Rational Truncation of Aptamer for Ultrasensitive Aptasensing of Chloramphenicol: Studies Using Bio-Layer Interferometry.

Aptamers are an excellent choice for the selective detection of small molecules. However, the previously reported aptamer for chloramphenicol suffers from low affinity, probably as a result of steric hindrance due to its bulky nature (80 nucleotides) leading to lower sensitivity in analytical assays. The present work was aimed at improving this binding affinity by truncating the aptamer without compromising its stability and three-dimensional folding. Shorter aptamer sequences were designed by systematically removing bases from each or both ends of the original aptamer. Thermodynamic factors were evaluated computationally to provide insight into the stability and folding patterns of the modified aptamers. Binding affinities were evaluated using bio-layer interferometry. Among the eleven sequences generated, one aptamer was selected based on its low dissociation constant, length, and regression of model fitting with association and dissociation curves. The dissociation constant could be lowered by 86.93% by truncating 30 bases from the 3' end of the previously reported aptamer. The selected aptamer was used for the detection of chloramphenicol in honey samples, based on a visible color change upon the aggregation of gold nanospheres caused by aptamer desorption. The detection limit could be reduced 32.87 times (1.673 pg mL-1) using the modified length aptamer, indicating its improved affinity as well as its suitability in real-sample analysis for the ultrasensitive detection of chloramphenicol.

Fluorescent aptasensor for the ultrasensitive detection of antibiotic residue in food samples based on dumbbell DNA-mediated signal amplification.

Sensitive and reliable detection of antibiotics is of great significance for environmental and food safety due to its high risk in trace concentrations. Herein, we developed a fluorescence sensing system for chloramphenicol (CAP) detection based on dumbbell DNA-mediated signal amplification. Two hairpin dimers (2H1 and 2H2) were employed as the building blocks to construct the sensing scaffolds. The CAP-aptamer binding in another hairpin H0 can liberate the trigger DNA, which then activates the cyclic assembly reaction between 2H1 and 2H2. The separation of FAM and BHQ in the formed product of cascaded DNA ladder yields a high fluorescence signal for CAP monitoring. Compared with the monomer hairpin assembly between H1 and H2, the dimer hairpin assembly between 2H1 and 2H2 exhibits enhanced signal amplification efficiency and reduced reaction time. The developed CAP sensor showed a wide linear range from 10 fM to 10 nM with a detection limit of 2 fM. Importantly, this sensing platform has been successfully applied to the determination of CAP in fish, milk, and water samples with satisfactory recovery and accuracy. With the advantages of high sensitivity, mix-and-read pattern, and robustness, our proposed CAP sensor can be used as a simple and routine tool for the detection of trace amounts of antibiotic residues.

Enhanced reductive degradation of chloramphenicol by sulfidated microscale zero-valent iron: Sulfur-induced mechanism, competitive kinetics, and new transformation pathway.

Crystalline iron sulfide (FeSx, i.e., FeS or FeS2) minerals as sulfur sources were used to prepare the mechanochemically sulfidated microscale zero-valent iron ((FeSx+ZVI)bm). Metastable FeS and FeS2 precursors were generated via aqueous coprecipitation and applied to fabricate FeSx@ZVI samples. (FeSx+ZVI)bm and FeSx@ZVI exhibited better chloramphenicol (CAP) degradation than ZVI due to the increase in specific surface areas, the decrease of electrochemical impedance, the formation of galvanic cells, and sulfur-induced pitting and local acidity. (FeSx+ZVI)bm had better CAP removal capacity than FeSx@ZVI under different S/Fe molar ratios, initial pH, and oxygen conditions. At the same time, FeSx@ZVI showed better electron utilization under oxic conditions, related to their Fe0 and sulfur spatial distribution. Nitro reduction and dechlorination of CAP by (FeSx+ZVI)bm produced nitroso, azoxy, amine, and monodechlorination products, while dechlorination was not involved in the degradation process of CAP by FeSx@ZVI. A new transformation pathway of nitroso-CAP to amine-CAP mediated by azoxy products is proposed via coupling a chain decay multispecies model and DFT calculations. The larger competitive reaction rates among O2, CAP, and its degradation products was determined by their lower LUMO energy. The contribution of direct electron transfer to nitro reduction was greater than that of atomic hydrogen, but the opposite was true for dechlorination. FeSx@ZVI had a larger DET contribution than (FeSx+ZVI)bm, and FeS2 promoted the DET contribution better than FeS. Toxicity assessment indicated that the rapid transformation of nitroso and azoxy products was crucial for eliminating the biotoxicity of CAP.

