Detection of human genomic mutations by chemical single-reaction DNA sequencing

Abstract

▼The ideal DNA sequencing method should yield complete and unambiguous information in a single electrophoretic pattern and should be simple, rapid and economical. A single-lane sequencing procedure is available, based upon the dideoxy Sanger methodology. This method cannot a priori be compressed further. Chemical DNA sequencing offers the potential of absolute compression: if one could obtain unambiguous and complete sequence information in a single pattern, then several different DNAs, each labeled with a different fluorochrome, could be analyzed in the same electrophoretic lane. This procedure could be quite relevant for mass genetic screenings. We have developed a chemical method (Ref. 1, 2) that yields a one-reaction one-lane sequence determination, thus allowing fast, multiple, simultaneous sequencing and direct sequence comparisons in the same electrophoretic lane. The method is based on the base-selective degradation (G>A>C>T) of DNA by N-methyl formamide (see Fig. 1). The chemical rationale of this method is as follows. Amides (as determined for formamide, N-methyl formamide and Ndimethyl formamide) react with DNA according to a multistep mechanism. (a) Degradation of the purine and pyrimidine bases: for purines, degradation occurs by nucleophilic attack in C-8, leading to degradative C-8-ring opening of the imidazole ring; for pyrimidines by nucleophilic attack in C-6, leading to degradative C-6-ring opening of the pyrimidine ring. (b) β-Elimination of the sugar-protons with consequent cleavage of the phosphate bonds. N-Methyl formamide has proved to be the best compound to carry out the sequencing reaction because of its efficiencies in base