The application of thermophilic DNA primase TtDnaG2 to DNA amplification

For DNA replication in vivo, DNA primase uses a complementary single-stranded DNA template to synthesize RNA primers ranging from 4 to 20 nucleotides in length, which are then elongated by DNA polymerase. Here, we report that, in the presence of double-stranded DNA, the thermophilic DNA primase TtDnaG2 synthesizes RNA primers of around 100 nucleotides with low initiation specificity at 70 °C. Analysing the structure of TtDnaG2, we identified that it adopts a compact conformation. The conserved sites in its zinc binding domain are sequestered away from its RNA polymerase domain, which might give rise to the low initiation specificity and synthesis of long RNA segments by TtDnaG2. Based on these unique features of TtDnaG2, a DNA amplification method has been developed. We utilized TtDnaG2 to synthesize RNA primers at 70 °C after 95 °C denaturation, followed by isothermal amplification with the DNA polymerase Bst3.0 or phi29. Using this method, we successfully amplified genomic DNA of a virus with 100% coverage and low copy number variation. Our data also demonstrate that this method can efficiently amplify circular DNA from a mixture of circular DNA and linear DNA, thus providing a tool to amplify low-copy-number circular DNA such as plasmids.