Triple-Helix Molecular Switch Triggered Cleavage Effect of DNAzyme for Ultrasensitive Electrochemical Detection of Chloramphenicol.

The abuse of chloramphenicol (CAP) in animal-derived products leads to serious food safety problems, so the sensitive and accurate determination of CAP residues has great noteworthiness for public health. Herein, we present a novel electrochemical aptasensor that incorporates a poly(diallyldimethylammonium chloride) functionalized graphene/Ag@Au nanosheets (PDDA-Gr/Ag@Au NSs) composite modified electrode and a DNAzyme signal amplification effect triggered by a triple-helix molecular switch (THMS) for detecting CAP. The PDDA-Gr/Ag@Au NSs composite has the advantages of high surface area, great conductivity, and dispersibility and has successfully improved the electrochemical performance of the electrode. Specific interaction with CAP will cause the signal transduction probe (STP) to be released from the THMS. After that, the DNAzyme will be activated with the help of Pb2+ and remove the immobilized signal probe on the electrode surface. The signal change was recorded by square wave voltammetry (SWV) and led to an accurate quantification of CAP. With all these features, the proposed sensing strategy yielded a satisfactory analytical performance with linearity between 1 pM and 1 µM and a limit of detection of 18.6 fM. Furthermore, the aptasensor shows excellent specificity for CAP in the presence of other antibiotics and resists interference with other common metal ions. Importantly, the performance is not diminished when the constructed aptasensor is applied to measuring CAP in milk powder. This THMS-based method is easy to design, and alteration to different targets can be achieved by simply replacing the aptamer sequence in the THMS. Therefore, this method shows significant prospects as a flexible platform for accurate monitoring of antibiotic residues in foodstuffs.

Structural basis for the context-specific action of the classic peptidyl transferase inhibitor chloramphenicol.

Ribosome-targeting antibiotics serve as powerful antimicrobials and as tools for studying the ribosome, the catalytic peptidyl transferase center (PTC) of which is targeted by many drugs. The classic PTC-acting antibiotic chloramphenicol (CHL) and the newest clinically significant linezolid (LZD) were considered indiscriminate inhibitors of protein synthesis that cause ribosome stalling at every codon of every gene being translated. However, recent discoveries have shown that CHL and LZD preferentially arrest translation when the ribosome needs to polymerize particular amino acid sequences. The molecular mechanisms that underlie the context-specific action of ribosome inhibitors are unknown. Here we present high-resolution structures of ribosomal complexes, with or without CHL, carrying specific nascent peptides that support or negate the drug action. Our data suggest that the penultimate residue of the nascent peptide directly modulates antibiotic affinity to the ribosome by either establishing specific interactions with the drug or by obstructing its proper placement in the binding site.

Green preparation of porous hierarchical TiO2(B)/anatase phase junction for effective photocatalytic degradation of antibiotics.

In this study, porous hierarchical bronze/anatase phase junction TiO2 assembled by ultrathin two-dimensional nanosheets was prepared by a novel, green and simple deep eutectic solvent-regulated strategy. Due to its structural features, the TiO2 sample exhibited enhanced photocatalytic activities for multiple kinds of antibiotics, including ofloxacin, ciprofloxacin and chloramphenicol.

Dual genetic selection of the theophylline riboswitch with altered aptamer specificity for caffeine.

