-quadruplexes (G4s) are ion-dependent structures, changes in the [Na+]/[K+] ratio may affect the folding of genomic G4s. More than 11000 putative G4 sequences in the human genome (hg19) contain at least two runs of three continuous cytosines, and these mixed G/C-rich sequences may form a quadruplex or a competing hairpin structure based on G-C base pairing. In this study, we examine how the [Na+]/[K+] ratio influences the structures of G/C-rich sequences. The natural G4 structure with a 9-nt long central loop, CEBwt, was chosen as a model sequence, and the loop bases were gradually replaced by cytosines. The series of CEB mutations revealed that the presence of cytosines in G4 loops does not prevent G4 folding or decrease G4 stability but increases the probability of forming a competing structure, either a hairpin or an intermolecular duplex. Slow conversion to the quadruplex in vitro (in a potassium-rich buffer) and cells was demonstrated by NMR. 'Shape-shifting' sequences may respond to [Na+]/[K+] changes with delayed kinetics.

Rice bran extract mitigates depressive-like behavior in dextran sulfate sodium-induced colitis: Involvement of the gut-brain axis and Sirt1 signaling pathway.

Inflammatory bowel disease (IBD) patients frequently suffer from depressive disorders as well. The present study was carried out to explore whether treatment with a standardized rice bran extract (RBE) could affect depression-like behavior in rats with dextran sulfate sodium (DSS)-induced colitis. Male Wistar rats were treated with RBE (100 mg/kg/day; p.o.) for 2 weeks. During the second week, colitis was induced by feeding the rats with 5 % (w/v) DSS in drinking water. RBE protected against DSS-induced body weight loss as well as against the macro- and microscopic inflammatory changes of the colon. Additionally, RBE mitigated DSS-induced dysregulation in blood-brain barrier tight junctional proteins, preserved the hippocampal histopathological architecture and improved the animal behavior in the forced swimming test. This was associated with modulation of hippocampal oxidative stress marker; GSH as well as hippocampal pro-inflammatory mediators; NF-ĸB and IL-1ß. Treatment with RBE also led to a profound increase in the hippocampal levels of Sirt1, PGC-1α, Nrf2, and HO-1, which were drastically dropped by DSS. In conclusion, the study revealed the protective effect of RBE against DSS-induced depressive-like behavior through modulation of different parameters along the gut-brain axis and up-regulated the Sirt1/PGC-1α/Nrf2/HO-1 signaling pathway.

Triple-tuned birdcage and single-tuned dipole array for quadri-nuclear head MRI at 7 T.

PURPOSE: The purpose of this work was to design and build a coil for quadri-nuclear MRI of the human brain at 7 T. METHODS: We built a transmit/receive triple-tuned (45.6 MHz for 2 $$ {}^2 $$ H, 78.6 MHz for 23 $$ {}^{23} $$ Na, and 120.3 MHz for 31 $$ {}^{31} $$ P) quadrature four-rod birdcage that was geometrically interleaved with a transmit/receive four-channel dipole array (297.2 MHz for 1 $$ {}^1 $$ H). The birdcage rods contained passive, two-pole resonant circuits that emulated capacitors required for single-tuning at three frequencies. The birdcage assembly also included triple-tuned matching networks, baluns, and transmit/receive switches. We assessed the performance of the coil with quality factor (Q) and signal-to-noise ratio (SNR) measurements, and performed in vivo multinuclear MRI and MR spectroscopic imaging (MRSI). RESULTS: Q measurements showed that the triple-tuned birdcage efficiency was within 33% of that of single-tuned baseline birdcages at all three frequencies. The quadri-tuned coil SNR was 78%, 59%, 44%, and 48% lower than that of single or dual-tuned reference coils for 1 $$ {}^1 $$ H, 2 $$ {}^2 $$ H, 23 $$ {}^{23} $$ Na, and 31 $$ {}^{31} $$ P, respectively. Quadri-nuclear MRI and MRSI was demonstrated in brain in vivo in about 30 min. CONCLUSION: While the SNR of the quadruple tuned coil was significantly lower than dual- and single-tuned reference coils, it represents a step toward truly simultaneous quadri-nuclear measurements.

Elucidating uranium interactions with synthetic Na-P1 zeolite/Ca2+-substituted alginate composite granules through batch and spectroscopic studies: Emphasizing the significance of ion exchange and complexation.

