Enzyme-Triggered Transforming of Assembly Peptide-Modified Magnetic Resonance-Tuned Probe for Highly Sensitive Imaging of Bacterial Infection In Vivo.

Confirming bacterial infection at an early stage and distinguishing between sterile inflammation and bacterial infection is still highly needed for efficient treatment. Here, in situ highly sensitive magnetic resonance imaging (MRI) bacterial infection in vivo based on a peptide-modified magnetic resonance tuning (MRET) probe (MPD-1) that responds to matrix metallopeptidase 2 (MMP-2) highly expressed in bacteria-infected microenvironments is achieved. MPD-1 is an assembly of magnetic nanoparticle (MNP) bearing with gadolinium ion (Gd3+ ) modified MMP-2-cleavable self-assembled peptide (P1 ) and bacteria-targeting peptide (P), and it shows T2 -weighted signal due to the assemble of MNP and MRET ON phenomenon between MNP assembly and Gd3+ . Once MPD-1 accumulates at the bacterially infected site, P1 included in MPD-1 is cleaved explicitly by MMP-2, which triggers the T2 contrast agent of MPD-1 to disassemble into the monomer of MNP, leading the recovery of T1 -weighted signal. Simultaneously, Gd3+ detaches from MNP, further enhancing the T1 -weighted signal due to MRET OFF. The sensitive MRI of Staphylococcus aureus (low to 104 CFU) at the myositis site and accurate differentiation between sterile inflammation and bacterial infection based on the proposed MPD-1 probe suggests that this novel probe would be a promising candidate for efficiently detecting bacterial infection in vivo.

Interference-Free Detection of Hydroxyl Radical and Arthritis Diagnosis by Rare Earth-Based Nanoprobe Utilizing SWIR Emission as Reference.

Due to the high oxidative potential of the hydroxyl radical (•OH), the accumulation of •OH in tissues can cause inflammation, such as that in arthritis. Therefore, the development of •OH detection with high efficiency and sensitivity is important for the treatment of related diseases. In this work, a cypate-modified core-shell NaErF4@NaLuF4 nanoprobe (csEr-Cy) was designed for detecting •OH on the basis of a typical reaction between cypate and •OH. The process resulted in the recovery of 654 nm upconversion luminescence emission of csEr because of a weakened inner filter effect (IFE) and Förster resonance energy transfer (FRET). The short-wavelength infrared (SWIR) emission at 1550 nm was not affected by •OH addition, thus enabling interference-free detection. Density functional theory (DFT) calculations were performed to explain the underlying mechanism. With the SWIR signal used as a reference for •OH detection, the csEr-Cy nanoprobe showed higher sensitivity and penetration than visible reference. This method was successfully used in mice for the diagnosis of arthritis in vivo. Our results provide novel insights into improving the sensitivity of nanoprobes for molecule detection and disease diagnosis.

An Easily Available Ratiometric Reaction-Based AIE Probe for Carbon Monoxide Light-up Imaging.

Carbon monoxide (CO) is a significant gasotransmitter that naturally modulates inflammatory responses. Visualization of CO in situ would help to reveal its physiological/pathological functions. Unfortunately, most existing CO fluorescent probes show aggregation-caused quenching (ACQ) properties. Herein, we report the reaction-based fluorescent probe (BTCV-CO) with aggregation-induced emission (AIE) characteristics for CO detection and imaging. This ratiometric AIE probe showed excellent stability, high sensitivity (detection limit of 30.8 nM), and superior selectivity. More importantly, this CO-responsive AIE probe could be facilely designed and easily obtained by two-step synthesis with high yield, providing an easy-to-handle AIE toolbox for real-time visualization of CO in a living system.

Yellow-emissive carbon dots with a large Stokes shift are viable fluorescent probes for detection and cellular imaging of silver ions and glutathione.

