Surface plasmon resonance detection of oligonucleotide sequences of the rpoB genes of Mycobacterium tuberculosis

Oligonucleotide sequences related to the normal and mutated rpoB genes of Mycobacterium tuberculosis are detected using a surface plasmon resonance (SPR) biosensor system. A bioselective element was prepared by immobilizing the thiol-modified oligonucleotides of the selected sequence (the capture probe P2) that contains the mutated TCG → TTG codon 531 (evoking drug resistance) of the rpoB gene of M. tuberculosis on a gold sensor surface. Specific hybridization between immobilized probe P2 and complementary target T2 gave the highest sensor response, single-base mismatched oligonucleotide TN (corresponding to the normal gene sequence) produced somewhat smaller response and no response was observed at injection of noncomplementary oligonucleotide TC. The P2-T2 hybridization efficiency is calculated ca. 30% (5 × 10¹² molecules cm⁻²), and the lowest detection limit of T2 was 10 nM. An extended T2E oligonucleotide sequence consisting of T2 sequence and additional 24 nucleotides was shown to cause more pronounced sensor response (at least 5 nM T2E was easily detected). Injection into the sensor cell of the oligonucleotides complementary to the free additional part of T2E after P2-T2E hybridization gave a significant additional SPR response, thus showing that the sandwich hybridization format further improves the sensor sensitivity and decreases the lowest detection limit. The experimental results on surface hybridization between the studied oligonucleotides were in good agreement with thermodynamic parameters of the hybridization calculated for solution conditions. The described approach could be proposed as a basis for creating a biosensor for real-time and label-free diagnostics of drug resistant tuberculosis.     

Comparative proteomics analysis between biofilm and planktonic cells of Mycobacterium tuberculosis

Tuberculosis is highly persistent and displays phenotypic resistance to high concentrations of antimicrobials. Recent reports exhibited that Mycobacterium tuberculosis biofilm was implicated to its pathogenicity and drug resistance. In this study, there were 47 kinds of differential proteins in the biofilm of M. tuberculosis H37Rv cells compared with the planktonic bacteria, and 37 proteins were nonredundant and identified by proteomics approach, such as 2DE and LC‐MS/MS. Moreover, six kinds of proteins were identified as HspX, which were conservative and highly expressed in biofilm. Note that 47 differential proteins were divided into seven categories, such as cell wall and cell processes, conserved hypotheticals, intermediary metabolism and respiration, and so on by TUBERCULIST. The Gene Ontology classification results showed that the largest protein group involved in metabolism, binding proteins, and catalytic function accounts for 30% and 57% of all identified proteins, respectively. Moreover, the protein interaction network analyzed by STRING showed that the minority proteins such as RpoA, SucC, Cbs, Tuf, DnaK, and GroeL in the interaction network have high network connectivity. These results implied that the proteins involved in metabolic process and catalytic function and the minority proteins mentioned above may play an important role in M. tuberculosis biofilm formation. To our knowledge, this is the first report about differential proteins between biofilm and planktonic M. tuberculosis, which provided the potential antigens for vaccines and target proteins for anti‐mycobacterial drugs.     

Graphene Doped Mn2O3 Nanofibers as a Facile Electroanalytical DNA Point Mutation Detection Platform for Early Diagnosis of Breast/Ovarian Cancer

This paper demonstrates a simple, label‐free detection methodology for detecting single point DNA mutations. Single point mutation detection is a key enabler for diagnosis and prevention of several genetic disorders that manifest into cancers. Specifically for this purpose, herein, an electrochemical biosensor utilizing electrospun graphene doped manganese III oxide nanofibers (GMnO) is developed. The charge transfer resistance offered by GMnO is extremely sensitive to the localized change in the conductivity. This sensitivity, attributed to the low band gap of Mn₂O₃ and high charge transfer kinetics of graphene, is explored in the proposed mutation detection platform. As a proof of concept, ultrasensitive detection of BRCA1 gene specific point mutation is demonstrated. The target specific single stranded probe DNA is immobilized onto GMnO modified glassy carbon working electrodes via chemisorption. Post target‐DNA hybridization, differential pulse voltammetry is employed to facilitate detection of targeted point mutation, wherein, difference in peak currents is used to distinguish the target DNA as normal or mutant. Efficiency of the proposed method is evaluated against a target concentration ranging from 10 pM−1 μM. With respect to the mutated target DNA, the LoD of the proposed device is found to be 0.8±0.069 pM. The proposed approach can be extended for detecting any mutation/hybridization of interest by simply adapting an appropriate functionalization protocol.     

