Oligonucleotídeos: desenho, produção e aplicações

Abstract

Oligonucleotides are small molecules of nucleic acids with great biotechnological potential for application in several areas of biology and medicine. The pathogen identification by PCR and the production of aptamers with bioactive or pharmacological effect can be cited among its main applications. In this context, the production and design of oligonucleotides are critical points for their application. The most widely used technique for the production of DNA oligonucleotides is chemical synthesis. Despite its effectiveness, this technique cannot be performed in house, making the user totally dependent on a supplier. This work aimed to design new oligonucleotides with potential for different applications, to develop a method for produce them, and to validate their application in a new protocol for the Flavivirus detection using reverse transcription polymerase chain reaction (RT-PCR). In the first stage of the work, a set of universal primers for Flavivirus identification was developed. For this, 1442 complete genomes of different representatives of the genus Flavivirus were aligned for selection of conserved regions (CRs). Twenty-six CRs were selected, allowing the design of 76 universal primers. Among them, it was chosen the primer pairs with the better characteristics related todegeneration and annealing temperature. These primers were used for the standardization of the in vitro RT-PCR protocol, which potentially amplifies an fragment of 800-806 bp in size from the coding region of NS5 protein. This fragment has sufficient variability to discriminate any species of the genus Flavivirus by sequencing. Once the flavivirus detection system was complete, a new step was taken for the design of specific primers. For this, the amplicon generated by the universal primers was defined as a target, in order to produce five new primers for specific identification of Zika virus and the four serotypes of the Dengue virus. Thus, a semi-nested RT-PCR system was developed. In the first step, some species of the genus Flavivirus are detected and in the second step, with the addition of a set of specific primers, are generated fragments of different sizes for discrimination between Zika virus and four dengue virus serotypes by agarose electrophoresis. In the second stage of the work, an enzymatic method for the production of DNA oligonucleotides was developed. The proposed method is based on rolling circle amplification (RCA) and involves four enzymatic steps: (1) phosphorylation of the 5 'end of the target sequence, (2) circularization of the target sequence, (3) polymerization of a new single strand of DNA containing the oligonucleotides of interest and, finally, (4) a restriction assay to release the oligonucleotides. All steps were performed in a single tube, adding the enzymes with their respective buffer solutions. The oligonucleotides produced were resolved using 8% polyacrylamide gel electrophoresis (PAGE) and visualized by silver staining. Potentially, any oligonucleotide that has no degenerate bases can be produced by the proposed enzymatic method in a single tube. To illustrate, the production of three variations of aptamer 31-TBA, a single chain oligonucleotide having anticoagulant action, was presented.