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  9. Design of primers for polymerase chain reaction (brief review of software and databases)

Design of primers for polymerase chain reaction (brief review of software and databases)

Year: 2016

Pages: 215-238

Number: Volume 8, issue 3

Type: scientific article

Topic: Articles

Authors: Chemeris D.A., Kiryanova O.Yu., Gubaidullin I.M., Chemeris A.V.

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Summary:

In three decades of the existence the polymerase chain reaction (PCR) as a method of molecular biology got practically into all modern physicochemical biology and related subjects. PCR is applied approximately in every eighth work where DNA is analyzed. Oligonucleotide primers are extremely important component of any PCR, and there is a number of requirements to their design. Now for this purpose the specialized computer software based on various algorithms are used. Many programs for primers design exist as free web services, also their distribution kits can be received from developers, quite often authors provide access to source code of their products. A number of programs are accessible from commercial sources. The existing software allow to design primers for various modifications among which there is multiplex, degenerate, metabisulfite PCR, PCR in real time, PCR with the subsequent cloning of multiple fragments, including ligase-free, PCR site-directed mutagenesis, PCR aimed for indel and mutations identification, SNP, etc. The multiple parameter analysis of oligonucleotides properties in silico (melting point definition, detection of secondary structures, dimers, etc.) is carried out. The programs which are carrying out design the oligonucleotide primers with various modifications, for example, containing ribonucleotides, LNA nucleotides are developed. Recently the programs of primers design considering the ploidy level of the concrete type of an organism genome began to appear. The large number of references to web services of software for primers design is given. Some databases in which information on the sequences of well proved primers collects are briefly characterized. The list of a references consist of more than 240 sources. In this work software complexes, and partly some algorithms which are applied to selection of primers are considered. A basis of any modern software complex, an efficient algorithm is the mathematical description in the form of systems of algebraic, differential equations, integral differential equations.

Keywords:

PCR, primer, primer annealing temperature, melting temperature, oligonucleotide, primer design, software, algorithm, database, databank

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