Yellow-emissive carbon dots (Y-CDs) were prepared by a solvothermal method using anhydrous citric acid and 2,3-phenazinediamine as the starting materials. The Y-CDs display a 24% fluorescence quantum yield, a 188-nm Stokes' shift and excellent stability. They are shown here to be excellent fluorescent probes for the determination of Ag(I) ion and glutathione (GSH). If exposed to Ag(I) ions, they are bound by the carboxy groups of the Y-CDs, and this causes quenching of fluorescence (with excitation/emission maxima at 380/568 nm) via a static quenching mechanism. This effect was used to design a fluorometric assay for Ag(I). The quenched fluorescence of the Y-CDs can be restored by adding GSH due to the high affinity of GSH for Ag(I). The calibration plot for Ag(I) is linear in the 1-4 µM Ag(I) concentration range, and the limit of detection is 31 nM. The respective values for GSH are 5-32 µM, and 76 nM, respectively. The method was applied to the detection of Ag(I) in spiked environmental water samples and gave recoveries ranging from 93 to 107%. It was also applied to the determination of GSH in tomatoes and purple grapes and gave satisfactory recoveries. The Y-CDs display low cytotoxicity and were successfully used to image Ag(I) and GSH in H1299 cells. Graphical abstract Schematic presentation of the mechanism of yellow fluorescent CDs for the detection of Ag+ and glutathione.

A silver(I) doped bud-like DNA nanostructure as a dual-functional nanolabel for voltammetric discrimination of methylated from unmethylated genes.

A small DNA structure, referred to as DNA nanobud (NB), was used for the first time to design a dual-functional nanolabel in order to recognize a particular oligonucleotide sequence, generate and amplify the electrochemical analytical signal. NBs containing numerous repetitive desired sequences were prepared through self-assembly of 8-h rolling circle amplification. Then, redox-active silver ions were loaded onto the NBs by over-night incubation with a solution of AgNO3. The incorporation of Ag+ into NBs was confirmed by field emission scanning electron microscopy, dynamic light scattering, UV-Vis spectroscopy, zeta potential measurements, and energy-dispersive X-ray spectroscopy. A DNA sandwich complex was created after hybridization of Ag+-NB with target sequence, which was captured by immobilized probe on a gold electrode. Cyclic voltammetry was applied to measure the redox signal of silver ions produced typically at a potential around 0.02 V vs. Ag/AgCl. The label can specifically discriminate fully methylated BMP3 gene from fully unmethylated bisulfate-converted part of the gene. The electrochemical signal produced by DNA sandwich complex of gold/probe/BMP3/Ag+-NB was linear toward BMP3 concentration from 100 pM to 100 nM. The method has a 100 pM BMP3 detection limit. Conceivably, this nanolabel can be designed and modified such that it may also be used to detect other sequences with lower detection limits. Graphical abstract Ag+-NB as a new nanolabel for genosensing was formed by loading Ag+ on a spherical DNA nanostructure, nanobud (NB), synthesized by rolling circle amplification process. By using a gold electrode (AuE), Ag+-NB with numerous electroactive cations and binding sites can detect targets and generate amplified electrochemical signals.

Choose and Use Your Chemical Probe Wisely to Explore Cancer Biology.

Small-molecule chemical probes or tools have become progressively more important in recent years as valuable reagents to investigate fundamental biological mechanisms and processes causing disease, including cancer. Chemical probes have also achieved greater prominence alongside complementary biological reagents for target validation in drug discovery. However, there is evidence of widespread continuing misuse and promulgation of poor-quality and insufficiently selective chemical probes, perpetuating a worrisome and misleading pollution of the scientific literature. We discuss current challenges with the selection and use of chemical probes, and suggest how biologists can and should be more discriminating in the probes they employ.

Two-Way Gold Nanoparticle Label-Free Sensing of Specific Sequence and Small Molecule Targets Using Switchable Concatemers.

