Abstract: Complexes, especially for the detection and separation of phosphoric-ester-containing compounds, are disclosed. The complexes according to the invention comprise at least one chelating agent, at least one central atom or central ion coordinated by the chelating agent(s), and at least one dye bonded to the chelating agent(s), etc.

Abstract: A technique is described for determining the effectiveness of medical therapy and dosage formulations by analyzing dot spectrograms representative of quantized hybridization activity in biological samples, such as DNA, RNA, or other protein biomolecular array samples, taken at different times from a patient undergoing the medical therapy. This technique enables disease progression analysis based on surrogate markers such as viral load. In accordance with the technique, a viral diffusion curve associated with a therapy of interest is generated and each dot spectrogram is then mapped to a viral diffusion curve using fractal filtering. Next, degree of convergence towards the peak of VDC, between the sample points on a filtered viral diffusion curve is determined. The technique allows for point-of-care viral load detection biosensors to accurately and reliably predict the likelihood of disease progression.

Abstract: Gene expression can be quantitatively analyzed by hybridizing fluor-tagged mRNA to targets on a cDNA micro-array. Comparison of gene expression levels arising from co-hybridized samples is achieved by taking ratios of average expression levels for individual genes. In an image-processing phase, a method of image segmentation identifies cDNA target sites in a cDNA micro-array image. The resulting cDNA target sites are analyzed based on a hypothesis test and confidence interval to quantify the significance of observed differences in expression ratios. In particular, the probability density of the ratio and the maximum-likelihood estimator for the distribution are derived, and an iterative procedure for signal calibration is developed.

Abstract: The present invention relates to methods of using labeled tracers to generate spatially addressable arrays of immobilized molecules, particularly polynucleotides, that can be normalized for differences in immobilization efficiencies at different addresses in the array. It also relates to the arrays generated by the method and to use of these arrays to enhance discrimination in array-based assays, particularly the discrimination between perfectly matched hybrids and hybrids containing a single mismatch in nucleic acid hybridization assays.

Abstract: A computer system (1) for analyzing nucleic acid sequences is provided. The computer system is used to perform multiple methods for determining unknown bases by analyzing the fluorescence intensities of hybridized nucleic acid probes. The results of individual experiments may be improved by processing nucleic acid sequences together. Comparative analysis of multiple experiments is also provided by displaying reference sequences in one area (814) and sample sequences in another area (816) on a display device (3).

Abstract: The present invention relates to a method for detecting and identifying mycobacterial species which comprises steps of amplifying 342 bp of rpoB gene fragments from clinically isolated mycobacterial using mycobacterial rpoB-specific PCR primers; sequencing 306 bp regions of the amplified 342 bp of rpoB gene fragments except the primer regions; and, inferring a phylogenetic tree with reference species. In accordance with the present invention, it was found that rpoB sequences from 44 mycobacterial species provide a basis for systematic phylogenetic relationship which can be used to identify clinically isolated mycobacteria that are pathogenic or potentially so. Accordingly, the amplification of rpoB DNA followed by automated sequencing and the analysis of phylogenetic relationships with the reference species can be used efficiently to detect and identify clinical isolates of mycobacteria which have not been identified by the conventional methods.

Abstract: The present invention relates to a method of producing covalently closed circular (ccc) DNA from a cultured cell or unicellular organism, preferably a bacterium, essentially free of genomic DNA. The method of the invention comprises the steps of precipitating a cleared lysate with an alcohol, washing and resuspension of the precipitate, digestion of the genomic DNA with a nuclease that cleaves linear DNA or circular DNA that includes a nick or a free 3′ or 5′ end but not ccc DNA, and finally, separation of the purified ccc DNA from the remainder of the product of the digestion step by contacting the product with an ion exchange material. ccc DNA obtained by the method, pharmaceutical compositions comprising the ccc DNA, and a kit for carrying out the method of the invention are also contemplated.

Abstract: The present invention relates to compositions, apparatus and methods useful for concurrently performing multiple, high throughput, biological or chemical assays, using repeated arrays of probes. A combination of the invention comprises a surface, which comprises a plurality of test regions, at least two of which, and in a preferred embodiment, at least twenty of which, are substantially identical, wherein each of the test regions comprises an array of generic anchor molecules. The anchors are associated with bifunctional linker molecules, each containing a portion which is specific for at least one of the anchors and a portion which is a probe specific for a target of interest. The resulting array of probes is used to analyze the presence or test the activity of one or more target molecules which specifically interact with the probes. In one embodiment of the invention, the test regions (which can be wells) are further subdivided into smaller subregions (indentations, or dimples).

Abstract: A method of fabricating a biopolymer array, and an apparatus which can execute the method. droplets of fluid carrying the biopolymer or a biomonomer are deposited onto a front side of a transparent substrate. Light is directed through the substrate from the front side, back through a substrate back side and a first set of deposited droplets on the first side to an image sensor. The substrate may be mounted by means of a chuck with parallel channels, and a scanning operation of a droplet dispensing head, light source, and sensor conducted in unison in the direction of the channels.

Abstract: The present invention also relates to single molecule optical sequencing methods and systems for determining the nucleotide sequence of individual double stranded nucleic acid molecules elongated and fixed to a solid-surface by nicking the nucleic acid molecule, enzymatically adding labeled nucleotides and imaging the labeled nucleotides.

