Data on multimerization efficiency for short linear DNA templates and phosphoryl guanidine primers during isothermal amplification with Bst exo- DNA polymerase

Data on multimerization efficiency for short linear DNA templates and phosphoryl guanidine primers during isothermal amplification with Bst exo- DNA polymerase Full article

Journal

Data in Brief
ISSN: 2352-3409

Output data

Year: 2020, Volume: 29, Article number : 105188, Pages count : DOI: 10.1016/j.dib.2020.105188

Tags

Isothermal amplification, Multimerization, Bst exo- DNA polymerase, Phosphoryl guanidine oligonucleotides (PGO)

Authors

Garafutdinov Ravil R. ¹ , Sakhabutdinova Assol R. ¹ , Kupryushkin Maxim S. ² , Pyshnyi Dmitrii V. ²

Affiliations

1	Institute of Biochemistry and Genetics, Ufa Federal Research Center of the Russian Academy of Sciences, Russian Federation
2	Institute of Chemical Biology and Fundamental Medicine, Siberian Branch of the Russian Academy of Sciences, Russian Federation

Over the last two decades, isothermal amplification of nucleic acids has gained more attention due to a number of advantages over the widely used polymerase chain reaction. For isothermal amplification, DNA polymerases with strand-displacement activity are needed, and Bst exo- polymerase is one of the most commonly used. Unfortunately, Bst exo- causes nonspecific DNA amplification (so-called multi- merization) under isothermal conditions that results in undesirable products (multimers) consisting of tandem nucleotide repeats. Multimerization occurs only for short ssDNA or primer dimers, and the ef- ficiency of multimerization depends significantly on the reaction conditions, but slightly depends on the sequence of DNA templates. In this study we report the prevention of DNA multimerization using a new type of modified oligonucleotide primers with internucleosidic phosphates containing 1,3-dimethyl-2- imino-imidazolidine moieties (phosphoryl guanidine (PG) groups). Primers with one, two or three PG groups located at the 30- or 50-ends or in the middle of the primers were designed. It turned out, such bulky groups interfere with the moving of Bst exo- polymerase along DNA chains. However, one modified phosphate does not notably affect the efficiency of polymerization, and the elongation is completely inhibited only when three contiguous modifications occur. Multimerization of the linear ssDNA tem- plates is blocked by three modifications in the middle of both primers whereas specific amplification of the circular ssDNA by rolling circle amplification is not inhibited. Thus, incorporation of three PG groups is sufficient to prevent multimerization and allows to create improved primers for reliable isothermal amplification with Bst exo- DNA polymerase.

Garafutdinov R.R. , Sakhabutdinova A.R. , Kupryushkin M.S. , Pyshnyi D.V.
Data on multimerization efficiency for short linear DNA templates and phosphoryl guanidine primers during isothermal amplification with Bst exo- DNA polymerase
Data in Brief. 2020. V.29. 105188 . DOI: 10.1016/j.dib.2020.105188 WOS Scopus OpenAlex

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