METHOD FOR THE DESIGN OF OLIGONUCLEOTIDES FOR MOLECULAR BIOLOGY TECHNIQUES

Abstract

The present invention discloses a method that can be used to identify one DNA sequence or one specific group of DNA sequences from a complex biological sample. Diverse molecular biology methods require the use of short DNA sequences, called oligonucleotides, that are artificially synthesized from a description of their composing bases. The disclosed method allows the design of oligonucleotides useful for said molecular biology procedures, like probe design procedures, and is characterized by the construction of a database of reference sequences, the selection of a subset of sequences belonging to target organisms, the selection of candidate oligonucleotides from such sequences, the depuration of these candidate oligonucleotides according to hybridization specificity and thermodynamic stability criteria, and the sorting of such oligonucleotides according to their taxonomic specificity. In a second aspect, a method is disclosed to design oligonucleotides pairs or primers, which are required in certain molecular biology techniques, like polymerase chain reaction (PCR) techniques. This method is similar to the first aspect of the invention, but thermodynamically compatible oligonucleotides pairs or primers that hybridize to the same sequence at a distance which is within a given range are evaluated.