Concentration Of Target Molecules Research Articles

Antioxidant reactivity evaluated by competitive kinetics: Influence of the target molecule concentration

In the present work, a competitive kinetic method using c-phycocyanin (from Arthospira maxima species) as target molecule was employed to estimate the reactivity of several phenols and flavonoids present in the human diet towards peroxyl radicals. The results obtained indicate that the protection afforded by a given compound strongly depends upon the experimental conditions employed and, in particular, on the concentration of the target molecule. This dependence is related to increased role of secondary reactions of the phenol-derived radicals initially formed. Secondary reactions can explain the strong downward curvature observed in R 0/ R (where R 0 is the rate of the process in the absence of additive, and R is the rate of the process in the presence of additive) vs. additive concentration plots, for compounds such as kaempferol and protocatechuic acid, particularly at high c-phycocyanin concentration. Also, it can explain the prooxidant role played by phenolic compounds of low reactivity, such as 3-hydroxyflavone at low c-phycocyanin concentrations.

Statistical methods for determining the accuracy of quantitative polymerase chain reaction‐based tests

Quantitative polymerase chain reaction (PCR)-based tests are used in several different scientific fields to determine levels of a target DNA sequence of interest (the target molecule). The accuracy of quantitative PCR-based tests can be assessed by using the assay to determine the number of copies of the target molecule in a sample with a known concentration of the target molecule. For example, a sample with a known concentration of a target DNA sequence is serially diluted into replicate aliquots and these are tested to determine if the observed quantity of the target is close to the expected quantity (given the concentration in the original sample and the dilution). Statistical methods that are conventionally used to assess the accuracy of these assays do not take into account the variability in the number of target molecules in each aliquot from the original sample. We develop methods that take into account this extra variation and which determine the accuracy of quantitative PCR-based tests in estimating the number of target molecules based on a set of assays of serial dilutions from an original sample with a known concentration of target molecules. These methods are applied to data from an experiment to test the accuracy of a real-time PCR assay at low HIV-1 DNA copy levels.

Lipid—Protein Interactions Revealed by Two‐Photon Microscopy and Fluorescence Correlation Spectroscopy

AbstractFor Abstract see ChemInform Abstract in Full Text.

Lipid−Protein Interactions Revealed by Two-Photon Microscopy and Fluorescence Correlation Spectroscopy

Cellular processes involve a multitude of chemical reactions that must be kept in delicate equilibrium to maintain cellular homeostasis. Powerful biophysical techniques are needed to measure the localization and concentration of target molecules as well as to quantify complex molecular processes in model and in vivo systems. Two-photon microscopy and fluorescence correlation spectroscopy (FCS) can measure association and dynamics of appropriate molecules under equilibrium conditions. FCS provides information on motility (diffusion coefficients), concentration (number of particles), association (molecular brightness), and localization (image) of the target molecules. All of this information, in conjunction with computational modeling techniques, can help us to better understand the network of complex molecular interactions, which are at the basis of cellular processes. Fluorescence imaging techniques add the beauty of visualization to the scientific information. Photons emitted by a fluorescent dye are digitized, and the associated spatial information and intensity can be translated into different colors and shades providing the researcher not only with quantitative intensity information but also with spatial resolution and visual comprehension of two- or three-dimensional images. In this Account, we review the use of two-photon excitation microscopy and FCS in the study of lipid-protein interactions. We discuss these new methodologies and techniques, and we present examples of different complexity from qualitative to quantitative, from simple model systems to studies in living cells.

Disrupted coordinate regulation of farnesoid X receptor target genes in a patient with cerebrotendinous xanthomatosis

Cerebrotendinous xanthomatosis (CTX), sterol 27-hydroxylase (CYP27A1) deficiency, is associated with markedly reduced chenodeoxycholic acid (CDCA), the most powerful activating ligand for farnesoid X receptor (FXR). We investigated the effects of reduced CDCA on FXR target genes in humans. Liver specimens from an untreated CTX patient and 10 control subjects were studied. In the patient, hepatic CDCA concentration was markedly reduced but the bile alcohol level exceeded CDCA levels in control subjects (73.5 vs. 37.8 +/- 6.2 nmol/g liver). Cholesterol 7alpha-hydroxylase (CYP7A1) and Na+/taurocholate-cotransporting polypeptide (NTCP) were upregulated 84- and 8-fold, respectively. However, small heterodimer partner (SHP) and bile salt export pump were normally expressed. Marked CYP7A1 induction with normal SHP expression was not explained by the regulation of liver X receptor alpha (LXRalpha) or pregnane X receptor. However, another nuclear receptor, hepatocyte nuclear factor 4alpha (HNF4alpha), was induced 2.9-fold in CTX, which was associated with enhanced mRNA levels of HNF4alpha target genes, CYP7A1, 7alpha-hydroxy-4-cholesten-3-one 12alpha-hydroxylase, CYP27A1, and NTCP. In conclusion, the coordinate regulation of FXR target genes was lost in CTX. The mechanism of the disruption may be explained by a normally stimulated FXR pathway attributable to markedly increased bile alcohols with activation of HNF4alpha caused by reduced bile acids in CTX liver.