The aptamer domain of the theophylline riboswitch was randomized to generate a library containing millions of different variants. Dual genetic selection utilizing the cat-upp fusion gene was performed for the library, which successfully led to the identification of a caffeine-specific synthetic riboswitch. When a chloramphenicol-resistance gene was expressed under control of this riboswitch, E. coli cells showed chloramphenicol resistance only in the presence of caffeine. When inserted upstream of the gfpuv or lacZ gene, the caffeine riboswitch induced the expression of green fluorescent protein or ß-galactosidase in the presence of caffeine, respectively. When tested with various concentrations of caffeine, the ß-galactosidase activity was proportional to the amount of caffeine, clearly indicating the caffeine-dependent gene regulation by the caffeine riboswitch.

The in situ formation of a hole-transporting material on bismuth tungstate for innovative photoelectrochemical aptasensing.

We present the in situ formation of a hole-transporting material (bismuth hexacyanoferrate) on the surface of bismuth tungstate aimed at an innovative photoelectrochemical strategy. This approach enabled a competent aptasensing platform for chloramphenicol that was amenable to homogenous, label-free, and split-mode detection.

Stimuli-Responsive Metal-Organic Framework on a Metal-Organic Framework Heterostructure for Efficient Antibiotic Detection and Anticounterfeiting.

Stimuli-responsiveness is an important characteristic that show promising potential in various applications. Herein, a novel ZIF-8-on-Tb-dpn (H3dpn = 5-(2',4'-dicarboxylphenyl)nicotic acid) heterostructure is constructed using a heteroepitaxial strategy combining the chemical-responsive (antibiotics) and light-responsive behaviors. The pyridine nitrogen of Tb-dpn acts as an anchor site for Zn2+, which helps to overcome the limit of lattice mismatch between two metal-organic frameworks (MOFs) and promotes the growth of ZIF-8 nanocrystals. Based on the synergy effect of two MOFs, ZIF-8-on-Tb-dpn exhibits an efficient turn-off response toward tetracycline and chloramphenicol via competitive absorption, Förster resonance energy transfer, and photoinduced electron transfer processes with limit of detection values of 5.6 and 37.6 nM, respectively, which are three- to -fivefold lower than those of Tb-dpn. Moreover, the nanocage of ZIF-8 is utilized to encapsulate photochromic spiropyran (SP) molecules and realize the reversible conversion between SP and merocyanine (MC) under visible light and ultraviolet light. The MC form is accompanied with strong adsorption at 555 nm, which can erase the emission of Tb3+. Therefore, a reversible invisible anticounterfeiting pattern is designed with SP ⊂ ZIF-8-on-Tb-dpn for information anticounterfeiting. The excellent stimuli-responsive ability makes the luminescent platform a potential candidate in luminescence applications.

Synthesis and biological evaluation of a novel anticancer agent CBISC that induces DNA damage response and diminishes levels of mutant-p53.

A novel nitrogen mustard CBISC has been synthesized and evaluated as an anticancer agent. CBISC has been shown to exhibit enhanced cell proliferation inhibition properties against mutant p53 cell lines colorectal cancer WiDr, pancreatic cancer (MIAPaCa-2 and PANC-1), and triple negative breast cancer (MDA-MB-231 and MDA-MB-468). In vitro mechanism of action studies revealed perturbations in the p53 pathway and increased cell death as evidenced by western blotting, immunofluorescent microscopy and MTT assay. Further, in vivo studies revealed that CBISC is well tolerated in healthy mice and exhibited significant in vivo tumor growth inhibition properties in WiDr and MIAPaCa-2 xenograft models. These studies illustrate the potential utility of CBISC as an anticancer agent.

Characterization of the multidrug efflux transporter styMdtM from Salmonella enterica serovar Typhi.

