Studies of Functional Nucleic Acids Modified Light Addressable Potentiometric Sensors: X‑ray Photoelectron Spectroscopy, Biochemical Assay, and Simulation

Functional nucleic acids (FNAs) are promising sensing elements, and extensive interests are excited to integrate FNAs with transducers for biochemical assays. However, efforts for FNAs modified light-addressable-potentiometric-sensor (FNA-LAPS) are rarely reported. LAPS is a versatile transducer with electrolyte-insulator-semiconductor (EIS) structure and can respond almost to any surface electronic deviation. Herein, organized studies for FNA-LAPS including experiments, theoretical derivations, and MEDICI (Synopsys) simulations are presented using Pb²⁺-DNAzyme GR-5 and Ag⁺-aptamer as proof-of-concepts, which are typical FNAs with distinctive sensing strategies. First, the on-LAPS occurrences of FNAs and their particular sensing actions are evidenced by tracking their X-ray photoelectron spectroscopy (XPS) core spectra of N 1s, P 2p, C 1s, Ag, etc. Then, applications of FNA-LAPS are executed by a homemade and mobile-phone controlled system, the limit-of-detection is 0.01 ppb, sensitivities are 2.86 (Pb²⁺) and 1.53 (Ag⁺) mV/log₁₀(ppb) (<i>R</i>² = 0.98), respectively. Furthermore, a charge and resistor mechanism (C&R) is proposed to illustrate the measured LAPS responding for FNAs and their sensing behaviors (Pb²⁺-mediated cleavage and Ag⁺-mediated folding), based on carefully analyzing basic LAPS’ experimental data and MEDICI calculated distributions of build-in potentials, energy-bands, carriers, etc., at the EIS microinterface (semiconductor side). Finally, demonstrations for C&R based FNA-LAPS principle are provided by the use of MEDICI, as a means to bridge experiments and theoretical deductions. In general, a cross-study for FNA-LAPS is proposed including XPS characterization, biochemistry detection, theoretical analysis, and MEDICI simulation, it is believed their powerful combination would provide an ideal workstation for analytical chemistry applications, not only the traditional determinations but also facilitations for investigating FNAs’ configurational transformations

Effect of waterlogging on carbon isotope discrimination during photosynthesis in <i>Larix gmelinii</i>

<p>Soil moisture is a major factor controlling carbon isotope discrimination (Δ¹³C), which has been demonstrated to decrease under dry conditions in many studies; however, few studies on Δ¹³C under waterlogging condition have been conducted. In this study, a pot experiment was conducted with <i>Larix gmelinii</i>, a major larch species in the east Siberian Taiga, to investigate the effect of waterlogging on Δ¹³C during photosynthesis. Assimilation rate and Δ¹³C_RD (instantaneous Δ¹³C calculated with Rayleigh distillation equation) decreased drastically soon after waterlogging, followed by recovery in their values, which was caused by a change in stomatal conductance. Thereafter, assimilation rate decreased gradually, whereas Δ¹³C_RD decreased more gently. These results were thought to be caused by the decrease in both stomatal conductance and carboxylation. Our results indicate that extreme wet events may cause a decrease in Δ¹³C, which is important information for detecting flooding events in the past using tree-ring isotope analyses and for studying impacts of flooding on plants in areas where waterlogging might occur.</p

Dopamine/Silica Nanoparticle Assembled, Microscale Porous Structure for Versatile Superamphiphobic Coating

Artificial superamphiphobic surfaces, which could repel both water and low surface tension organic liquids, have been limited to particular kinds of materials or surfaces thus far. In this work, a kind of microscale porous coating was developed. Taking dopamine and hydrophilic fumed silica nanoparticles as initial building blocks, microscale porous coating was constructed <i>via</i> ice templation. Polydopamine bound silica nanoparticles together to form a porous structure network and rendered the coating to have potential for further postfunctionalization. After two-step CVD, the microscale porous coating changes from superhydrophilic to superamphiphobic, exhibiting super-repellency to droplets with surface tension of 73–23 mN/m. The influences of concentration of initial dopamine, hydrophilic fumed silica nanoparticles, and dry conditions on the formation of the porous structure have been studied to optimize the conditions. Coatings with different pore sizes and pore heights have been fabricated to discover the relationship between the structure parameters and the repellency of the porous coatings. Only with optimal pore size and pore height can the porous coating display superamphiphobicity. Compared with nanoscale, the microscale structure favors the achievement of superamphiphobicity. Given the outstanding adhesive ability of polydopamine, the superamphiphobic coatings have been successfully applied to various materials including artificial materials and natural materials

MOESM1 of A VP24-truncated isolate of white spot syndrome virus is inefficient in per os infection

Additional file 1. A schematic diagram showing the organization of the circular genome of WSSV-CN04. Positions of the predicted protein coding genes and their transcription directions are indicated with arrows

Side Chain Conformational Distributions of a Small Protein Derived from Model-Free Analysis of a Large Set of Residual Dipolar Couplings

