Polymerase chain reaction amplification efficiency

Iqbal, S. Robinson, J. Deere, D. Saunders, J. R. Edwards, C. Porter, J. Efficiency of the polymerase chain reaction amplification of the uid gene for detection of Escherichia coli in contaminated water. Lett. Appl. Microbiol. 1997,24,498-502. 

Synthetic oligonucleotides are very important tools in the study and manipulation of DNA, including such techniques as site-directed mutagenesis and DNA amplification by the polymerase chain reaction. The techniques for chemical synthesis of oligonucleotides are highly developed. Very efficient automated methodologies based on solid phase synthesis are used extensively in fields that depend on the availability of defined DNA sequences.52... 

Zhou et al. [175] described the determination of severe acute respiratory syndrome (SARS) coronavirus by a microfluidic chip system. The unit included an LIF microfluidic chip analyzer, a glass microchip for both PCR and capillary electrophoresis, a chip thermal cycler based on dual Peltier thermoelectric elements, a reverse transcription-polymerase chain reaction (RT-PCR) SARS diagnostic kit, and a DNA electrophoretic sizing kit. According to the authors, the system allowed efficient DNA amplification of the SARS coronavirus followed by electrophoretic sizing and detection on the same chip. 

AuNPs have also been used for DNA-specific sequence detection. Lee and co-workers developed silicon/glass-based devices for simultaneous Polymerase Chain Reaction (PCR) target amplification and sequence-specific electrochemical detection. A PCR closed chamber was connected to patterned indium tin oxide (ITO) or gold electrodes modified with specific DNA sequences, which served as an efficient electrochemical... 

An important technical difference between NGS techniques is whether the input DNA or RNA must be amplified in quantity before sequencing. This matters because the methods of amplifying DNA/ RNA can introduce errors in the sequence and also introduce biases in the sequences that are amplified. Typical thermostable polymerases, used for amplifying DNA/RNA in polymerase chain reactions (PCR), introduce mutations at a rate of 1 in 9000 nucleotides. This rate sounds rare, but the multiple amplification cycles necessarily (up to 40) can yield a number of sequence errors. Furthermore, particular types of sequences called microsatellites, such as long stretches of adenine nucleotides, may cause an even higher error rate. Likewise, polymerases often amplify GC-rich sequences at lower efficiency... 

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