Salmonellae are foodborne pathogens and the major cause of gastroenteritis in humans. Salmonellae express multidrug efflux transporters that play a key role in their drug resistance, which is becoming an increasing problem for therapeutic intervention. Despite their biomedical importance, the mechanisms underlying substrate transport by multidrug efflux transporters remain poorly understood. Here, we describe the first characterization of a multidrug transporter belonging to the major facilitator superfamily from the genus Salmonella. We show that several clinical Salmonella Typhi (S. Typhi) isolates constitutively express the styMdtM (STY4874) gene, which encodes a known multidrug-resistance (MDR) transporter. Guided by the structure of the Escherichia coli (E. coli) homolog, we studied two residues critical for substrate transport, Asp25 and Arg111. Mutation of Asp25 to glutamate did not affect the transport function of styMdtM, whereas mutation to alanine reduced its transport activity, suggesting that a negative charge at this position is critical for substrate translocation across the membrane. Substrate-affinity measurements by intrinsic fluorescence spectroscopy showed that the Asp25Ala mutant retained its capacity to bind substrate, albeit at a lower level. Mutation of Arg111 to alanine resulted in a decrease in secondary structure content of the transporter, and mutation to lysine completely destabilized the structure of the transporter. A homology model of styMdtM suggests that Arg111 is important for stabilizing the transmembrane domain by mediating necessary interactions between neighboring helices. Together, our studies provide new structural and mechanistic insights into the Salmonella MDR transporter styMdtM.

Multiplexed complexome profiling using tandem mass tags.

Complexome profiling is a rapidly spreading, powerful technique to gain insight into the nature of protein complexes. It identifies and quantifies protein complexes separated into multiple fractions of increasing molecular mass using mass spectrometry-based, label-free bottom-up proteomics. Complexome profiling enables a sophisticated and thorough characterization of the composition, molecular mass, assembly, and interactions of protein complexes. However, in practice, its application is limited by the large number of samples it generates and the related time of mass spectrometry analyses. Here, we report an improved process workflow that implements tandem mass tags for multiplexing complexome profiling. This workflow substantially reduces the number of samples and measuring time without compromising protein identification or quantification reliability. In profiles from mitochondrial fractions of cells recovering from chloramphenicol treatment, tandem mass tags-multiplexed complexome profiling exhibited migration patterns of mature ATP synthase (complex V) and assembly intermediates that were consistent in composition and abundance with profiles obtained by the label-free approach. Reporter ion quantifications of proteins and complexes unaffected by the chloramphenicol treatment presented less variation in comparison to the label-free method. Incorporation of tandem mass tags enabled an efficient and robust complexome profiling analysis and may foster broader application for protein complex profiling in biomedical research and diagnostics.

An electrochemical aptasensor based on PEI-C3N4/AuNWs for determination of chloramphenicol via exonuclease-assisted signal amplification.

An electrochemical aptasensor, including the polyethyleneimine-graphite-like carbon nitride/Au nanowire nanocomposite (PEI-C3N4/AuNWs) and exonuclease-assisted signal amplification strategy was constructed for the determination of chloramphenicol (CAP). Initially, a nanocomposite with substantial electrocatalytic property was synthesized by PEI-C3N4/AuNWs. This improves the conductivity and specific surface area of the PEI-C3N4/AuNW-modified gold electrode. Next, a DNA with a complementary sequence to a CAP aptamer (cDNA) was immobilized on the PEI-C3N4/AuNW-modified electrode, followed by the CAP aptamer hybridized with cDNA. The lower signal at this time is due to the negatively charged phosphate group of the oligonucleotide and [Fe (CN)6]3-/4- electrostatically repelling each other. The presence of the CAP would cause aptamer on the electrode surface to fall off and be digested by Recjf exonuclease, which resulted in target recycling, and a significant increase in DPV signal can be observed at a potential of 0.176 V (vs. Ag/AgCl). Under optimal conditions, there is a linear relationship between the peak current and the logarithm of CAP concentration in the range 100 fM-1 µM, and the detection limit of this aptasensor is 2.96 fM (S/N = 3). Furthermore, the resultant aptasensor has excellent specificity, reproducibility, and long-term stability, and has been applied to the detection of CAP in milk samples. Graphical abstract The detection principle of the electrochemical aptasensor for CAP detection was based on PEI-C3N4/AuNWs and exonuclease-assistant signal amplification. It is based on the fact that PEI-C3N4/AuNWs nanocomposites on the surface of the electrode can effectively improve the performance of the aptasensor, and Recjf exonuclease initiates the target recycling process, causes signal amplification.

Interaction of Chloramphenicol Cationic Peptide Analogues with the Ribosome.