Accurate quantitative measurement of structural dispersion in proteins remains a prime challenge to both X-ray crystallography and NMR spectroscopy. Here we use a model-free approach based on measurement of many residual dipolar couplings (RDCs) in differentially orienting aqueous liquid crystalline solutions to obtain the side chain χ₁ distribution sampled by each residue in solution. Applied to the small well-ordered model protein GB3, our approach reveals that the RDC data are compatible with a single narrow distribution of side chain χ₁ angles for only about 40% of the residues. For more than half of the residues, populations greater than 10% for a second rotamer are observed, and four residues require sampling of three rotameric states to fit the RDC data. In virtually all cases, sampled χ₁ values are found to center closely around ideal <i>g</i>^–, <i>g</i>⁺ and <i>t</i> rotameric angles, even though no rotamer restraint is used when deriving the sampled angles. The root-mean-square difference between experimental ³J_HαHβ couplings and those predicted by the Haasnoot-parametrized, motion-adjusted Karplus equation reduces from 2.05 to 0.75 Hz when using the new rotamer analysis instead of the 1.1-Å X-ray structure as input for the dihedral angles. A comparison between observed and predicted ³J_HαHβ values suggests that the root-mean-square amplitude of χ₁ angle fluctuations within a given rotamer well is ca. 20°. The quantitatively defined side chain rotamer equilibria obtained from our study set new benchmarks for evaluating improved molecular dynamics force fields, and also will enable further development of quantitative relations between side chain chemical shift and structure

Discovery of Highly Potent Inhibitors Targeting the Predominant Drug-Resistant S31N Mutant of the Influenza A Virus M2 Proton Channel

With the emergence of highly pathogenic avian influenza (HPAI) H7N9 and H5N1 strains, there is a pressing need to develop direct-acting antivirals (DAAs) to combat such deadly viruses. The M2-S31N proton channel of the influenza A virus (A/M2) is one of the validated and most conserved proteins encoded by the current circulating influenza A viruses; thus, it represents a high-profile drug target for therapeutic intervention. We recently discovered a series of S31N inhibitors with the general structure of adamantyl-1-NH₂⁺CH₂–aryl, but they generally had poor physical properties and some showed toxicity in vitro. In this study, we sought to optimize both the adamantyl as well as the aryl/heteroaryl group. Several compounds from this study exhibited submicromolar EC₅₀ values against S31N-containing A/WSN/33 influenza viruses in antiviral plaque reduction assays with a selectivity index greater than 100, indicating that these compounds are promising candidates for in-depth preclinical pharmacology

A Homogeneous Signal-On Strategy for the Detection of <i>rpoB</i> Genes of Mycobacterium tuberculosis Based on Electrochemiluminescent Graphene Oxide and Ferrocene Quenching

Tuberculosis (TB) remains one of the leading causes of morbidity and mortality all over the world and multidrug resistance TB (MDR-TB) pose a serious threat to the TB control and represent an increasing public health problem. In this work, we report a homogeneous signal-on electrochemiluminescence (ECL) DNA sensor for the sensitive and specific detection of <i>rpoB</i> genes of MDR-TB by using ruthenium­(II) complex functionalized graphene oxide (Ru–GO) as suspension sensing interface and ferrocene-labeled ssDNA (Fc–ssDNA) as ECL intensity controller. The ECL of Ru–GO could be effectively quenched by Fc–ssDNA absorbed on the Ru–GO nanosheets. The Ru–GO has good discrimination ability over ssDNA and dsDNA. Mutant ssDNA target responsible for the drug resistant tuberculosis can hybridize with Fc–ssDNA and release Fc–ssDNA from Ru–GO surface, leading to the recovery of ECL. Mutant ssDNA target can be detected in a range from 0.1 to 100 nM with a detection limit of 0.04 nM. The proposed protocol is sensitive, specific, simple, time-saving and polymerase chain reaction free without complicated immobilization, separation and washing steps, which creates a simple but valuable tool for facilitating fast and accurate detection of disease related specific sequences or gene mutations

Quantitative Residue-Specific Protein Backbone Torsion Angle Dynamics from Concerted Measurement of ³<i>J</i> Couplings

Three-bond ³<i>J</i>_C′C′ and ³<i>J</i>_HNHα couplings in peptides and proteins are functions of the intervening backbone torsion angle ϕ. In well-ordered regions, ³<i>J</i>_HNHα is tightly correlated with ³<i>J</i>_C′C′, but the presence of large ϕ angle fluctuations differentially affects the two types of couplings. Assuming the ϕ angles follow a Gaussian distribution, the width of this distribution can be extracted from ³<i>J</i>_C′C′ and ³<i>J</i>_HNHα, as demonstrated for the folded proteins ubiquitin and GB3. In intrinsically disordered proteins, slow transverse relaxation permits measurement of ³<i>J</i>_C′C′ and ³<i>J</i>_HNH couplings at very high precision, and impact of factors other than the intervening torsion angle on ³<i>J</i> will be minimal, making these couplings exceptionally valuable structural reporters. Analysis of α-synuclein yields rather homogeneous widths of 69 ± 6° for the ϕ angle distributions and ³<i>J</i>_C′C′ values that agree well with those of a recent maximum entropy analysis of chemical shifts, <i>J</i> couplings, and ¹H–¹H NOEs. Data are consistent with a modest (≤30%) population of the polyproline II region

Sequences of the overlapping polypeptides from TMUV NS1 (SDSG strain, Accession number: KJ740747.1).

<p>Sequences of the overlapping polypeptides from TMUV NS1 (SDSG strain, Accession number: KJ740747.1).</p

IFA and western-blot identification of mAb 3G2.

<p>A: Western-blot identification Lane 1, Control, GST-tag didn’t react with mAb 3G2; Lane 2, The band of NS1-GST fusion protein was reacted with mAb 3G2; Lane M, Blue plusIIprotein Marker (14-120kda, Transgen Biotech). B: IFA identification Monoclonal antibody against TMUV NS1 protein was used to perform IFA on TMUV-infected BHK-21 cells. BHK-21 cells infected with TMUV yielded significant fluorescence with six MAbs in the cytoplasm; Control BHK-21 cells didn’t yield any fluorescence.</p