Shortening of Amino Acids from C-terminal of PZase as Basis of Pyrazinamide Resistance in P14 Isolate of Mycobacterium Tuberculosis Strain

Pyrazinamide (PZA) is one of the mainstays WHO-recommended drugs for therapy of tuberculosis (TB). The emergence of PZA resistance in clinical isolates of M. tuberculosis is often associated with pncA gene mutations encoding PZase. A local clinical isolate of Mycobacterium tuberculosis strain showed phenotipe resistant to PZA at concentration of 10 μg/mL. The ORF of pncA gene of the isolate showed deletion of guanine base at position 81, then followed by shortening of 70 amino acids from C-terminal of PZAse which has 186 amino acid residues. The mutant of PZase took frame shift of amino acids after the residue at position 27. The pncA gene mutation at the level of genotype, that produced a physical-chemical alteration of the active site or the metal-binding site of PZase, in this case perturbing or lossing its activity was proposed as trigering the PZA resistance in P14 clinical isolate of M. tuberculosis strain.     

Lable‐Free Electrochemical DNA Sensor Based on Gold Nanoparticles/Poly(neutral red) Modified Electrode

We present a new strategy for the label‐free electrochemical detection of DNA hybridization based on gold nanoparticles (AuNPs)/poly(neutral red) (PNR) modified electrode. Probe oligonucledotides with thiol groups at the 5‐end were covalently linked onto the surface of AuNPs/PNR modified electrode via S‐Au binding. The hybridization event was monitored by using differential pulse voltammetry (DPV) upon hybridization generates electrochemical changes at the PNR‐solution interface. A significant decrease in the peak current was observed upon hybridization of probe with complementary target ssDNA, whereas no obvious change was observed with noncomplementary target ssDNA. And the DNA sensor also showed a high selectivity for detecting one‐mismatched and three‐mismatched target ssDNA and a high sensitivity for detecting complementary target ssDNA, the detection limit is 4.2×10^?12 M for complementary target ssDNA. In addition, the DNA biosensor showed an excellent reproducibility and stability under the DNA‐hybridization conditions.     

Cluster‐based molecular docking study for in silico identification of novel 6‐fluoroquinolones as potential inhibitors against Mycobacterium tuberculosis

A classical protein sequence alignment and homology modeling strategy were used for building three Mycobacterium tuberculosis‐DNA gyrase protein models using the available topoII‐DNA‐6FQ crystal structure complexes originating from different organisms. The recently determined M. tuberculosis‐DNA gyrase apoprotein structures and topoII‐DNA‐6FQ complexes were used for defining the 6‐fluoroquinolones (6‐FQs) binding pockets. The quality of the generated models was initially validated by docking of the cocrystallized ligands into their binding site, and subsequently by quantitative evaluation of their discriminatory performances (identification of active/inactive 6‐FQs) for a set of 145 6‐FQs with known biological activity values. The M. tuberculosis‐DNA gyrase model with the highest estimated discriminatory power was selected and used afterwards in an additional molecular docking experiment on a mixed combinatorial set of 427 drug‐like 6‐FQ analogs for which the biological activity values were predicted using a prebuilt counter‐propagation artificial neural network model. A novel three‐level Boolean‐based [T/F (true/false)] clustering algorithm was used to assess the generated binding poses: Level 1 (geometry properties assessment), Level 2 (score‐based clustering and selection of the (T)‐signed highly scored Level 1 poses), and Level 3 (activity‐based clustering and selection of the most “active” (T)‐signed Level 2 hits). The frequency analysis of occurrence of the fragments attached at R₁ and R₇ position of the (T)‐signed 6‐FQs selected in Level 3 revealed several novel attractive fragments and confirmed some previous findings. We believe that this methodology could be successfully used in establishing novel possible structure‐activity relationship recommendations in the 6‐FQs optimization, which could be of great importance in the current antimycobacterial hit‐to‐lead processes. © 2012 Wiley Periodicals, Inc.     

