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IP Watch: Recent Patents Related to PCR, Nucleic Acid Amplification, and Sample Prep: Jun 28, 2011

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BioArray Solutions has been awarded US Patent No. 7,970,553, "Concurrent optimization in selection of primer and capture probe sets for nucleic acid analysis."

Michael Seul, Tatiana Vener, and Xiongwu Xia are named as inventors on the patent.

Discloses a method of iteratively optimizing two (or more) interrelated sets of probes for the multi-step analysis of sets of designated sequences, each such sequence requiring, for conversion, at least one conversion probe, or primer; and each converted sequence requiring, for detection, at least one capture probe. The patent describes an iterative method for the concurrent optimization of primer and probe selection invoking fast logical string matching functions to perform a complete cross-correlation of probe sequences and target sequences. The score function assigns to each probe-target alignment a "degree of matching" score on the basis of position-weighted Hamming distance functions. Pairs of probes in the final selection may differ in several positions, while other pairs of probes may differ in only a single position. Not all such positions are of equal importance, and a score function is introduced, reflecting the position of the mismatch within the probe sequence.


DuPont has been awarded US Patent No. 7,968,856, "Fluorometer with low heat-generating light source."

Jerald Lee and Stanley Dabell are named as inventors on the patent.

The patent describes a fluorometer preferably combined with a thermal cycler useful in biochemical protocols such as PCR and DNA melting curve analysis. The fluorometer features a low heat-generating light source such as a light-emitting diode having a one-to-one correspondence to each of a plurality of sample containers, such as capped PCR tubes in a standard titer tray. The fluorometer further comprises an optical path between each LED and its correspondingly positioned container, and another optical path between each fluorescing sample within the positioned container and an optical signal sensing means. The instrument can be computer controlled.


Becton Dickinson has been awarded US Patent No. 7,968,292, "Compositions and methods for the identification of a carbapenemase gene."

Craig Whiteford and Charles Yu are named as inventors on the patent.

Provides compositions and methods, and novel primer and probe compositions, for the rapid and sensitive detection of the enzyme carbapenemase in a sample. The primers and probe sets can be used in amplification methods such as PCR, particularly quantitative PCR, and packaged into kits for use in amplification methods for the purpose of detecting carbapenemase in a test sample, particularly a patient sample and particularly a direct sample.

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In Nature this week: nautilus genome gives peek into its evolution, computational tool to analyze single-cell ATAC-seq data, and more.