[Subtractive hybridization. Theoretical analysis, and a principle of the trap]

An analysis of the kinetics of the subtractive hybridization and the extent of enrichment of sequence differences between two otherwise identical genomes or transcripts has been carried out for different conditions. The hybridization of single- or double-stranded DNA (tracer) containing the difference (target) to the large excess of single-stranded complementary DNA not having the sequence (driver) gives a much higher enrichment of the target than hybridization of double-stranded driver and tracer or double-stranded driver with single-stranded tracer. The conclusion is that the first approach can give means for efficient extraction of the target without artificial simplifications of the genomes before subtraction. A principle of the "trapper", preventing the hybrids formed from dissociation in the course of PCR amplification of the target enriched, is proposed as a complement to the single-stranded DNA hybridization in the process of highly efficient subtraction.