Multiplex identification of drug‐resistant Gram‐positive pathogens using stuffer‐free MLPA system

Early detection of pathogens from blood and identification of their drug resistance are essential for sepsis management. However, conventional culture‐based methods require relatively longer time to identify drug‐resistant pathogens, which delays therapeutic decisions. For precise multiplex detection of drug‐resistant Gram‐positive pathogens, we developed a method by using stuffer‐free multiplex ligation‐dependent probe amplification (MLPA) coupled with high‐resolution CE single‐strand conformation polymorphisms (CE‐SSCP) system. We designed three probe sets for genes specific to Gram‐positive species (Staphylococcus aureus: nuc, Enterococcus faecium: sodA, and Streptococcus pneumoniae: lytA) and two sets for genes associated with drug resistance (mecA and vanA) to discriminate major Gram‐positive pathogens with the resistance. A total of 94 different strains (34 reference strains and 60 clinical isolates) were used to validate this method and strain‐specific peaks were successfully observed for all the strains. To improve sensitivity of the method, a target‐specific preamplification step was introduced and, consequently, the sensitivity increased from 10 pg to 100 fg. We also reduced a total assay time to 8 h by optimizing hybridization time without compromising test sensitivity. Taken together, our multiplex detection system can improve detection of drug‐resistant Gram‐positive pathogens from sepsis patients’ blood.     

Design,Synthesis, and in vitro Anti‐mycobacterial Activities of Propylene‐tethered Heteronuclear Bis‐isatin Derivatives

A series of novel propylene‐tethered heteronuclear bis‐isatin derivatives were designed, synthesized, and assessed for their in vitro and anti‐mycobacterial activities. All hybrids exhibited considerable antibacterial and anti‐mycobacterial activities against Mycobacterium tuberculosis H37Rv and multi‐drug‐resistant tuberculosis (MDR‐TB) with minimum inhibitory concentration (MIC) ranging from 16 to 256 μg/mL. In particular, the heteronuclear bis‐isatin 4i (MIC: 25 and 16 μg/mL) was most active against M. tuberculosis H₃₇Rv and MDR‐TB strains, which was fourfold and greater than eightfold more potent than the first‐line anti‐tubercular agents rifampicin (MIC: 64 μg/mL) and isoniazid (MIC: >128 μg/mL) against MDR‐TB, could act as a lead for further optimization.     

The Structural Basis of Mycobacterium tuberculosis RpoB Drug-Resistant Clinical Mutations on Rifampicin Drug Binding

Tuberculosis (TB), caused by the Mycobacterium tuberculosis infection, continues to be a leading cause of morbidity and mortality in developing countries. Resistance to the first-line anti-TB drugs, isoniazid (INH) and rifampicin (RIF), is a major drawback to effective TB treatment. Genetic mutations in the β-subunit of the DNA-directed RNA polymerase (rpoB) are reported to be a major reason of RIF resistance. However, the structural basis and mechanisms of these resistant mutations are insufficiently understood. In the present study, thirty drug-resistant mutants of rpoB were initially modeled and screened against RIF via a comparative molecular docking analysis with the wild-type (WT) model. These analyses prioritized six mutants (Asp441Val, Ser456Trp, Ser456Gln, Arg454Gln, His451Gly, and His451Pro) that showed adverse binding affinities, molecular interactions, and RIF binding hinderance properties, with respect to the WT. These mutant models were subsequently analyzed by molecular dynamics (MD) simulations. One-hundred nanosecond all-atom MD simulations, binding free energy calculations, and a dynamic residue network analysis (DRN) were employed to exhaustively assess the impact of mutations on RIF binding dynamics. Considering the global structural motions and protein–ligand binding affinities, the Asp441Val, Ser456Gln, and His454Pro mutations generally yielded detrimental effects on RIF binding. Locally, we found that the electrostatic contributions to binding, particularly by Arg454 and Glu487, might be adjusted to counteract resistance. The DRN analysis revealed that all mutations mostly distorted the communication values of the critical hubs and may, therefore, confer conformational changes in rpoB to perturb RIF binding. In principle, the approach combined fundamental molecular modeling tools for robust “global” and “local” level analyses of structural dynamics, making it well suited for investigating other similar drug resistance cases.     

