Factors Influencing Dna Expansion in the Course of Polymerase Chain Reaction

Abstract

We performed more than 3,500 polymerase chain reactions (PCRs) under various conditions with more than 400 DNA fragments of 4–150 nucleotides in length. Some of the PCRs provided expanded DNA molecules of kilobase lengths whereas others led to no expansion. Repetitiveness of the primary structure was mostly found to be necessary but not sufficient for the expansion. (A+T)-rich fragments expand better than (G+C)-rich ones and pyrimidine-rich fragments expand better than purine-rich fragments. Terminal nucleotides and the fragment length also are important for the expansion. Examples are presented when relatively small alterations of the DNA primary structure caused a dramatic change in the expansion. For example, A₈T₈ expanded a lot whereas T₈A₈ did not expand at all. The present work has implications for pathological expansions of microsatellites in the human genome as well as regarding the genome evolution in general.

Keywords:

• DNA expansion
• PCR
• Microsatellites

This project was supported by grant NM/7634–3 from the Ministry of Health of the Czech Republic.