Designing of sequencing assay assisted by capillary electrophoresis based on DNA folding analysis: an application to the VCAM1 gene

In this work, we describe a fast standardized molecular method for DNA sequencing assisted by capillary electrophoresis with a particular emphasis on bioinformatic approaches to avoid sequencing errors due to complex DNA regions. In this case, the method was applied on the human vascular adhesion molecule 1 (VCAM1) gene. VCAM1 sequence, in fact, shows many thermodynamically critical parameters such as very low GC content (30-40%), many nucleotide stack areas, i.e. hairpins, self-complementary regions. With a traditional primer design approach it was difficult to design correct PCR oligonucleotides, thus sometimes, the chromatogram showed an illegible profile. By a strategy involving various bioinformatic tools (Mfold, Oligo, Highter), we investigated the role of the DNA-folding analysis in the assistance of primer design for the DNA sequencing of fragments with high -ΔG stem-loop regions. This new approach allowed us to sequence nine different VCAM1 regions each containing the respective exon. Our results, based on different DNA samples recruited from oral brushes taken from ten different subjects, identified four different SNPs (c.662-7C/T, c.1793-79A>G, c.2079C/T, c.2208A>G) with high reproducibility.