Impedance labelless detection-based polypyrrole DNA biosensor

Microelectrodes were fabricated to study impedance labelless detection of DNA hybridization. The probe molecule was attached onto the platinum microelectrode surface by electrochemically copolymerizing pyrrole and the probe oligonucleotides. Measured impedance complexes showed that an electrochemical redox-reaction occurred and the electron-transfer resistance increased after DNA hybridization. It was proposed that the hybridization of DNA in the conductive polymer matrix slowed down the anionic doping/undoping process, resulting impedance changes for the target DNA detection. Impedance measurements were conducted at the complementarily hybridized probe oilgomer-attached polypyrrole film electrodes in different anionic solutions to exam the anionic effects. Results showed that higher concentration and smaller size of anions had the lower electron-transfer resistance. The results not only provide further evidence to support the detection mechanism proposed, but also offer a method to improve the signal to noise ratio for the DNA biosensor. The research also tested the specificity of the methods and experimental results, indicating good specificity of the method. A concept array chip was fabricated and used to demonstrate the capability of the labelless detection method. Nano-Molar concentrations were detected and showed fairly linear responses versus the target molecule concentrations. The method is simple and inexpensive. The technique based genosensors could have potential applications in clinical diagnosis, drug discovery, environmental and food analysis.

Specific Chemical Effects on Surface-Enhanced Raman Spectroscopy for Ultra-Sensitive Detection of Biological Molecules

Achieving high signal amplification in surface-enhanced Raman scattering (SERS) is important for reaching single molecule level sensitivity and has been the focus of intense research efforts. We introduce a novel chemical enhancer, lithium chloride, that provides an additional order of magnitude increase in SERS relative to previously reported enhancement results. We have duplicated single molecule detection of the DNA base adenine that has previously been reported, thereby providing independent validation of this important result. Building upon this work, we show that the chemical enhancer LiCl produces strong SERS signal under a wide range of experimental conditions, including multiple laser excitation wavelengths and target molecule concentrations, for nucleotides, nucleosides, bases, and dye molecules. This is significant because while selection of anions used in chemical enhancement is well known to affect the degree of amplification attained, cation selection has previously been reported to have no major effect on the magnitude of SERS enhancement. Our findings indicate that cation selection is quite important in ultra-sensitive SERS detection, opening the door to further discussion and theory development involving the role of cations in SERS.

Microsphere Bead Arrays and Sequence Validation of 5/7/9T Genotypes for Multiplex Screening of Cystic Fibrosis Polymorphisms

The development of simple and rapid methods for the detection of the common genetic mutations associated with cystic fibrosis (CF) requires access to positive-control samples including the 5/7/9T variants of intron 8. We used PCR and a simple multiplex bead-array assay to identify 5/7/9T control samples from 29 commercially available DNA samples. Unpurified PCR products were directly hybridized to color-coded beads containing allele-specific capture probes for 5/7/9T detection. The performance of the assay was investigated using reverse-complement oligonucleotides, individual PCR products, and multiplex PCR products for 5/7/9T detection within a complex CFTR screening assay. Samples were genotyped by grouping the relative signal intensities from each capture probe. Of 29 commercially available DNA samples analyzed, 2 5T/7T, 2 5T/9T, 9 7T/9T, 11 7T/7T, and 5 9T/9T genotypes were identified. The genotype within each sample group was confirmed by DNA sequencing. The assay was compatible with the analysis of 10 to 1000 ng of genomic DNA isolated from whole blood and allowed for the separate identification of primary CFTR mutations from reflex variants. The correct identification of positive controls demonstrated the utility of a simple bead-array assay and provided accessible samples for assay optimization and for routine quality control in the clinical laboratory.

High-density, microsphere-based fiber optic DNA microarrays

A high-density fiber optic DNA microarray has been developed consisting of oligonucleotide-functionalized, 3.1-μm-diameter microspheres randomly distributed on the etched face of an imaging fiber bundle. The fiber bundles are comprised of 6000–50 000 fused optical fibers and each fiber terminates with an etched well. The microwell array is capable of housing complementary-sized microspheres, each containing thousands of copies of a unique oligonucleotide probe sequence. The array fabrication process results in random microsphere placement. Determining the position of microspheres in the random array requires an optical encoding scheme. This array platform provides many advantages over other array formats. The microsphere-stock suspension concentration added to the etched fiber can be controlled to provide inherent sensor redundancy. Examining identical microspheres has a beneficial effect on the signal-to-noise ratio. As other sequences of interest are discovered, new microsphere sensing elements can be added to existing microsphere pools and new arrays can be fabricated incorporating the new sequences without altering the existing detection capabilities. These microarrays contain the smallest feature sizes (3 μm) of any DNA array, allowing interrogation of extremely small sample volumes. Reducing the feature size results in higher local target molecule concentrations, creating rapid and highly sensitive assays. The microsphere array platform is also flexible in its applications; research has included DNA–protein interaction profiles, microbial strain differentiation, and non-labeled target interrogation with molecular beacons. Fiber optic microsphere-based DNA microarrays have a simple fabrication protocol enabling their expansion into other applications, such as single cell-based assays.

