Chemical development in the design of oligonucleotide probes for binding to DNA and RNA

Abstract

This paper deals with the chemical synthesis of natural and modified oligodeoxyribonucleotides and chimeric oligoribo-oligodeoxyribo-nucleotides. The first part describes the synthesis of oligonucleotide probes bearing different types of spacer groups (aminoalkyl-, hydroxyalkyl-, amino acids), bound to the 5'- or 3'-terminal phosphate group of oligonucleotides. Two types of reagents have been used to convert the oligonucleotide phosphomonoester group into chemically reactive groups in aqueous media: water-soluble carbodiimide and N-hydroxybenzotriazole. The second part involves the description of the chemical ligase method for template-dependent coupling of oligonucleotides. Application of these techniques to replace natural internucleotide bonds in oligonucleotides with modified phosphoramide, pyrophosphate, chimeric ribo-deoxyribo, arabino-deoxyribo, deoxyxylo-deoxyribo, as well as phosphoramidate-alkyl-phosphoramidate internucleotide linkages is described. The final part involves some examples of the interaction of modified oligonucleotide probes with DNA and proteins (restriction enzymes). The use of modified oligonucleotide probes (chimeric oligoribo-oligodeoxyribo-nucleotides linked via the pyrophosphate internucleotide bond) allows the elaboration of a method of regiospecific cleavage of RNA. This method is equivalent to restriction enzyme cleavage of DNA.