A two-way colorimetric biosensor based on unmodified gold nanoparticles (GNPs) and a switchable double-stranded DNA (dsDNA) concatemer have been demonstrated. Two hairpin probes (H1 and H2) were first designed that provided the fuels to assemble the dsDNA concatemers via hybridization chain reaction (HCR). A functional hairpin (FH) was rationally designed to recognize the target sequences. All the hairpins contained a single-stranded DNA (ssDNA) loop and sticky end to prevent GNPs from salt-induced aggregation. In the presence of target sequence, the capture probe blocked in the FH recognizes the target to form a duplex DNA, which causes the release of the initiator probe by FH conformational change. This process then starts the alternate-opening of H1 and H2 through HCR, and dsDNA concatemers grow from the target sequence. As a result, unmodified GNPs undergo salt-induced aggregation because the formed dsDNA concatemers are stiffer and provide less stabilization. A light purple-to-blue color variation was observed in the bulk solution, termed the light-off sensing way. Furthermore, H1 ingeniously inserted an aptamer sequence to generate dsDNA concatemers with multiple small molecule binding sites. In the presence of small molecule targets, concatemers can be disassembled into mixtures with ssDNA sticky ends. A blue-to-purple reverse color variation was observed due to the regeneration of the ssDNA, termed the light-on way. The two-way biosensor can detect both nucleic acids and small molecule targets with one sensing device. This switchable sensing element is label-free, enzyme-free, and sophisticated-instrumentation-free. The detection limits of both targets were below nanomolar.

Impedimetric PSA aptasensor based on the use of a glassy carbon electrode modified with titanium oxide nanoparticles and silk fibroin nanofibers.

This article describes an impedimetric aptasensor for the prostate specific antigen (PSA), a widely accepted prostate cancer biomarker. A glassy carbon electrode (GCE) was modified with titanium oxide nanoparticles (TiO2) and silk fibroin nanofiber (SF) composite. The aptasensor was obtained by immobilizing a PSA-binding aptamer on the AuNP-modified with 6-mercapto-1-hexanol. The single fabrication steps were characterized by cyclic voltammetry and electrochemical impedance spectroscopy. The assay has two linear response ranges (from 2.5 fg.mL-1 to 25 pg.mL-1, and from 25 pg.mL-1 to 25 ng.mL-1) and a 0.8 fg.mL -1 detection limit. After optimization of experimental conditions, the sensor is highly selective for PSA over bovine serum albumin and lysozyme. It was successfully applied to the detection of PSA in spiked serum samples. Graphical abstract Schematic of the fabrication of an aptasensor for the prostate specific antigen (PSA). It is based on the use of a glassy carbon electrode modified with gold nanoparticles and titanium oxide-silk fibroin. The immobilization process of aptamer and interaction with PSA were followed by electrochemical impedance spectroscopy technique.

Development and Validation of Broad-Range Qualitative and Clade-Specific Quantitative Molecular Probes for Assessing Mercury Methylation in the Environment.

Two genes, hgcA and hgcB, are essential for microbial mercury (Hg) methylation. Detection and estimation of their abundance, in conjunction with Hg concentration, bioavailability, and biogeochemistry, are critical in determining potential hot spots of methylmercury (MeHg) generation in at-risk environments. We developed broad-range degenerate PCR primers spanning known hgcAB genes to determine the presence of both genes in diverse environments. These primers were tested against an extensive set of pure cultures with published genomes, including 13 Deltaproteobacteria, nine Firmicutes, and nine methanogenic Archaea genomes. A distinct PCR product at the expected size was confirmed for all hgcAB(+) strains tested via Sanger sequencing. Additionally, we developed clade-specific degenerate quantitative PCR (qPCR) primers that targeted hgcA for each of the three dominant Hg-methylating clades. The clade-specific qPCR primers amplified hgcA from 64%, 88%, and 86% of tested pure cultures of Deltaproteobacteria, Firmicutes, and Archaea, respectively, and were highly specific for each clade. Amplification efficiencies and detection limits were quantified for each organism. Primer sensitivity varied among species based on sequence conservation. Finally, to begin to evaluate the utility of our primer sets in nature, we tested hgcA and hgcAB recovery from pure cultures spiked into sand and soil. These novel quantitative molecular tools designed in this study will allow for more accurate identification and quantification of the individual Hg-methylating groups of microorganisms in the environment. The resulting data will be essential in developing accurate and robust predictive models of Hg methylation potential, ideally integrating the geochemistry of Hg methylation to the microbiology and genetics of hgcAB IMPORTANCE: The neurotoxin methylmercury (MeHg) poses a serious risk to human health. MeHg production in nature is associated with anaerobic microorganisms. The recent discovery of the Hg-methylating gene pair, hgcA and hgcB, has allowed us to design and optimize molecular probes against these genes within the genomic DNA for microorganisms known to methylate Hg. The protocols designed in this study allow for both qualitative and quantitative assessments of pure-culture or environmental samples. With these protocols in hand, we can begin to study the distribution of Hg-methylating organisms in nature via a cultivation-independent strategy.

