Specific primer design for the polymerase chain reaction.pdf

REVIEW Specific primer design for the polymerase chain reaction Li-Yeh Chuang ? Yu-Huei Cheng ? Cheng-Hong Yang Received: 2 December 2012 / Accepted: 23 May 2013 / Published online: 21 June 2013  Springer Science+Business Media Dordrecht 2013 Abstract The design of primers has a major impact on the success of PCR in relation to the specificity and yield of the amplified product. Here, we introduce the applications of PCR as well as the definition and characteristics for PCR primer design. Recent primer design tools based on Primer3, along with several computational intelligence-based primer design meth- ods which have been applied in primer design, are also reviewed. In addition, characteristics of population- based methods used in primer design are discussed in detail. Keywords Algorithm  Computational intelligence  Polymerase chain reaction  Primer design Introduction Polymerase chain reaction (PCR) is a common and indispensable technique applied in the biological and medical fields. Before performing PCRs, suitable primers have to be designed. In primer design, many constraining conditions have to be considered simul- taneously, with the typical considerations being the primer length, length difference of a primer pair, primer GC content, nucleotide composition in a primer 30 end (i.e. GC clamp), PCR product size, concentra- tions of the PCR buffer reagents, stable secondary structures (i.e. elimination of dimers and hairpins), primer melting temperature, and the melting temper- ature difference of a primer pair (Yuryev et al. 2002; Housley et al. 2006; Andreson et al. 2008; Boyle et al. 2009). Manually designed primers may easily yield incorrect results and thus designing feasible primer sets by automatic computation is preferable. To date, various computational tools and methods for facilitat- ing primer design have been developed and applied in biology and medicine, such as large scale sequencing (Haas et al. 1998), clinical diagnostic applications (Elnifr