Abstract: A method for performing highly accurate PCR employing an assembly, a heated cover and an internal computer. The assembly is made up of a sample block, a number of Peltier thermal electric devices and heat sink, clamped together. The sample block temperature is changed exclusively by the thermoelectric devices controlled by the computer. The control software includes calibration diagnostics which permit variation in the performance of thermoelectric coolers from instrument to instrument to be compensated for such that all instruments perform identically. The block heat sink assembly can be changed to another of the same or different design. The assembly carries the necessary information required to characterize its own performance in an on-board memory device, allowing the assembly to be interchangeable among instruments while retaining its precision operating characteristics. The instrument monitors the thermoelectric devices and warns of changes in resistance that may result in failure.

Abstract: A method of generating a single-stranded nucleic acid molecule comprising (a) combining in a mixture under conditions suitable for a polymerase extension reaction, (i) a polymerase, (ii) an initial polynucleotide comprising a 5? portion and a 3? portion, wherein the polynucleotide forms the nucleic acid molecule 5? end; and (iii) a plurality of overlapping template oligonucleotides each having a 5? template portion and a 3? portion.

Abstract: The invention provides methods and materials for the conversion of cytosine to uracil. A nucleic acid, such a gDNA, is reacted with bisulfate, such as magnesium bisulfite, in the presence of a quaternary amine catalyst. Examples of suitable quaternary amine catalysts include but are not limited to quaternary ammonium compounds, quaternary alkyl ammonium salts, quaternary alkyl ammonium halides, quaternary methyl ammonium bromide, quaternary ammonium chloride, tetraethylammonium hydroxide, tetraethylammonium chloride, tetrabutylammonium chloride, tetrabutylammonium bromide. The invention also contemplates kits of premeasured ingredients for carrying out the methods of the invention either on an individual sample or on a plurality of samples.

Abstract: The present invention provides a two-step multiplex amplification reaction wherein the first step truncates the standard initial multiplex amplification round to “boost” the sample copy number by only a 100-1000 fold increase in the target. Following the first step the product is divided into optimized secondary single amplification reactions, each containing one of the primer sets that were used previously in the first or multiplexed booster step. The booster step can occur using an aqueous target nucleic acid or using a solid phase archived nucleic acid. In particular, nucleic acid sequences that uniquely identify E. Coli were identified using the multiplex amplification method.

Abstract: Disclosed, among other things, are primers containing certain modified nucleobases in the 3? terminal region of the primers that provide reduced formation of primer-dimers during amplification reactions, and various methods of use thereof.

Abstract: The present invention concerns methods and compositions to prepare biological samples to preserve the macromolecules in the samples. Embodiments of the invention concern the use of a soak solution that contains one or more water-miscible solvents. A sample is incubated with the soak solution to the point of saturation at a temperature above the melting temperature of the water-miscible solvent but below 0° C. The use of methods and compositions of the invention allow for subsequent preparation or analysis of the samples.

Abstract: Disclosed are methods and apparatus for compensating for mass error for a time-of-flight mass spectrometer. A reference flight distance for a pulse of ions corresponding to a reference temperature of one or more components of an ion flight path assembly is determined, and the temperature of one or more components of the ion flight path assembly is measured. Correlating the thermal expansion of the flight path assembly with the temperature measurement allows the measured flight times to be adjusted to correspond with the reference flight distance to thereby compensate for the thermal expansion of the flight path assembly. A mass spectrum is obtained using the adjusted flight times. In various embodiments, the temperature signal is used with pre-determined thermal expansion correction factors for the flight path assembly to calculate a correction factor to control another component of the TOF MS, such as the voltage applied to a power supply system or a signal to control clock frequencies.

Abstract: Disclosed is a method of determining when to calibrate a time-of-flight mass spectrometer. In various embodiments, the method comprises storing within a controller a set of parameters for the mass spectrometer; providing an updated set of parameters while retaining at least one set of previously stored parameters; computing at least one rate of change of the updated set of parameters with respect to the at least one set of previously stored parameters; and determining when to calibrate the mass spectrometer from the results of computing the rate of change of at least one of the parameters. In various embodiments, a parameter stored can be a set of temperatures derived from obtaining system temperature measurements of those components whose changing temperature is an indication of mass drift.

Abstract: A thermal cycler for automatic performance of the polymerase chain reaction is provided. The thermal cycler comprises a heater control that provides close temperature control of the reaction.

Abstract: An instrument is provided that can monitor nucleic acid sequence amplifications reactions, for example, PCR amplification of DNA and DNA fragments. The instrument includes a multi-notch filter disposed along one or both of an excitation beam path and an emission beam path. Methods are also provided for monitoring nucleic acid sequence amplifications using an instrument that includes a multi-notch filter disposed along a beam path.

Abstract: A fluid processing device is provided that enables the controlled flow of a liquid sample along a fluid processing pathway through various sample-containment regions and is free of fluid flow blockages or valves along the processing pathway. A system is also provided for processing the device and includes a rotatable platen and alignment features that can hold the fluid processing device in two or more different orientations on the rotatable platen. A method is also provided for processing a sample, in the device, with the system.