Virtual screening of all possible tripeptide analogues of chloramphenicol was performed using molecular docking to evaluate their affinity to bacterial ribosomes. Chloramphenicol analogues that demonstrated the lowest calculated energy of interaction with ribosomes were synthesized. Chloramphenicol amine (CAM) derivatives, which contained specific peptide fragments from the proline-rich antimicrobial peptides were produced. It was demonstrated using displacement of the fluorescent erythromycin analogue from its complex with ribosomes that the novel peptide analogues of chloramphenicol were able to bind bacterial ribosome; all the designed tripeptide analogues and one of the chloramphenicol amine derivatives containing fragment of the proline-rich antimicrobial peptides exhibited significantly greater affinity to Escherichia coli ribosome than chloramphenicol. Correlation between the calculated and experimentally evaluated levels of the ligand efficiencies was observed. In vitro protein biosynthesis inhibition assay revealed, that the RAW-CAM analogue shows activity at the level of chloramphenicol. These data were confirmed by the chemical probing assay, according to which binding pattern of this analogue in the nascent peptide exit tunnel was similar to chloramphenicol.

Structure-switching fluorescence aptasensor for sensitive detection of chloramphenicol.

The performance of chloramphenicol aptamer, including binding thermodynamics, structure switching, and binding domain, was investigated by isothermal titration calorimetry, circular dichroism, and molecular docking. Then, a new fluorescence aptasensor was developed with signal amplification mediated by exonuclease I-catalyzed reaction and hybridization chain reaction (HCR) for chloramphenicol detection. In this system, the aptamer-binding domain is blocked by the initiator of HCR, the aptamer undergoes structure switching in the presence of chloramphenicol, and DNA dissociation occurs. The released aptamer is subsequently recognized and cleaved by Exo I to set free chloramphenicol. With the Exo I-assisted chloramphenicol recycling, an increasing number of initiators were exposed from the digestion of the initiator-aptamer complex. Then, the chain-like assembly of FAM labeled H1 and H2 through HCR was triggered by the initiator, generating a long DNA polymer. Under optimum conditions, the aptasensor exhibited a log-linear range from 0.001 to 100 nM of chloramphenicol and a detection limit of 0.3 pM. Additionally, the designed biosensing platform was applied to determine chloramphenicol in milk and lake water with high accuracy. The current approach provides a new avenue to develop sensitive aptasensors with the assistance of binding mechanism between aptamer and target compounds. Graphical abstract.

"Plug and Play" logic gate construction based on chemically triggered fluorescence switching of gold nanoparticles conjugated with Cy3-tagged aptamer.

Gold nanoparticles (AuNPs) conjugated with Cy3-tagged aptamer which can specifically recognize chloramphenicol (CAP) (referred to as AuNPs-AptCAP) are described. CAP can trigger the configuration change of CAP binding aptamer, and thus switching the fluorescence of AuNPs-AptCAP through changing the efficiency of the fluorescence resonance energy transfer (FRET) system with Cy3 as donors and AuNPs as recipients. AuNPs-AptCAP exhibits a linear range of CAP concentrations from 26.0 to 277 µg L-1 with a limit of detection of 8.1 µg L-1 when Cy3 was excited at 530 nm and emission was measured at 570 nm. More importantly, AuNPs-AptCAP can be utilized as signal transducers for the build-up of a series of logic gates including YES, PASS 0, INH, NOT, PASS 1, and NAND. Utilizing the principle of a metal ion-mediated fluorescence switch together with a strong metal ion chelator, the fluorescence of AuNPs-AptCAP could be modulated by adding metal ions and EDTA sequentially. Therefore, a "Plug and Play" logic system based on AuNPs-AptCAP has been realized by simply adding other components to create new logic functions. This work highlights the advantages of simple synthesis and facile fluorescence switching properties, which will provide useful knowledge for the establishment of molecular logic systems. Graphical abstract.

Theoretical Insight into the Interaction between Chloramphenicol and Functional Monomer (Methacrylic Acid) in Molecularly Imprinted Polymers.

