BACKGROUND The majority of established techniques for monitoring real-time PCR amplification involve individual target-specific fluorogenic probes. For analysis of numerous different targets the synthesis of these probes contributes to the overall cost during assay development. Sequence-dependent universal detection techniques overcome this drawback but are prone to detection of unspecific ampl...

The microreaction volumes of PCR chips (a microfabricated silicon chip bonded to a piece of flat glass to form a PCR reaction chamber) create a relatively high surface to volume ratio that increases the significance of the surface chemistry in the polymerase chain reaction (PCR). We investigated several surface passivations in an attempt to identify 'PCR friendly' surfaces and used those surfac...

Background: A reliable method to detect gene polymorphisms must be established to eliminate genotyping errors due to false PCR amplification. In the previous study, we have developed AS-PCR (Allele Specific-Polymerase Chain Reaction) to detect HER2 Ile655Val gene polymorphism with good specificity and sensitivity, yet it produces some errors. This study is aimed to eliminate the source of genot...

Amplification of a product in PCR with specific primers may be viewed as an artificial Darwinian-type "selection of the fittest". In other selective systems, such as general evolution, immune system and probably brain cortex, the stringency of selection is not absolute but rather degenerate, with selection of many highly fit units, not limited, however, to only the fittest. In PCR also, anneali...

The incorporation of locked nucleic acids (LNAs) into oligonucleotide primers has been shown to increase template binding strength and specificity for DNA amplification. Real-time PCR and DNA sequencing have been shown to be significantly enhanced by the use of LNAs. Theoretically, increasing primers' binding strength may also increase the sensitivity of conventional PCR, reducing minimum templ...

DNA amplification by the polymerase chain reaction (PCR) was used to detect DNA of the Lyme disease spirochaete Borrelia burgdorferi. Primers that specify the amplification of a 145 basepair DNA fragment of the OspA gene of B. burgdorferi were used. The amplification product was detected by gel electrophoresis and ethidium bromide staining or by hybridization to a radiolabelled oligonucleotide ...

Selective amplification in PCR is principally determined by the sequence of the primers and the temperature of the annealing step. We have developed a new PCR technique for distinguishing related sequences in which additional selectivity is dependent on sequences within the amplicon. A 5' extension is included in one (or both) primer(s) that corresponds to sequences within one of the related am...

Human epidermal growth factor receptor 2 (HER2) and topoisomerase II alpha (TOP2A) genes have been proposed as predictive biomarkers of sensitivity to anthracycline chemotherapy. Recently, chromosome 17 centromere enumeration probe (CEP17) duplication has also been associated with increased responsiveness to anthracyclines. However, reports are conflicting and none of these tumor markers can ye...

Multi-tag pyrosequencing has become a key method in the analysis of microbial community composition. However, it is well known that kinetic bias during the initial PCR amplification of such microbial communities can dramatically distort amplicon abundance prior to downstream emulsion PCR and pyrosequencing. Here we present a simple protocol combining length-heterogeneity PCR fingerprinting with...

It is sometimes useful to amplify DNA before labeling it. Degenerate oligonucleotide primed-polymerase chain reaction (DOP-PCR) allows amplification of any complex DNA, regardless of sequence. DOP-PCR is performed using a single primer that has a fixed sequence at its 5' end and several degenerate bases near its 3' end that allow it to anneal at low stringency to many sites in complex DNA. Foll...