Abstract

DE LA FUENTE, ARIEL; ROMERO CALLE, DANITZA XIOMARA; CARDENAS ALEGRIA, OSCAR  and  ALVAREZ ALIAGA, MARÍA TERESA. Design and Evaluation of primers in silico of the E1 gene of chukungunya virus for Real-Time PCR (q PCR). Rev.Cs.Farm. y Bioq [online]. 2018, vol.6, n.1, pp.107-124. ISSN 2310-0265.

Abstract Primer design is a substantial part of PCR assays, which is used in characteriza-tion of microorganisms, sequencing, quanti-fication, etc. In recent years, new tools have been added for this purpose, new variants and approaches have been created, many of these tools are commercial and others are free including open source, giving the pos-sibility to improve or modify as required. In this work, we compared the basic charac-teristics of the primers design, using 2 types of free and open source web tools, Primer-BLAST and Primer3Plus, in this sense the in silico design, analysis of secondary struc-tures and verification of primers designed. The results showed that the use of addi-tional variables or use of penalties using the software Primer3 Plus affect in specificity, secondary structures formation in primers and in the products of amplification. In ad-dition, default parameters, that many software have, do not imply that suitable and / or specific primers can be obtained, mean-ing the importance of the use of penalties. Therefore, the use of Primer3Plus has al-lowed to decrease the formation of second-ary structures without affecting the ampli-fication specificity of the selected marker.

Keywords : Design of primers; secondary structures; qPCR; software.

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