Quantitative PCR to evaluate small amounts of BCL2 mRNA in human peripheral T cells: implication of equimolar target and competitor end products

Background: It is difficult to reliably and reproducibly quantitate small amounts of mRNA by conventional PCR. The method we describe here enabled us to more accurately quantitate a small amount of BCL2 mRNA in human peripheral T cells. Methods: The sample was amplified in four tubes containing three-fold serial dilutions of competitor so that when the PCR products in the four tubes were totaled, the number of target and competitor components were approximately equal. An unknown concentration of target molecules should be assessed only within a narrow range, requiring that several reactions be performed for each sample. Results and Conclusion: With this method, conventional PCR machines can be used to perform quantitative PCR on very small amounts of BCL2, and would be especially useful for samples that contain substance(s) that affect PCR amplification efficiency.

Nanomechanics – The Link to Biology and Chemistry

Biological and chemical processes can be transduced into nanomechanical motion via change of surface stress on a cantilever. By coating the surface of each cantilever of a micro-fabricated array of silicon cantilevers with a different polymer, a versatile vapor sensor is obtained that is able to discriminate between various solvent vapors using principal-component analysis techniques. In liquids such sensors allow rapid quantitative and qualitative detection of non-labeled biomolecules. Differential measurements of cantilever deflection (with respect to an unspecific reference cantilever) allow the detection of sequence-specific DNA hybridization. Single-stranded thiolated DNA 12-mer sequences, anchored onto the surface of the gold-coated cantilevers of the array, provide a biosensor for the detection of their complementary strands in buffer solution. The influence of the target-molecule concentration on the cantilever deflection is studied, and a value for the thermodynamic surface-solution equilibrium constant is derived from measurements on a cantilever.

Signal amplification through nucleotide extension and excision on a dendritic DNA platform.

Techniques that provide strong signal amplification are useful in diagnostic applications, especially in detecting low concentrations of non-amplifiable target molecules. A versatile and strong signal amplification method based on activities of a DNA polymerase to generate high concentrations of pyrophosphate (PPi) is described. The generation of PPi is catalyzed by nucleotide extension and excision activities of a DNA polymerase on an oligonucleotide cassette. The signal is generated upon enzymatic conversion of PPi to ATP and ATP levels subsequently detected with firefly luciferase. Bioluminescence produced by an oligonucleotide cassette consisting of just two polymerase reaction sites is sufficient to detect them at low attomole levels. The attachment of a large number of these oligonucleotide cassettes to DNA dendrimers enabled the detection of such poly-valent substrate molecules at low zeptomole (10(-21)mol) concentrations. The extent of signal amplification obtained with dendrimer substrates is comparable to exponential target amplifications provided by nucleic acid amplification methods. The attachment of such PPi-generating dendritic DNA platforms to ligands that mediate target recognition would potentially permit detection of extremely low concentrations of analytes in diagnostic assays.

Biosensor using magnetically detected label

This method and apparatus for detecting target molecules in a liquid phase. The apparatus monitors whether the target molecule has selectively bound to recognition agents on the surface of a magnetic field sensor by monitoring the output of the sensor. The recognition agents which selectively bind target molecules are covalently bound to microfabricated magnetic field sensors. These sensors are then exposed to a sample suspected of containing the target molecules, whereupon the recognition agents bind to and immobilize any target molecules present. Depending on the embodiment, recognition agents that selectively bind the target molecule, or recognition agents that selectively bind the sensor-bound recognition agents, are covalently bound to magnetizable particles. These particles are then added to the sensors and, again depending on the embodiment, attach either to any immobilized target molecules or to sensor-bound recognition agents. Unattached particles are removed, and the magnetic particles are then magnetized. A change in the output of the magnetic field sensors indicates the presence of magnetic particles bound to the sensors, and thereby indicates the presence and concentration of target molecule in the sample.

Quantitative RT-PCR: limits and accuracy.

In this paper we determine the limits and accuracy of quantitative reverse transcription (RT)-PCR using a modification of the original protocol. The quantification of mRNA with this procedure requires a preliminary estimation of the target molecule (TM) concentration, established from experiments with an internal control molecule (ICM). A definitive quantification is then attained from serial dilutions of the reverse transcription reaction. The success of this latter step is dependent on maintaining an equivalent number of TM and ICM in the reaction. The purpose of our study was to evaluate the influence of the deviation between the TM and the ICM on the result. We show here that we can control the accuracy of the assay by fixing the limit of the TM/ICM ratio. Indeed, when the TM/ICM ratio is between 0.66 and 1.5 (i.e., the difference between TM and ICM is 1.5-fold), the final result has an error of approximately 10%. Exceeding this limit produces errors approaching 60%, as in the case of TM/ICM = 2. When the above conditions are respected, a difference as small as 20% between two samples can be determined with an accuracy of 95%.