Recombinase polymerase amplification using novel thermostable strand-displacing DNA polymerases from Aeribacillus pallidus and Geobacillus zalihae

J Biosci Bioeng. 2023 Apr;135(4):282-290. doi: 10.1016/j.jbiosc.2023.01.009. Epub 2023 Feb 17.


Recombinase polymerase amplification (RPA) is an isothermal DNA amplification reaction at around 41 °C using recombinase (Rec), single-stranded DNA-binding protein (SSB), and strand-displacing DNA polymerase (Pol). Component instability and the need to store commercial kits in a deep freezer until use are some limitations of RPA. In a previous study, Bacillus stearothermophilus Pol (Bst-Pol) was used as a thermostable strand-displacing DNA polymerase in RPA. Here, we attempted to optimize the lyophilization conditions for RPA with newly isolated thermostable DNA polymerases for storage at room temperature. We isolated novel two thermostable strand-displacing DNA polymerases, one from a thermophilic bacterium Aeribacillus pallidus (H1) and the other from Geobacillus zalihae (C1), and evaluated their performances in RPA reaction. Urease subunit β (UreB) DNA from Ureaplasma parvum serovar 3 was used as a model target for evaluation. The RPA reaction with H1-Pol or C1-Pol was performed at 41 °C with the in vitro synthesized standard UreB DNA. The minimal initial copy numbers of standard DNA from which the amplified products were observed were 600, 600, and 6000 copies for RPA with H1-Pol, C1-Pol, and Bst-Pol, respectively. Optimization was carried out using RPA components, showing that the lyophilized RPA reagents containing H1-Pol exhibited the same performance as the corresponding liquid RPA reagents. In addition, lyophilized RPA reagents with H1-Pol showed almost the same activity after two weeks of storage at room temperature as the freshly prepared liquid RPA reagents. These results suggest that lyophilized RPA reagents with H1-Pol are preferable to liquid RPA reagents for onsite use.

Keywords: Aeribacillus pallidus; Geobacillus zalihae; Isothermal DNA amplification; Recombinase polymerase amplification; Strand-displacing DNA polymerase.

MeSH terms

  • DNA-Directed DNA Polymerase / genetics
  • Geobacillus* / genetics
  • Nucleic Acid Amplification Techniques / methods
  • Recombinases* / genetics
  • Recombinases* / metabolism
  • Sensitivity and Specificity


  • Recombinases
  • DNA-Directed DNA Polymerase

Supplementary concepts

  • Geobacillus zalihae
  • Aeribacillus pallidus