Composition dependent separation of oligonucleotides by capillary electrophoresis in acidic buffers with application to the quality control of synthetic oligonucleotides

Oligonucleotides have become a widely used tool in molecular biology and mo lecular diagnostics, Their parallel synthesis in large numbers has raised t he request for fast and informative analytical tools for their quality cont rol. Here we propose an alternative to current analytical methodologies bas ed on capillary electrophoresis at very low pH in free solution. In these n on-classical analytical conditions oligonucleotides can be discriminated fo r their base composition, thus adding a further dimension to the classical electrophoretic sizing performed in sieving media at moderately basic pH. W e have tested several separating conditions at various pH values on a very large set of samples (about 200 synthetic oligonucleotides) ranging from 10 to 50 residues and with different terminal modification including amine, p hosphate, biotin, fluorescein and other fluorescent dyes. We have been able to characterize the quality of these synthetic products and to detect base redundancies (i.e, the copresence of different bases in a single position of the oligonucleotide chain) in oligonucleotides up to 50 bases long, thus posing the basis for the application of this method to the emerging held o f detection mutation in complex genomes analysis. (C) 1999 Elsevier Science B.V. All rights reserved.