Abstract: The present invention is drawn to A method of managing HIV chemotherapy of patients who are HIV positive, which comprises transfecting a cell line susceptible to infection by HIV with a sequence from the pol gene of HIV, which sequence encodes a desired target enzyme, obtained by isolating viral RNA from a sample of a biological material from a patient and reverse transcribing the desired region of the pol gene, and a HIV-DNA construct from which the sequence has been deleted, culturing the transfected cells so as to create a stock of chimeric viruses providing an indication of the resistance profile of the circulating virus, assessing the phenotypic sensitivity of the chimeric viruses to an inhibitor of the enzyme encoded by the pol gene of HIV and assigning a value thereto, constructing a data set comprising the value for chimeric virus sensitivity and the corresponding value for a chimeric wild-type strain of HIV, repeating the sensitivity assessment for at least two further inhibitors and thereby construc

Abstract: The present invention relates to an automated method of quantifying DNA strand breaks in intact cells whereby (a) cells are lysed in order to release DNA, (b) the lysate is subjected to an alkaline denaturation process, (c) neutralization occurs, (d) a fluorescent dye is added, and (e) fluorescence is read off a fluorometer, and the method is characterized in that all pipetting stages are carried out in automated fashion by means of a pipetting device in a lightproof housing. The invention further relates to a device to carry out said method, comprising a lightproof housing, a temperature controlled base plate, a system of pipetting nozzles and a fluorometer to measure the fluorescent intensity of DNA.

Abstract: Methods for preparing double stranded, circular DNA molecules comprising a region encoding a protein of interest are disclosed. One or more donor DNA fragments encoding the protein of interest are combined with an acceptor plasmid, a first DNA linker, and a second DNA linker in a Saccharomyces cerevisiae host cell whereby the donor DNA fragment is joined to the acceptor plasmid by homologous recombination of the donor DNA, acceptor plasmid, and linkers to form the closed, circular plasmid.

Abstract: The invention is directed to the design of DNA-binding proteins (DBP's) with capabilities of binding to any predetermined target double-stranded DNA sequence. Disclosed are the rules for design of the proteins; an algorithm for screening for the optimal DBP's; a computer system employing the rules and the algorithm; general formulae encompassing the proteins; and methods of use of the proteins.

Abstract: Disclosed are a number of methods that can be used in a variety of embodiments, including, creation of a nucleic acid terminated at one or more selected bases, sequence analysis of nucleic acids, mapping of sequence motifs within a nucleic acid, positional mapping of nucleic acid clones, and analysis of telomeric regions. The methods utilize double-stranded templates, and in most aspects involve a strand replacement reaction initiated at one or more random or specific locations created in a nucleic acid molecule, and in certain aspects utilizing an oligonucleotide primer.

Abstract: The present invention discloses a methodology which is directed to providing positive confirmation that nucleic acids, possessing putatively identified sequence predicted to generate observed GeneCalling™ signals, are actually present within the sample from which the signal was originally derived.

Abstract: The present invention relates to apparatus and methods for quantitative protein design and optimization.

Abstract: A procedure for the detection of high virus concentrations in blood plasma and/or blood serum by means of the polymerase chain reaction (PCR) is described, in which the sensitivity of the PCR is restricted by the use of suboptimal nucleic acid extraction, amplification or detection conditions. This procedure is suitable, for example, for the detection of parvovirus DNA in plasma or serum, it being possible to adjust the sensitivity of the PCR such that the parvovirus DNA is only detected in samples whose DNA content is greater than 106 to 107 genome equivalents/ml. The detection of the parvovirus DNA amplification carried out is carried out in the sample by measurements of the fluorescence.

Abstract: There are beforehand prepared a monomer having a reaction residue and a polynucleotide probe set comprising plural kinds of polynucleotide probes having a residue bonded to the reaction residue. The monomer is mixed with each kind of polynucleotide probes comprising any plural probes selected from the polynucleotide probe set. Each kind of the resultant mixtures is added to each of different small holes to make the mixture into gel matrix. Thus, a polynucleotide probe chip is produced. Sample DNA is forcibly migrated in the gels by electrophoresis. Laser light is projected onto the side face of the chip. The fluorescence emitted from the whole surface of the chip is collectively detected with a high-sensitive two-dimensional detector. Thus, the polynucleotide probe chip, holding various kinds of DNA probes, for detecting DNA can be provided. This chip has high hybridization-efficiency and makes high-sensitivity and high-speed DNA detection possible.

Abstract: A new method to analyze and predict the binding energy for enzyme-transition state inhibitor interactions is presented. Computational neural networks are employed to discovery quantum mechanical features of transition states and putative inhibitors necessary for binding. The method is able to generate its own relationship between the quantum mechanical structure of the inhibitor and the strength of binding. Feed-forward neural networks with back propagation of error can be trained to recognize the quantum mechanical electrostatic potential at the entire van der Waals surface, rather than a collapsed representation, of a group of training inhibitors and to predict the strength of interactions between the enzyme and a group of novel inhibitors. The experimental results show that the neural networks can predict with quantitative accuracy the binding strength of new inhibitors.