Effect of metal ions on isothermal amplification with Bst exo- DNA polymerase

Over the last two decades, the isothermal amplification has become actively used for nucleic acids analysis. To perform isothermal techniques, DNA polymerases with strand-displacement activity are needed, and Bst exo- polymerase is one of the most widely used. However, Bst exo- is prone to non-speci...

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Bibliographic Details
Published in:International journal of biological macromolecules 2020-10, Vol.161, p.1447-1455
Main Authors: Garafutdinov, Ravil R., Gilvanov, Aidar R., Kupova, Olga Yu, Sakhabutdinova, Assol R.
Format: Article
Language:English
Subjects:
Bst exo- DNA polymerase
Cofactors
DNA - chemistry
DNA - genetics
DNA Replication
DNA-Directed DNA Polymerase - chemistry
Ions - chemistry
Isothermal amplification
Metals - chemistry
Models, Molecular
Molecular Conformation
Molecular docking simulations
Molecular Structure
Multimerization
Rolling circle amplification (RCA)
Structure-Activity Relationship
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Summary:Over the last two decades, the isothermal amplification has become actively used for nucleic acids analysis. To perform isothermal techniques, DNA polymerases with strand-displacement activity are needed, and Bst exo- polymerase is one of the most widely used. However, Bst exo- is prone to non-specific DNA synthesis (e.g., DNA multimerization) occurring in the absence of the DNA target of interest. Here, we report on the activity of Bst exo- in the presence of Mg2+, Mn2+, Ca2+, Cd2+, Co2+, Cu2+, Ni2+ and Zn2+ in the model molecular systems which included amplification of circular and linear DNA templates; conditions providing effective and highly specific isothermal amplification were determined. It was found that amplification can proceed not only with Mg2+ but with Mn2+, Ca2+, Cd2+ and Cu2+ depending on the type of Bst exo- polymerase and the buffer. Manganese ions turned out to be the most suitable alternative cofactor, which prevents multimerization in some buffers. Molecular docking simulations showed the highest stability for the quaternary ‘polymerase-DNA-triphosphate-cations’ complexes containing Mg2+ and Mn2+, and the moderate one for complexes with Ca2+, Cd2+ and Cu2+. The frequency of nucleotide misincorporation increased in the following row: Mg2+ ≈ Mn2+ ≤ Cd2+ 
ISSN:0141-8130
1879-0003
DOI:10.1016/j.ijbiomac.2020.08.028