Exploiting extension bias in polymerase chain reaction to improve primer specificity in ensembles of nearly identical DNA templates.

@article{Wright2014ExploitingEB,
  title={Exploiting extension bias in polymerase chain reaction to improve primer specificity in ensembles of nearly identical DNA templates.},
  author={Erik S. Wright and Luftu Safak Yilmaz and Satya Sai Ram and Jeremy M Gasser and Gregory W. Harrington and Daniel R. Noguera},
  journal={Environmental microbiology},
  year={2014},
  volume={16 5},
  pages={1354-65}
}
We describe a semi-empirical framework that combines thermodynamic models of primer hybridization with experimentally determined elongation biases introduced by 3'-end mismatches for improving polymerase chain reaction (PCR)-based sequence discrimination. The framework enables rational and automatic design of primers for optimal targeting of one or more sequences in ensembles of nearly identical DNA templates. In situations where optimal targeting is not feasible, the framework accurately… CONTINUE READING
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DECIPHER: Database Enabled Code for Ideal Probe Hybridization Employing R [WWW document

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