Dual nano-sized contrast agents in PET/MRI: a systematic review.

Nowadays molecular imaging plays a vital role in achieving a successful targeted and personalized treatment. Hence, the approach of combining two or more medical imaging modalities was developed. The objective of this review is to systematically compare recent dual contrast agents in Positron Emission Tomography (PET)/Magnetic Resonance Imaging (MRI) and in some cases Single photon emission computed tomography (SPECT)/MRI in terms of some their characteristics, such as tumor uptake, and reticuloendothelial system uptake (especially liver) and their relaxivity rates for early detection of primary cancer tumor. To the best of our knowledge, this is the first systematic and integrated overview of this field. Two reviewers individually directed the systematic review search using PubMed, MEDLINE and Google Scholar. Two other reviewers directed quality assessment, using the criteria checklist from the CAMARADES (Collaborative Approach to Meta-Analysis and Review of Animal Data from Experimental Studies) tool, and differences were resolved by consensus. After reviewing all 49 studies, we concluded that a size range of 20-200 nm can be used for molecular imaging, although it is better to try to achieve as small a size as it is possible. Also, small nanoparticles with a hydrophilic coating and positive charge are suitable as a T2 contrast agent. According to our selected data, the most successful dual probes in terms of high targeting were with an average size of 40 nm, PEGylated using peptides as a biomarker and radiolabeled with copper 64 and gallium 68. Copyright © 2017 John Wiley & Sons, Ltd.

Learning from PAINful lessons.

Chemical probes are important both as tools to understand biology and as starting points for drug leads, but not every active molecule makes a good probe; many react nonspecifically with thiols. These promiscuous inhibitors are worse than useless because they can mislead researchers and muddy the literature. Understanding the mechanisms of such compounds can prevent scientists from following false hits down blind alleys.

DNA sensor with a dipyridophenazine complex of osmium(lI) as an electrochemical probe.

Application of a dipyrido[3,2-a:2',3'-c]phenazine (DPPZ)-type metal complex as an DNA electrochemical probe was studied. The introduction of electron-donating groups (NH2) was effective for controlling the redox potential and binding affinities of the DPPZ-type osmium complex. The [Os(DA-bpy)2DPPZ]2+ complex (DA-bpy; 4,4'-diamino-2,2'-bipyridine) had a lower half-wave potential (E 1/2) of 147 mV (vs Ag/AgCl) and higher binding affinity with DNA (binding constant, K = 3.1 x 10(7) M(-1)) than those of other complexes. With a single-stranded DNA immobilized gold electrode, the hybridization signal (deltaI) of the [Os(DA-bpy)2DPPZ]2+ complex was linear in the concentration range of 1.0 pg mL(-1) - 0.12 microg mL(-1) for the targeted DNA with a regression coefficient of 0.999. The detection limit was 0. 1 pg mL(-1). The 400-bp yAL3 gene was also detected with good sensitivity and selectivity using the [Os(DA-bpy)2DPPZ]2+ complex.

Optimisation of probe concentration in indirect photometric detection in capillary electrophoresis using highly absorbing dyes.

