Modelling viral evolution in vitro using exo- Klenow polymerase: continuous selection of strand displacement amplified DNA that binds an oligodeoxynucleotide to form a triple-helix.

Evolution comprises cycles of amplification, mutagenesis and selection. To study evolutionary phenomena, isothermal strand displacement amplification (SDA) of double-stranded DNA as an in vitro model for rolling-circle replication of viruses has been coupled to a positive selection procedure. First, two subsequent amplification reactions utilizing exo- Klenow polymerase were performed under direct observation using the fluorescent dye thiazole orange. Under the chosen conditions, the mutation rate was 1.5 x 10(-3) and 0.4 x 10(-3) for base substitutions and deletions, respectively. Then, a 16mer oligodeoxynucleotide with an acridine moiety coupled to its 5' end was used to select for double strands that retained their ability to form a triple-helix with the oligodeoxynucleotide. Conditions for triple-helix formation were chosen such that only 10 to 40% of the SDA products were allowed to bind the third strand. Non-denaturing polyacrylamide gel electrophoresis was used to separate triple-helices from unmodified double strands, and only triplex strands were used to initiate a new round of error-prone amplification and selection. Nine such rounds with about 270 molecular generations were performed. The final mutant spectrum was characterized and compared with those of amplification reactions without additional selection pressure. While without selection pressure base substitutions and deletions throughout the initial wild-type rapidly produce a diverse mutant distribution, the consensus after nine selection rounds clearly shows two mutational hotspot positions. Using gel shift assays and a newly developed non-radioactive DNase I footprinting technique, it could be shown that both the initial wild-type and the final consensus do not differ significantly in their triplex formation ability. As opposed to this, they do show different amplification efficiencies. The final consensus sequence is amplified with the highest rate in the exponential reaction phase, while the most abundant clone, which is characterized by two additional point deletions, is the sequence with the highest amplification rate in the linear growth phase.