DNA sensor: A novel electrochemical gene detection method using carbon electrode immobilized DNA probes

Abstract

The authors have developed a novel, rapid, convenient, and specific gene detection method, named the ‘DNA sensor,’ using a graphite electrode loaded with DNA probes. Synthesized oligonucleotide (5-TGCAGTTCCGGTGGCTGATC-3′) complementary to oncogene v-myc was employed for a model probe. The oligonucleotide was chemically adsorbed on a basal plane pyrolytic graphite (BPPG) electrode. The sensor was able to be applied to a hybridization reaction (40°C) in a linearized pVM623 solution carrying the Pst I fragment of v-myc (1.5 kbp).

After the hybridization reaction, the sensor was immersed into an acridine orange solution (1 μM) and washed with a phosphate buffer (pH 7.0). Acridine orange intercalated between base pairs of the formed double stranded DNAs on the electrode. The anodic peak potential of acridine orange that interacted with the DNAs on the electrode was measured. The positive shift of the peak potential increased in proportional to the pVM623 concentration in the hybridization reaction. 10^?1 g/ml of pVM623 was able to be detected in the buffer solution using the sensor. This gene detection was completed within an hour.     

Macozinone: revised synthesis and crystal structure of a promising new drug for treating drug‐sensitive and drug‐resistant tuberculosis

Mycobacterium tuberculosis (Mtb), the principal etiological agent of tuberculosis (TB), infects over one‐quarter of humanity and is now the leading cause of infectious disease mortality by a single pathogen. Macozinone {2‐[4‐(cyclohexylmethyl)piperazin‐1‐yl]‐8‐nitro‐6‐(trifluoromethyl)‐4H‐1,3‐benzothiazin‐4‐one, C₂₀H₂₃F₃N₄O₃S} is a promising new drug for treating drug‐sensitive and drug‐resistant TB that has successfully completed phase I clinical trials. We report the complete spectroscopic and structural characterization by ¹H NMR, ¹³C NMR, HRMS, IR, and X‐ray crystallography. The cyclohexyl moiety is observed to be nearly perpendicular to the core formed by the 1,3‐benzothiazin‐4‐one and piperazine groups. The central piperazine ring adopts a slightly distorted chair conformation caused by sp²‐hybridization of the nitro N atom, which donates into the electron‐deficient 1,3‐benzothiazin‐4‐one group.     

p16基因甲基化的芯片定量检测

p16基因的失活与多种肿瘤相关,但p16基因缺失率较低,突变更为罕见,p16基因启动子区CpG岛甲基化与其蛋白表达密切相关．DNA甲基化已成为目前研究的热点,现有的技术包括：Southernblot法、限制性内切酶-PCR法、DNA测序法、甲基化特异性PCR(MSP)、     

Screen-printed electrochemical hybridization biosensor for the detection of DNA sequences from the Escherichia coli pathogen

An electrochemical biosensor for the specific detection of short DNA sequences from the E. coli pathogen is described. This hybridization device relies on the immobilization of a 25-mer oligonucleotide probe, from the E. coli lacZ gene, onto a screen-printed carbon electrode. Chronopotentiometric detection of the Co(bpy)₃⁺³ indicator is used for monitoring the hybridization event. Numerous variables of the assay protocol, including those of the probe immobilization step, the hybridization event, and the indicator association/detection, are characterized and optimized. Hybridization times of 2- and 30-min are sufficient for detecting 300- and 50 ng/mL, respectively, of the E. coli DNA target. Applicability to analysis of untreated environmental water samples is illustrated. Such single-use electrochemical sensors hold great promise for decentralized environmental and food testing for the E. coli pathogen.     