Uranium, a key member of the actinides series, is radioactive and may cause severe environmental hazards once discharged into the water due to high toxicity. Removal of uranium via adsorption by applying tailored, functional adsorbents is at the forefront of tackling such pollution. Here, we report the optimized functionalization of the powder coal fly-ash (CFA) derived Na-P1 synthetic zeolite to the form of granules by employing the biodegradable polymer-calcium alginate (CA) and their application to remove aqueous U. The optimized synthesis showed that granules are formed at the CA concentration equals to 0.5 % wt., and that application of 1% wt. solution renders the most effective U scavengers. The maximum U adsorption capacity (qmax) increases significantly after CA modification from 44.48 mgU/g for native, powder Na-P1 zeolite to 62.53 mg U/g and 76.70 mg U/g for 0.5 % wt. and 1 % wt. CA respectively. The U adsorption follows the Radlich-Peterson isotherm model, being the highest at acidic pH (pHeq∼4). The U adsorption kinetics reveals swift U uptake, reaching equilibrium after 2h for 1 % ZACB and 3 h for 0.5 % wt. ZACB following the pseudo-second-order (PSO) kinetic model. SEM-EDXS investigation elucidates that adsorbed U occurs onto materials as an inhomogenous, well-dispersed, and micrometer-scale aggregate. Further, XPS and µ-XRF spectroscopies complementarily confirmed the hexavalent oxidation state of adsorbed U and its altered distribution on ZACBs with varying CA concentrations. U distribution was probed "in-situ" onto materials while correlations between the major elements (Al, Si, Ca, U) contributing to U scavenging were calculated and compared. Finally, a real-life coal mine wastewater (CMW) polluted by 238U and 228,226Ra was successfully purified, satisfying WHO guidelines after treatment using ZACBs. These findings offer new insights on successful yet optimized Na-P1 zeolite modification using biodegradable polymer (Ca2+-exchanged alginate) aimed at efficient U removal, displaying a near-zero environmental impact.

Selective modulation of alkali metal ions on acetylcholinesterase.

Acetylcholinesterase (AChE) is an important hydrolase in cholinergic synapses and a candidate target in the treatment of Alzheimer's disease. The lithium treatment widely used in neurological disorders can alter the AChE activity, yet the underlying mechanism of how the ion species regulate the enzymatic activity remains unclear. In this work, we performed combined quantum mechanics/molecular mechanics (QM/MM) and molecular dynamics (MD) simulations and well-tempered metadynamics to understand the modulation of human AChE (hAChE) activity using three alkali metal ions (Li+, Na+, and K+) in different concentrations. Our simulations show that the binding affinity and catalytic activity are affected by different ion species through allosteric ion coordination geometries on the hAChE complex and distant electrostatic screening effect. A Li+ cluster involving D330, E393, and D397 residues and three Li+ ions was found to be highly conserved and can be critical to the enzyme activity. Binding energy calculations indicate that the electrostatic screening from allosterically bound cations can affect the key residues at the catalytic site and active-site gorge, including E199. Furthermore, an increase in ion concentration can lead to lower reactivity, especially for Li+ ions, which exhibit more cation-hAChE contacts than Na+ and K+. The selective ion binding and their preferred modulation on hAChE are highly related to ion species. This work provides a molecular perspective on selective modulation by different ion species of the enzyme catalytic processes.

Structural Characterization of the Metalized Radical Cations of Adenosine ([Ade+Li-H]•+ and [Ade+Na-H]•+) by Infrared Multiphoton Dissociation Spectroscopy and Theoretical Studies.

Nucleoside radicals are key intermediates in the process of DNA damage, and alkali metal ions are a common group of ions in living organisms. However, so far, there has been a significant lack of research on the structural effects of alkali metal ions on nucleoside free radicals. In this study, we report a new method for generating metalized nucleoside radical cations in the gas phase. The radical cations [Ade+M-H]•+ (M = Li, Na) are generated by the 280 nm ultraviolet photodissociation (UVPD) of the precursor ions of lithiated and sodiated ions of 2-iodoadenine in a Fourier transform ion cyclotron resonance (FT ICR) cell. Further infrared multiphoton dissociation (IRMPD) spectra of both radical cations were recorded in the region of 2750-3750 cm-1. By combining these results with theoretical calculations, the most stable isomers of both radicals can be identified, which share the common characteristics of triple coordination patterns of the metal ions. For both radical species, the lowest-energy isomers undergo hydrogen transfer. Although the sugar ring in the most stable isomer of [Ade+Li-H]•+ is in a (South, syn) conformation similar to that of [Ado+Na]+, [Ade+Na-H]•+ is distinguished by the unexpected opening of the sugar ring. Their theoretical spectra are in good agreement with experimental spectra. However, due to the flexibility of the structures and the complexity of their potential energy surfaces, the hydrogen transfer pathways still need to be further studied. Considering that the free radicals formed directly after C-I cleavage have some similar spectral characteristics, the existence of these corresponding isomers cannot be ruled out. The findings imply that the structures of nucleoside radicals may be significantly influenced by the attached alkali metal ions. More detailed experiments and theoretical calculations are still crucial.

