Selection of aptamers against live bacterial cells.

 Anal Chem. 2008 Oct 15;80(20):7812-9. Epub 2008 Sep 20

Single-stranded DNA or RNA aptamer molecules have usually been selected against purified target molecules. To eliminate the need of purifying target molecules on the cell surface, we have developed a selection technique using live bacterial cells in suspension as targets, to select for ssDNA aptamers specific to cell surface molecules. Lactobacillus acidophilus cells were chosen to demonstrate proof of principle based on their high abundance of surface molecules (potential targets). Aptamer pools obtained after 6-8 rounds of selection demonstrated high affinity for and selective binding with L. acidophilus cells when tested via flow cytometry, microscopy, and fluorescence measurements. Out of 27 aptamers that were cloned and sequenced, one sequence, hemag1P, was found to bind to L. acidophilus much more strongly and specifically than other cells tested. This aptamer was predicted to have a tight hairpin secondary structure. On average, an estimated 164 +/- 47 aptamer molecules were bound to a target cell with an apparent K d of 13 +/- 3 nM. A likely putative molecular target of hemag1P is the S-layer protein on the cell surface.

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Systematic Investigation of Optimal Aptamer Immobilization for Protein−Microarray Applications

Anal. Chem., 80 (19), 7372–7378, 2008. 10.1021/ac801081v 

Aptamers are short single-stranded DNA or RNA oligonucleotides that can bind to a wide range of target molecules with high affinity and specificity. As nucleic acids, aptamers can undergo denaturation, but the process is reversible. As a result of this stability and the possibility of automated selection of aptamers, these oligonucleotides are highly promising capture molecules in microarray formats. In this study, his-tagged proteins and an aptamer directed against the his-tag were chosen as a model system. Different factors affect the activity of aptamers immobilized on a solid support like a microarray surface. The orientation of the immobilized aptamer plays an important role in correct aptamer folding and, thus, in effective binding of the corresponding target. Other important parameters identified in this work are the microarrays’ surface charge as well as the length of the spacer between aptamer and solid support. These parameters were investigated systematically, resulting in the development of an aptamer-based microarray for detection of his-tagged proteins. The general applicability of the developed immobilization strategy was demonstrated by utilization of three different aptamers.

 

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Detecting Simulated Patterns of Lung Cancer Biomarkers by Random Network of Single-Walled Carbon Nanotubes Coated with Nonpolymeric Organic Materials

An array of chemiresistive random network of single-walled carbon nanotubes coated with nonpolymeric organic materials shows a high potential for diagnosis of lung cancer via breath samples. The sensors array shows excellent discrimination between the volatile organic compounds (VOCs) found in the breath of patients with lung cancer, relative to healthy controls, especially if the sensors array is preceded with either water extractor and/or preconcentrator of VOCs. The pattern compositions of the healthy and cancerous states were determined by gas-chromatography linked with mass-spectroscopy (GC-MS) analysis of real exhaled breath. 

http://pubs.acs.org/cgi-bin/asap.cgi/nalefd/asap/pdf/nl801577u.pdf?isMac=477783

A 200-Antibody Microarray Biochip for Environmental Monitoring: Searching for Universal Microbial Biomarkers through Immunoprofiling

ASAP Anal. Chem., ASAP Article, 10.1021/ac8008093
Web Release Date: October 7, 2008

Environmental biomonitoring approaches require the measurement of either unequivocal biomarkers or specific biological profiles. Antibody microarrays constitute new tools for fast and reliable analysis of up to hundreds of biomarkers simultaneously. Herein we report 150 new polyclonal antibodies against microbial strains and environmental extracts, as well as the construction and validation of an antibody microarray (EMCHIP200, for “Environmental Monitoring Chip”) containing 200 different antibodies. Each antibody was tested against its antigen for its specificity and cross-reactivity by a sandwich microarray immunoassay. The limit of detection was 0.2 ng mL⁻¹ for some proteins and 10⁴−10⁵ cells mL⁻¹ for bacterial cells and spores. Partial biochemical characterization allowed identification of polymeric compounds (proteins and polysaccharides) as some of the targets recognized by the antibodies. We have successfully used the EMCHIP200 for the detection of biological polymers in samples from extreme environments around the world (e.g., a deep South African mine, Antarctica’s dry valleys, Yellowstone National Park, Iceland, and Rio Tinto surface and subsurface). Clustering analysis permitted us to associate similar immunoprofiles or patterns to samples from apparently very different environments, indicating that they indeed share similar universal biomarkers. Our EMCHIP200 constitutes a new generation of immunosensors for biomarker detection and profiling, for either environmental, industrial, biotechnological, or astrobiological applications.

Disposable Magnetic DNA Sensors for the Determination at the Attomolar Level of a Specific Enterobacteriaceae Family Gene

 

 

ASAP Anal. Chem., ASAP Article, 10.1021/ac801319b
Web Release Date: October 7, 2008

Disposable magnetic DNA sensors using an enzyme-amplified strategy for the specific detection of a gene related to the Enterobacteriaceae bacterial family, based on the coupling of streptavidin-peroxidase to biotinylated lacZ gene target sequences, has been developed. A biotinylated 25-mer capture probe was attached to streptavidin-modified magnetic beads and hybridization with the biotinylated target was allowed to proceed. Then, a streptavidin-peroxidase polymer was attached to the biotinylated target, and the resulting modified magnetic beads were captured by a magnetic field on the surface of tetrathiafulvalene (TTF) modified gold screen-printed electrodes (Au/SPEs). The amperometric response obtained at −0.15 V after the addition of hydrogen peroxide was used to detect the hybridization process. In order to improve the sensitivity of the determination and reduce the assay time, different variables of the assay protocol were optimized. A low detection limit (5.7 fmol) with good stability (RSD = 7.1%, n = 10) was obtained. The DNA nonspecific adsorption at the magnetic beads was negligible, the obtained results thus demonstrating the possibility to detect the hybridization event with great specificity and sensitivity. The developed method was used for the analysis of Escherichia coli DNA fragments (326 bases) in polymerase chain reaction (PCR) amplicons extracted from a cell culture. As low as 2.5 aM asymmetric PCR product could be detected with the developed methodology.