Molecular imprinting technology is a promising method for detecting chloramphenicol (CAP), a broad-spectrum antibiotic with potential toxicity to humans, in animal-derived foods. This work aimed to investigate the interactions between the CAP as a template and functional monomers required for synthesizing efficient molecularly imprinted polymers for recognition and isolation of CAP based on density functional theory. The most suitable monomer, methacrylic acid (MAA), was determined based on interaction energies and Gibbs free energy changes. Further, the reaction sites of CAP and MAA was predicted through the frontier molecular orbitals and molecular electrostatic potentials. Atoms in molecules topology analysis and non-covalent interactions reduced density gradient were applied to investigate different types of non-covalent and inter-atomic interactions. The simulation results showed that CAP was the main electron donor, while MAA was the main electron acceptor. Moreover, the CAP-MAA complex simultaneously involved N-H···O and C=O···H double hydrogen bonds, where the strength of the latter was greater than that of the former. The existence of hydrogen bonds was also confirmed by theoretical and experimental hydrogen nuclear magnetic resonance and Fourier transform infrared spectroscopic analyses. This research can act as an important reference for intermolecular interactions and provide strong theoretical guidance regarding CAP in the synthesis of molecularly imprinted polymers.

Comparative Genomics Determines Strain-Dependent Secondary Metabolite Production in Streptomyces venezuelae Strains.

Streptomyces venezuelae is well known to produce various secondary metabolites, including chloramphenicol, jadomycin, and pikromycin. Although many strains have been classified as S. venezuelae species, only a limited number of strains have been explored extensively for their genomic contents. Moreover, genomic differences and diversity in secondary metabolite production between the strains have never been compared. Here, we report complete genome sequences of three S. venezuelae strains (ATCC 10712, ATCC 10595, and ATCC 21113) harboring chloramphenicol and jadomycin biosynthetic gene clusters (BGC). With these high-quality genome sequences, we revealed that the three strains share more than 85% of total genes and most of the secondary metabolite biosynthetic gene clusters (smBGC). Despite such conservation, the strains produced different amounts of chloramphenicol and jadomycin, indicating differential regulation of secondary metabolite production at the strain level. Interestingly, antagonistic production of chloramphenicol and jadomycin was observed in these strains. Through comparison of the chloramphenicol and jadomycin BGCs among the three strains, we found sequence variations in many genes, the non-coding RNA coding regions, and binding sites of regulators, which affect the production of the secondary metabolites. We anticipate that these genome sequences of closely related strains would serve as useful resources for understanding the complex secondary metabolism and for designing an optimal production process using Streptomyces strains.

An enzyme-free fluorometric nanoprobe for chloramphenicol based on signal amplification using graphene oxide sheets.

A sensitive and selective method for the determination of the antibiotic chloramphenicol (CAP) is described, which is based on double signal amplification and GO as an efficient fluorescence quencher. The nucleic acid probe is composed of three well-defined regions, viz. the signal probe I, the signal probe II, and the capture probe. The capture probe will bind to CAP specifically and the signal probes produce a significant fluorescence signal. One end of the signal probes is labeled with the fluorophore 6-carboxyfluorescein (FAM). The labeled probes can be adsorbed on graphene oxide (GO) via π-stacking interactions, upon which the green fluorescence of FAM (measured at excitation/emission wavelengths of 490/514 nm) is quenched. On addition of CAP, the aptamer/CAP complexes are formed, and this leads to the restoration of fluorescence due to the removal of the probes from GO. The double signal probes, together with GO as quencher, improve the fluorescence signal significantly and lower the detection limit. Under optimized conditions, the assay works in the 20- to 200-ppb CAP concentration range and has a 0.3-ppb detection limit. It is also successfully applied to the determination of CAP in spiked swine urine samples. The recoveries from spiked swine urine samples are between 97.73 and 108.56%, and the repeatability (expressed as the RSD) is between 4.66 and 8.90%. Graphical abstract The constructed DNA probes form a stable structure and bind to chloramphenicol specifically. One end of signal probes was labeled with the fluorophore 6-carboxyfluorescein (FAM). The detection sensitivity of chloramphenicol was significantly enhanced by using double signal amplification, which was superior to the traditional methods. The quantities of CAP can be achieved by fluorescence increment.