Abstract: A DNA microarray, preferably in the form of a chip, contains probes which hybridize to generate primers capable of amplifying approximately 89 HPV types. These target the E1 region of the gene. The design of the chip allows for the detection of any known HPV type, based on a unique probe sequence derived from the HPV E1 region. The present assay utilizes a number of primers that can amplify from about one to six different types of HPV. A large number of primers can be used together. After amplification, the amplicons are contacted with specific probes that are unique for each HPV type. The array further employs a control sequence, which normalizes variability due to sample size.

Abstract: The invention is directed to novel methods of multiplexing nucleic acid reactions, including amplification, detection and genotyping. The invention relies on the use of precircle probes that are circularized in the presence of the corresponding target nucleic acids, cleaved, and then amplified.

Abstract: Methods and apparatus for direct detection of chemical reactions are provided. In a preferred embodiment, electric charge perturbations of the local environment during enzyme-catalyzed reactions are sensed by an electrode system with an immobilized target molecule. The target molecule is preferably DNA. The charge perturbation caused by the polymerase reaction can uniquely identify a DNA sequence. The polymerization process generates local perturbations of charge in the solution near the electrode surface and induces a charge in a polarazible gold electrode. This event is detected as a transient current by a voltage clamp amplifier. Detection of single nucleotides in a sequence can be determined by dispensing individual dNTPs to the electrode solution and detecting the charge perturbations. Alternatively, multiple bases can be determined at the same time using a mix of all dNTPs with subsequent analysis of the resulting signal.

Abstract: The invention encompasses methods for enriching for and identifying a polymorphism within a nucleic acid sample either by separating a subset of a nucleic acid sample or by selectively replicating a subset of a nucleic acid sample such that the polymorphism is contained within a nucleic acid population with reduced complexity, and then identifying the polymorphism within the enriched nucleic acid sample.

Abstract: Methods and apparatus for direct detection of chemical reactions are provided. In a preferred embodiment, electric charge perturbations of the local environment during enzyme-catalyzed reactions are sensed by an electrode system with an immobilized target molecule. The target molecule is preferably DNA. The charge perturbation caused by the polymerase reaction can uniquely identify a DNA sequence. The polymerization process generates local perturbations of charge in the solution near the electrode surface and induces a charge in a polarazible gold electrode. This event is detected as a transient current by a voltage clamp amplifier. Detection of single nucleotides in a sequence can be determined by dispensing individual dNTPs to the electrode solution and detecting the charge perturbations. Alternatively, multiple bases can be determined at the same time using a mix of all dNTPs with subsequent analysis of the resulting signal.

Abstract: The invention is directed to novel methods of multiplexing nucleic acid reactions, including amplification, detection and genotyping. The invention relies on the use of precircle probes that are circularized in the presence of the corresponding target nucleic acids, cleaved, and then amplified.

Abstract: Described here is an automated robotic device that isolates circulating tumor cells (CTCs) or other biological structures with extremely high purity. The device uses powerful magnetic rods covered in removable plastic sleeves. These rods sweep through blood samples, capturing, e.g., cancer cells labeled with antibodies linked to magnetically responsive particles such as superparamagnetic beads. Upon completion of the capturing protocol, the magnetic rods undergo several rounds of washing, thereby removing all contaminating blood cells. The captured target cells are released into a final capture solution by removing the magnetic rods from the sleeves. Additionally, cells captured by this device show no reduced viability when cultured after capture. Cells are captured in a state suitable for genetic analysis. Also disclosed are methods for single cell analysis. Being robotic allows the device to be operated with high throughput.

Abstract: Methods and compositions for detecting an analyte in a sample are provided. In practicing the subject methods, a sample is combined with at least a pair of proximity probes that each include an analyte binding domain and a nucleic acid domain. The resultant mixture is then contacted with a pair of asymmetric nucleic acid connectors. Proximity dependent connector mediated interaction between the nucleic acid domains of the proximity probes is then detected to determine the presence of the analyte in the sample. Also provided are kits and systems for practicing the subject methods.

Abstract: A rapid diagnostic assay for influenza virus, particularly avian influenza and more particularly H5N1, is described. The assay is based on amplification of a significant portion of the hemagglutinin (HA) gene and sequencing of several loci within the HA gene, using techniques which can obtain real time sequence information from multiple sites of a target DNA, in particular pyrosequencing and bioluminescence regenerative cycle. The assay contemplates the use of information-rich subsequences within the HA gene, e.g., (1) a glycosylation sequon; (2) receptor binding site; and (3) HA1/HA2 cleavage site. Other subsequences for sequencing include strain and clade markers, which vary among H5N1 strains.

Abstract: A method of determining the length of a polynucleotide target is provided. With this method, a target is first hybridized to an array of first probes having different, determined lengths, resulting in the formation of duplexes between the polynucleotide target and the first probes. These duplexes have a single stranded section of target if the target is longer than the first probe it is in a duplex with, and a single stranded section of probe if the target is shorter than the first probe it is in a duplex with. Next, a series of probes is hybridized to the duplexes, breaking apart duplexes in which the target and probe have unequal lengths through the process of branch migration. Thus, the target only remains bound in the duplex if the target and probe are of equal lengths. The length of the polynucleotide target can thereby be determined.