A Biosensor for Genetic Modified Soybean DNA Determination via Adsorption of Anthraquinone‐2‐sulphonic Acid in Reduced Graphene Oxide

An electrochemical DNA biosensor for DNA determination of genetically modified (GM) soybean (CaMV 35S target genes) was developed utilizing a new detection concept based on the adsoption of anthraquinone‐2‐sulphonic acid (AQMS) on the reduced graphene oxide nano‐particles (rGO) during DNA hybridization events. The aminated DNA probe for CaMV 35S was immobilized onto poly(n‐butyl acrylate) film modified with succinimide functional groups [poly(nBA‐NAS)] via peptide covalent bond. Nanosheets of rGO were entrapped in the poly(nBA‐NAS) film to form a conducting [poly(nBA‐NAS)‐rGO] film of the DNA biosensor. Besides facilitating the electron transfer reactions, the rGO also functioned as an adsorbent for AQMS. The sensing mechanism of the proposed DNA biosensor involved measuring the oxidation current of the AQMS adsorbed on the electrode surface at −0.50 V using differential pulse voltammetry (DPV) before and after a DNA hybridization event. Under optimum conditions, the DNA biosensor demonstrated a linear proportionality between AQMS oxidation signal and logarithm cDNA concentration from 1.0×10⁻¹⁵ M to 1.0×10⁻⁸ M target DNA with a detection limit of 6.3×10⁻¹⁶ M. The electrochemical DNA biosensor possessed good selectivity and a shelf life of about 40 days with relative standard deviation of reproducibility obtained in the range of 3.7–4.6% (n=5). Evaluation of the DNA biosensor using GM soybean DNA extracts showed excellent recovery percentages of 97.2–104.0.     

Synthesis of Photolabile 5′‐O‐Phosphoramidites for the Photolithographic Production of Microarrays of Inversely Oriented Oligonucleotides

The photolabile 3′‐O‐{[2‐(2‐nitrophenyl)propoxy]carbonyl}‐protected 5′‐phosphoramidites ( 16 – 18 ) were synthesized (see Scheme) for an alternative mode of light‐directed production of oligonucleotide arrays. Because of the characteristics of these monomeric building blocks, photolithographic in situ DNA synthesis occurred in 5′→3′ direction, in agreement with the orientation of enzymatic synthesis. Synthesis yields were as good as those of conventional reactions. The resulting oligonucleotides are attached to the surface via their 5′‐termini, while the 3′‐hydroxy groups are available as substrates for enzymatic reactions such as primer extension upon hybridization of a DNA template (see Fig. 2). The production of such oligonucleotide chips adds new procedural avenues to the growing number of applications of DNA microarrays.     

A Subtractively Optimized DNA Microarray Using Non-sequenced Genomic Probes for the Detection of Food-Borne Pathogens

In this study, we present the successful detection of food-borne pathogens using randomly selected non-sequenced genomic DNA probes-based DNA microarray chips. Three food-borne pathogens, Staphylococcus aureus, Salmonella enterica subsp. enterica serovar Typhimurium (S. Typhimurium), and Bacillus cereus, were subjected for the preparation of the DNA microarray probes. Initially, about 50 DNA probes selected randomly from non-sequenced genomic DNA of each pathogen were prepared by using a set of restriction enzyme pairs. The proto-type of DNA microarray chip for detecting three different pathogens simultaneously was fabricated by using those DNA probes prepared for each pathogen. This proto-type DNA microarray has been tested with three target pathogens and additional seven bacteria, and successfully verified with a few cross-hybridized probes. After this primary verification of the DNA microarray hybridization, this proto-type DNA microarray chip was redesigned and successfully optimized by eliminating a few cross-hybridized probes. The specificity of this redesigned DNA microarray chip to each pathogen was confirmed without any serious cross-hybridizations, and its multiplexing capability in its pathogen detection was found to be possible. This randomly selected non-sequenced genomic DNA probes-based DNA microarray was successfully proved to be the high-throughput simultaneous detection chip for the detection of food-borne pathogens, without knowing the exact sequence information of the target bacteria. This could be the first fabrication of DNA microarray chip for the simultaneous detection of different kinds of food-borne pathogens.     

Synthesis and investigation of binding interactions of 1,4-benzoxazine derivatives on topoisomerase IV in Acinetobacter baumannii$

