Identification of putative G-quadruplex DNA structures in S. pombe genome by quantitative PCR stop assay

Jamroskovic J, Obi I, Movahedi A, Chand K, Chorell E, Sabouri N (2019)

Publication Language: English

Publication Type: Journal article, other

Publication year: 2019

Journal

DNA Repair Elsevier

Book Volume: 82

Article Number: 102678

DOI: 10.1016/j.dnarep.2019.102678

Open Access Link: https://doi.org/10.1016/j.dnarep.2019.102678

Abstract

In order to understand in which biological processes the four-stranded G-quadruplex (G4) DNA structures play a role, it is important to determine which predicted regions can actually adopt a G4 structure. Here, to identify DNA regions in Schizosaccharomyces pombe that fold into G4 structures, we first optimized a quantitative PCR (qPCR) assay using the G4 stabilizer, PhenDC3. We call this method the qPCR stop assay, and used it to screen for G4 structures in genomic DNA. The presence of G4 stabilizers inhibited DNA amplification in 14/15 unexplored genomic regions in S. pombe that encompassed predicted G4 structures, suggesting that at these sites the stabilized G4 structure formed an obstacle for the DNA polymerase. Furthermore, the formation of G4 structures was confirmed by complementary in vitro assays. In vivo, the S. pombe G4 unwinder Pif1 helicase, Pfh1, was associated with tested G4 sites, suggesting that the G4 structures also formed in vivo. Thus, we propose that the confirmed G4 structures in S. pombe form an obstacle for replication in vivo, and that the qPCR stop assay is a method that can be used to identify G4 structures. Finally, we suggest that the qPCR stop assay can also be used for identifying G4 structures in other organisms, as well as being adapted to screen for novel G4 stabilizers.

Authors with CRIS profile

Anahita Movahedi Lehrstuhl für Fertigungsmesstechnik (FMT)

Involved external institutions

Umeå University SE Sweden (SE)

How to cite

APA:

Jamroskovic, J., Obi, I., Movahedi, A., Chand, K., Chorell, E., & Sabouri, N. (2019). Identification of putative G-quadruplex DNA structures in S. pombe genome by quantitative PCR stop assay. DNA Repair, 82. https://dx.doi.org/10.1016/j.dnarep.2019.102678

MLA:

Jamroskovic, Jan, et al. "Identification of putative G-quadruplex DNA structures in S. pombe genome by quantitative PCR stop assay." DNA Repair 82 (2019).

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