Abstract: The present invention provides a method of synthesizing phosphoramidite linkers that are useful for the production of synthesizing two or more oligonucleotides in tandem. The inventive linker has the following desirable properties: (i) enhanced stability to alkali conditions versus the linkers previously published, (ii) cleaves to produce 5? and 3? ends that are fully biologically compatible, (iii) cleaves completely under conditions that are already used in cleavage/deprotection processes so it is fully compatible with conditions that are common in laboratories and does not require additives that necessitate further purification after cleavage, (iv) integrates easily onto commercially available synthesizers because it is compatible with standard coupling chemistry, and (v) is compatible with DNA, RNA, forward, reverse, and LNA, synthesis chemistries. In addition, the inventive linkers may be coupled to a solid support. Thus, the inventive linkers provide a significant advancement in the state of the art.

Abstract: The present invention provides phosphoramidite linkers that are useful for the production of synthesizing two or more oligonucleotides in tandem. The inventive linkers have the following desirable properties: (i) enhanced stability to alkali conditions versus the linkers previously published, (ii) cleave to produce 5? and 3? ends that are fully biologically compatible, (iii) cleave completely under conditions that are already used in cleavage/deprotection processes so they are fully compatible with conditions that are common in laboratories and do not require additives that necessitate further purification after cleavage, (iv) integrate easily onto commercially available synthesizers because they are compatible with standard coupling chemistry, and (v) are compatible with DNA, RNA, forward, reverse, and synthesis chemistries. In addition, the inventive linkers may be coupled to a solid support. Thus, the inventive linkers provide a significant advancement in the state of the art.

Abstract: The present invention features methods and compositions for the renaturation, hybridization, association, or reassociation of nucleic acids that combines both acceleration of the reaction rate and improved specificity.

Abstract: A method of determining the length of a polynucleotide target is provided. With this method, a target is first hybridized to an array of first probes having different, determined lengths, resulting in the formation of duplexes between the polynucleotide target and the first probes. These duplexes have a single stranded section of target if the target is longer than the first probe it is in a duplex with. Next, a second probe having a determined length is hybridized to these duplexes. If the length of the target is greater than the length of the first probe it is displaced during this hybridization step by the process of branch migration. In contrast, if the length of the target is less than or equal to the length of the first probe, it is not displaced. Thus, the length of the polynucleotide target can be determined.

Abstract: The present invention features methods and compositions for the renaturation, hybridization, association, or reassociation of nucleic acids that combines both acceleration of the reaction rate and improved specificity.

Abstract: A safety and performance enhancement arrangement for primary explosive detonators. This arrangement involves a circuit containing an energy storage capacitor and preset self-trigger to protect the primary explosive detonator from electrostatic discharge (ESD). The circuit does not discharge into the detonator until a sufficient level of charge is acquired on the capacitor. The circuit parameters are designed so that normal ESD environments cannot charge the protection circuit to a level to achieve discharge. When functioned, the performance of the detonator is also improved because of the close coupling of the stored energy.

Abstract: The invention relates to proteins or polypeptides that comprise intramolecular dimers of fluorescent protein monomers. More specifically, the invention relates to recombinant polypeptides comprising a monomer of a fluorescent polypeptide, a linker peptide, and a second monomer of that fluorescent polypeptide, where the monomers form an intramolecular dimer. The invention also relates to nucleic acids encoding Intramolecular Dimer Fluorescent Proteins (IDFPs) and vectors comprising such nucleic acids. The invention further relates to methods of making IDFPs and methods of using them. IDFPs are, useful in any application suited for fluorescent proteins and are particularly useful in applications in which more than one fluorescent protein sharing complementary dimerization interfaces is present in the same mixture or is expressed in the same cell, because IDFPs do not form heterodimers.

Abstract: The invention is directed to novel methods of multiplexing nucleic acid reactions, including amplification, detection and genotyping. The invention relies on the use of precircle probes that are circularized in the presence of the corresponding target nucleic acids, cleaved, and then amplified.

Abstract: Methods of selecting tag nucleic acids and VLSIPS™ arrays and the arrays made by the methods are used to label and track compositions, including cells and viruses, e.g., in libraries of cells or viruses. In addition to providing a way of tracking compositions in mixtures, the tags facilitate analysis of cell and viral phenotypes.

Abstract: The invention features methods of high throughput screening of candidate drug agents and rapid identification of drug targets by examining induction of the stress response in a host cell, e.g., the stress response in wildtype host cells and/or in host cells that differ in target gene product dosage (e.g., host cells that have two copies of a drug target gene product-encoding sequence relative to one copy). In general, induction of the stress response in wildtype host cells indicates that a candidate agent has activity of the drug. Induction of a relatively lower or undetectable stress response in a host cell comprising an alteration in gene product dosage indicates that the host cell is drug-sensitive and is altered in a gene product that plays a role in resistance to the drug.