Open Bridge-Structured Gold Nanoparticle Array for Label-Free DNA Detection

 

A very interesting approach to detect DNA.

ASAP Anal. Chem., ASAP Article, 10.1021/ac801088u
Web Release Date: October 7, 2008

We focused on changes in the electrical property of the open bridge-structured gold nanoparticles array consisting of 46-nm parent and 12-nm son gold nanoparticles by hybridization and applied it for a simple electrical DNA detection. Since a target DNA of a 24-mer oligonucleotide was added to the probe DNA modified 12-nm Au nanoparticles, which was arranged on the gap between the 46-nm Au particles, the response was read by an electrical readout system. Even in a simple measuring method, we obtained a rapid response to the cDNA with a high S/N ratio of 30 over a wide concentration range and a detection limit of 5.0 fmol. Moreover, the array discriminated 1-base mismatches, regardless of their location in the DNA sequence, which enabled us to detect single-nucleotide polymorphism, which is one of the important diagnoses, without any polymerase chain reaction amplification, sophisticated instrumentation, or fluorescent labeling through an easy-to-handle electrical readout system

Self-Assembly of Quantum Dots and Carbon Nanotubes for Ultrasensitive DNA and Antigen Detection

http://pubs.acs.org/cgi-bin/abstract.cgi/ancham/asap/abs/ac800992m.html

A highly selective, ultrasensitive, fluorescence detection method for DNA and antigen based on self-assembly of multiwalled carbon nanotubes (CNTs) and CdSe quantum dots (QDs) via oligonucleotide hybridization is reported. Mercaptoalkyloligonucleotide molecules bind to the quantum dots, while amineoalkyloligonucleotides bind to CNTs with −COCl surface groups. QDs and CNTs further assemble into nanohybrids through DNA hybridization in the presence of target complementary oligonucleotides. The method is achieved with good repeatability with the detection limit of 0.2 pM DNA molecules and 0.01 nM antigen molecules. This novel detection system can also be used for multicomponent detection and antigen−antibody immunoreaction. The novel system has great potential in applications such as ultrasensitive pathogen DNA or antigen or antibody detection, molecular imaging, and photoelectrical biosensors

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Digitized Molecular Diagnostics: Reading Disk-Based Bioassays with Standard Computer Drives

http://pubs.acs.org/cgi-bin/abstract.cgi/ancham/asap/abs/ac8012434.html

We report herein a digital signal readout protocol for screening disk-based bioassays with standard optical drives of ordinary desktop/notebook computers. Three different types of biochemical recognition reactions (biotin−streptavidin binding, DNA hybridization and protein−protein interaction) were performed directly on a compact disk in a line array format with the help of microfluidic channel plates. Being well-correlated with the optical darkness of the binding sites (after signal enhancement by gold nanoparticle-promoted autometallography), the reading error levels of prerecorded audio files can serve as a quantitative measure of biochemical interaction. This novel readout protocol is about 1 order of magnitude more sensitive than fluorescence labeling/scanning and has the capability of examining multiplex microassays on the same disk. Because no modification to either hardware or software is needed, it promises a platform technology for rapid, low-cost, and high-throughput point-of-care biomedical diagnostics.

Multidimensional LC Separations in Shotgun Proteomics

This feature article summarizes the key concepts of the MUDPIT(Multidimensional Protein Identification Technology) and how an LC-MS/MS experiment is carried out for biomarker discovery.

http://pubs.acs.org/cgi-bin/sample.cgi/ancham/2008/80/i19/html/ac8013669.html

Femtomolar sensitivity with matrix-free LDI MS

http://pubs.acs.org/cgi-bin/abstract.cgi/ancham/2008/80/i19/abs/ac801190e.html

A nanostructured diamond-like carbon (DLC) coated digital versatile disk (DVD) target is presented as a matrix-free sample support for application in laser desorption/ionization mass spectrometry (LDI-MS). A large number of vacancies, defects, relative sp² carbon content, and nanogrooves of DLC films support the LDI phenomenon. The observed absorptivity of DLC is in the range of 305−330 nm (nitrogen laser, 337 nm). The universal applicability is demonstrated through different analytes like amino acids, carbohydrates, lipids, peptides, and other metabolites. Carbohydrates and amino acids are analyzed as sodium and potassium adducts. Peptides are detectable in their protonated forms, which avoid the extra need of additives for ionization. A bovine serum albumin (BSA) digest is analyzed to demonstrate the performance for peptide mixtures, coupled with the material-enhanced laser desorption/ionization (MELDI) approach. The detection limit of the described matrix-free target is investigated to be 10 fmol/μL for [Glu¹]-fibrinopeptide B (m/z 1570.6) and 1 fmol/μL for L-sorbose (Na⁺ adduct). The device does not require any chemical functionalization in contrast to other matrix-free systems. The inertness of DLC provides longer lifetimes without any deterioration in the detection sensitivity. Broad applicability allows high performance analysis in metabolomics and peptidomics. Furthermore the DLC coated DVD (1.4 GB) sample support is used as a storage device for measured and processed data together with sampling on a single device.

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