In indirect photometric detection in capillary electrophoresis, the concentration of the absorbing probe ion in the background electrolyte should be as high as possible in order to increase the dynamic range of the detection method. For relatively low absorptivity probes (epsilon < 2000 L mol(-1)cm(-1)) used under typical conditions (75 microm ID capillary) the maximum probe concentration is normally limited by the separation current. However, for medium (epsilon approximately/= 2000-15000 L mol(-1)cm(-1)) and especially for high (epsilon > 15000 L mol(-1)cm(-1)) absorptivity probes such as dyes, the maximum concentration may be limited by the background absorbance of the electrolyte which must fall within the linearity range of the detector. In this work, it is shown that another practical factor limiting the probe concentration is the adsorption of probe onto the capillary wall at higher concentrations, resulting in unstable baseline and increased noise. Use of a zwitterionic surfactant to suppress adsorption enabled the concentration of a model probe anion (tartrazine) to be increased by a factor of six times (to 3 mM). This resulted in significant improvements in peaks shapes, resolution between peaks, detection sensitivity and linear calibration range for the analyte anions. Baseline separation of a test mixture was maintained up to 7.5 mM total concentration of sample coions injected (13.7 nL) for the 3 mM electrolyte, with detection limits ranging from 0.63 to 0.94 microM. Peak height reproducibility (over 20 consecutive injections) was improved (values ranging from 1.1 to 1.9%) compared with electrolytes containing lower concentrations of the probe. Overall, the optimised, higher concentration probe electrolyte provided the sensitivity benefits of highly absorbing probes with the additional benefits of ruggedness and improved stacking, peak shapes and resolution.

Molecular analysis of the immunoglobulin heavy chain gene in the diagnosis of primary cutaneous B cell lymphoma.

The diagnosis of primary cutaneous B cell lymphoma can be difficult on the basis of histologic and immunophenotypic features alone. Previous polymerase chain reaction studies for detection of a clonal population in nodal B cell lymphomas have employed different primer pairs with detection sensitivities varying between 34% and 94% but there have been no comprehensive studies of primary cutaneous B cell lymphoma. We compared the sensitivity of different sets of consensus primers to amplify the CDR3 VDJ region of the immunoglobulin heavy chain gene in combination with an immunoglobulin heavy chain joining region consensus primer to detect a monoclonal population in 39 cases of primary cutaneous B cell lymphoma. Radiolabeled products were analyzed with denaturing 6% polyacrylamide gel electrophoresis. Sequence analysis was used to confirm amplification of clonal immunoglobulin heavy chain gene rearrangements and to establish whether somatic hypermutation can interfere with primer binding. Clonal immunoglobulin heavy chain gene rearrangements were demonstrated in 79% of cases (74% with leader sequences, 64% with FR1, and 45% with FR3 primers). Somatic hypermutation at primer binding sites was confirmed in cases where a false negative result was obtained with the FR3 primer. Although monoplex polymerase chain reaction amplification using the leader sequence primers is the most sensitive method for detecting a clonal population, six primers are required in six different reactions. Our findings suggest initial analysis with the FR3 primer and subsequent analysis using leader sequences in negative cases. Our data indicate that the FR3 consensus primer alone is not sufficient for a comprehensive analysis of primary cutaneous B cell lymphoma.

Thermal cycle labeling: zeptomole detection sensitivity and microgram probe amplification using CviJl* restriction-generated oligonucleotides.

A new method for efficiently labeling and amplifying DNA probes from anonymous samples has been developed. The two/three base recognition endonuclease CviJI* restricts DNA to numerous small fragments primarily 20-60 bp in size. Thermal denaturation of these fragments results in sequence-specific oligonucleotides complementary to their cognate template. Repeated cycles of denaturation, annealing, and extension of such a multiprimed template by a thermostable DNA polymerase results in a significant amplification of the starting material. This method of amplification, referred to as thermal cycle labeling (TCL), appears to generate a large fraction of rearranged and presumably branched products. The inclusion of nucleotide analogs in the TCL reaction generates microgram amounts of haptentagged probe with a detection limit of 25 zmol (2.5 x 10(-20) mol). Reactions containing [alpha-33P]dCTP yield high-specific-activity probes (2.6 x 10(9) cpm/microgram) with reduced radiolytic decay and a useful shelf life of 1 month. CviJI* -generated primers circumvent the need for synthetic oligos while providing microgram amounts of amplified and labeled probes using the described TCL protocol.