Biomics

The efficiency of Polymerase Chain Reaction (PCR) depends on multiple factors. The primers are very important components of PCR which determine the specificity of amplification. In this review, considerable attention is paid to the principles of selection of primers and the requirements for their design with the help of appropriate software. The problems of elimination of primer dimers, as well as the thermodynamics of DNA duplex structures and their melting temperatures, largely dependent not only on the GC-composition, but also on the stacking interactions of neighboring nucleotides, are considered. The applicability of the NN-model of DNA thermodynamics to determine the melting and annealing temperatures of primers is shown. Various formulas for calculating these temperatures are given. The so-called degenerate primers, primers with extra-sequences at the 5'-end, modified and discriminating primers are described separately. The topics of chemical and enzymatic synthesis of oligonucleotides, which also include historical aspects, are also discussed.

primer, DNA, oligonucleotide, chemical synthesis of oligonucleotides, thermodynamics, stacking interaction, neighbor nucleotides, NN model, 5’-end, 3’-end, temperature of melting, temperature of annealing, design of primers, software

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