Novel phenolate salts of bioactive agents: Cannabidiol phenolate salts.

Bioactive phenolic compounds are commonly found in medications, with examples including apomorphine, estrone, thymol, estradiol, propofol, o-phenylphenol, l-Dopa, doxorubicin, tetrahydrocannabinol (THC), and cannabidiol (CBD). This study is the first to explore the creation and assessment of metal and ammonium phenolate salts using CBD as an example. CBD is used in medicine to treat anxiety, insomnia, chronic pain, and inflammation, but its bioavailability is limited due to poor water solubility. In this study exploit a synthetic route to convert CBD into anionic CBD-salts to enhance water solubility. Various CBD-salts with metal and ammonium counterions such as lithium (Li+), sodium (Na+), potassium (K+), choline hydroxide ([(CH3)3NCH2CH2OH]+), and tetrabutylammonium ([N(C4H9)4]+) have been synthesized and characterized. These salts are obtained in high yields, ranging from 74 % to 88 %, through a straightforward dehydration reaction between CBD and alkali metal hydroxides (LiOH, NaOH, KOH) or ammonium hydroxides (choline hydroxide, tetrabutylammonium hydroxide). These reactions are conducted in either ethanol, methanol, or a methanol:water mixture, maintaining a 1:1 molar ratio between the reactants. Comprehensive characterization using Fourier-Transform Infrared Spectroscopy (FT-IR), Nuclear Magnetic Resonance (NMR) spectroscopy, and elemental (CHN) analysis confirms the formation of CBD-salts, as evidenced by the absence of aromatic hydroxyl resonances or stretching frequencies. The molecular formulas of CBD salts were determined based on CHN analysis, and CBD quantification from acid regeneration experiments. Characterization data confirms that each CBD phenolate in a specific CBD salt was electrostatically stabilized by one of the either alkali metal or ammonium ion. The CBD-salts are highly susceptible to acidic conditions, readily reverting back to the original CBD. The percentage and purity of CBD in the CBD-metal/ammonium salts have been studied using High-Performance Liquid Chromatography (HPLC) analysis. Solubility studies indicate that the conversion of CBD into CBD salts significantly enhances its solubility in water, ranging from 110 to 1606 folds greater than pure CBD. Furthermore, the pharmacokinetic evaluation of oral administration of CBD-salts compared to CBD were determined in rats.

Why Na+ has higher propensity than K+ to condense DNA in a crowded environment.

Experimentally, in the presence of the crowding agent polyethylene glycol (PEG), sodium ions compact double-stranded DNA more readily than potassium ions. Here, we have used molecular dynamics simulations and the "ion binding shells model" of DNA condensation to provide an explanation for the observed variations in condensation of short DNA duplexes in solutions containing different monovalent cations and PEG; several predictions are made. According to the model we use, externally bound ions contribute the most to the ion-induced aggregation of DNA duplexes. The simulations reveal that for two adjacent DNA duplexes, the number of externally bound Na+ ions is larger than the number of K+ ions over a wide range of chloride concentrations in the presence of PEG, providing a qualitative explanation for the higher propensity of sodium ions to compact DNA under crowded conditions. The qualitative picture is confirmed by an estimate of the corresponding free energy of DNA aggregation that is at least 0.2kBT per base pair more favorable in solution with NaCl than with KCl at the same ion concentration. The estimated attraction free energy of DNA duplexes in the presence of Na+ depends noticeably on the DNA sequence; we predict that AT-rich DNA duplexes are more readily condensed than GC-rich ones in the presence of Na+. Counter-intuitively, the addition of a small amount of a crowding agent with high affinity for the specific condensing ion may lead to the weakening of the ion-mediated DNA-DNA attraction, shifting the equilibrium away from the DNA condensed phase.

Kinetic and Thermodynamic Control of G-Quadruplex Polymorphism by Na+ and K+ Cations.