Abstract

Acinetobacter baumannii has emerged as an important pathogen for nosocomial infections having high morbidity and mortality. This pathogen is notorious for antimicrobial resistance to many common antimicrobial agents including fluoroquinolones, which have both intrinsic and acquired resistance mechanisms. Fluoroquinolones targeting the bacterial topoisomerase II (DNA gyrase and Topo IV) show potent broad-spectrum antibacterial activity by the stabilization of the covalent enzyme–DNA complex. However, their efficacy is now being threatened by an increasing prevalence of resistance. Fluoroquinolones cause stepwise mutations in DNA gyrase and Topo IV, having alterations of their binding sites. Furthermore, the water–Mg⁺² bridge, which provides enzyme–fluoroquinolone interactions, has a significant role in resistance. In this study, 13 compounds were synthesized as 1,4-benzoxazine derivatives which act as bacterial topoisomerase II inhibitors and their antibacterial activities were determined against multi-drug resistant Acinetobacter strains which have ciprofloxacin (CIP) resistant and GyrA mutation. Afterwards we performed docking studies with Topo IV (pdb:2XKK) of these compounds to comprehend their binding properties in Discovery Studio 3.5. The results of this study show significant conclusions to elucidate the resistance mechanism and lead to the design of new antibacterial agents as bacterial topoisomerase II inhibitors.     

Oligodeoxynucleotides Containing Diastereomeric O2′,C3′‐linked Bicyclic Nucleotide Units for Functionalization of the Major Groove of Nucleic Acid Duplexes: A Summary and Novel Derivatives*

The synthesis and evaluation of a range of piperazino‐derivatized diastereomeric O2′,C3′‐linked bicyclic nucleotides are described. A new and optimized protocol is presented for the synthesis of the bicyclic scaffold on which the piperazino moiety is appended. At low salt concentration, the C2″‐S‐configured piperazino‐modified oligonucleotides display significantly enhanced hybridization affinity toward complementary DNA and RNA targets relative to the unmodified oligonucleotide control, whereas no melting transition is observed for hybrids formed with the C2″‐R‐configured piperazino‐modified oligonucleotides. Upon derivatization of the piperazino moiety with a 1‐pyrenebutanoyl group, all modified oligonucleotides display strong DNA binding and profound DNA hybridization selectivity.     

A new peptide nucleotide acid biosensor for electrochemical detection of single nucleotide polymorphism in duplex DNA via triplex structure formation

In this paper, we report a new PNA biosensor for electrochemical detection of point mutation or single nucleotide polymorphism (SNP) in p53 gene corresponding oligonucleotide based on PNA/ds-DNA triplex formation following hybridization of PNA probe with double-stranded DNA (ds-DNA) sample without denaturing the ds-DNA into single-stranded DNA (ss-DNA). As p53 gene is mutated in many human tumors, this research is useful for cancer therapy and genomic study. In this approach, methylene blue (MB) is used for electrochemical signal generation and the interaction between MB and oligonucleotides is studied by differential pulse voltammety (DPV). Probe-modified electrode is prepared by self-assembled monolayer (SAM) formation of thiolated PNA molecules on the surface of Au electrode. A significant increase in the reduction signal of MB following hybridization of the probe with the complementary double-stranded oligonucleotide (ds-oligonucleotide) confirms the function of the biosensor. The selectivity of the PNA sensor is investigated by non-complementary ds-oligonucleotides and the results support the ability of the sensor to detect single-base mismatch directly on ds-oligonucleotide. The influence of probe and ds-DNA concentrations on the effective discrimination against complementary sequence and point mutation is studied and the concentration of 10^?6 M is selected as appropriate concentration. Diagnostic performance of the biosensor is described and the detection limit is found to be 4.15 × 10^?12 M.     

Ciprofloxacin–Isatin Hybrids and Their Antimycobacterial Activities

A series of diethylene glycol tethered ciprofloxacin–isatin hybrids 5a–j were designed, synthesized, and evaluated for their in vitro antimycobacterial activity against both drug‐sensitive and multidrug‐resistant (MDR) Mycobacterium tuberculosis strains in this paper. The preliminary results revealed that all hybrids with greater lipophilicity than the parent ciprofloxacin displayed considerable activity against the tested strains with minimum inhibitory concentration (MIC) in a range of 1.56–64 μg/mL. In particular, hybrid 5f (MIC: 1.56 and 2 μg/mL) with low cytotoxicity in VERO cell line was comparable with the parent ciprofloxacin (MIC: 0.78 and 2 μg/mL) against M. tuberculosis H₃₇Rv and MDR tuberculosis strains and ≥16‐fold more potent than isoniazid and rifampicin (MIC: >128 and 32 μg/mL, respectively) against MDR tuberculosis, suggesting that it may serve as a new and promising candidate for further study.