G-Quadruplexes (G4s) are ubiquitous nucleic acid folding motifs that exhibit structural diversity that is dependent on cationic conditions. In this work, we exploit temperature-controlled single-molecule fluorescence resonance energy transfer (smFRET) to elucidate the kinetic and thermodynamic mechanisms by which monovalent cations (K+ and Na+) impact folding topologies for a simple G-quadruplex sequence (5'-GGG-(TAAGGG)3-3') with a three-state folding equilibrium. Kinetic measurements indicate that Na+ and K+ influence G4 formation in two distinctly different ways: the presence of Na+ modestly enhances an antiparallel G4 topology through an induced fit (IF) mechanism with a low affinity (Kd = 228 ± 26 mM), while K+ drives G4 into a parallel/hybrid topology via a conformational selection (CS) mechanism with much higher affinity (Kd = 1.9 ± 0.2 mM). Additionally, temperature-dependent studies of folding rate constants and equilibrium ratios reveal distinctly different thermodynamic driving forces behind G4 binding to K+ (ΔH°bind > 0, ΔS°bind > 0) versus Na+ (ΔH°bind < 0, ΔS°bind < 0), which further illuminates the diversity of the possible pathways for monovalent facilitation of G-quadruplex folding.

A smartphone-based ratiometric fluoroprobe based on blue-red dual-emission signals of thiochrome and copper nanoclusters for sensitive assay of metam-sodium in cucumbers.

It is of great importance to develop the highly efficient fluorescence strategy for rapid/sensitive detection of metam-sodium (MES) in evaluating its residual safety, especially in fresh vegetables. Herein, we prepared an organic fluorophore (thiochrome, TC) and glutathione-capped copper nanoclusters (GSH-CuNCs), and their combination (TC/GSH-CuNCs) was sucessfully employed as a ratiometric fluoroprobe by means of the blue-red dual emission. The fluorescence intensities (FIs) of TC decreased upon the addition of GSH-CuNCs via the fluorescence resonance energy transfer (FRET) process. When fortified at the constant levels of GSH-CuNCs and TC, MES substantially reduced the FIs of GSH-CuNCs, while this was not the case in the FIs of TC except for the prominent red-shift of ∼30 nm. Compared to the previous fluoroprobes, the TC/GSH-CuNCs based fluoroprobe supplied wider linear range of 0.2-500 µM, lower detection limit (60 nM), and satisfactory fortification recoveries (80-107%) for MES in the cucumber samples. Based on the fluorescence quenching phenomenon, a smartphone application was used to output RGB values of the captured images for the colored solution. The smartphone-based ratiometric sensor could be utilized for the visual fluorescent quantitation of MES by virtue of the R/B values in cucumbers, which gave linear range (1-200 µM) and LOD (0.3 µM). By means of blue-red dual-emission fluorescence, the smartphone-based fluoroprobe provides a cost-effective, portable and reliable avenue for the on-site, rapid and sensitive assay of MES's residues in complex vegetable samples.

Computational study of the role of counterions and solvent dielectric in determining the conductance of B-DNA.

DNA naturally exists in a solvent environment, comprising water and salt molecules such as sodium, potassium, magnesium, etc. Along with the sequence, the solvent conditions become a vital factor determining DNA structure and thus its conductance. Over the last two decades, researchers have measured DNA conductivity both in hydrated and almost dry (dehydrated) conditions. However, due to experimental limitations (the precise control of the environment), it is very difficult to analyze the conductance results in terms of individual contributions of the environment. Therefore, modeling studies can help us to gain a valuable understanding of various factors playing a role in charge transport phenomena. DNA naturally has negative charges located at the phosphate groups in the backbone, which provides both the connections between the base pairs and the structural support for the double helix. Positively charged ions such as the sodium ion (Na^{+}), one of the most commonly used counterions, balance the negative charges at the backbone. This modeling study investigates the role of counterions both with and without the solvent (water) environment in charge transport through double-stranded DNA. Our computational experiments show that in dry DNA, the presence of counterions affects electron transmission at the lowest unoccupied molecular orbital energies. However, in solution, the counterions have a negligible role in transmission. Using the polarizable continuum model calculations, we demonstrate that the transmission is significantly higher at both the highest occupied and lowest unoccupied molecular orbital energies in a water environment as opposed to in a dry one. Moreover, calculations also show that the energy levels of neighboring bases are more closely aligned to ease electron flow in the solution.