Molecular architecture of G-quadruplex structures generated on duplex Rif1-binding sequences

The Journal of Biological Chemistry
Hisao MasaiKazuo Nagasawa

Abstract

G-quadruplexes (G4s) are four-stranded DNA structures comprising stacks of four guanines, are prevalent in genomes, and have diverse biological functions in various chromosomal structures. A conserved protein, Rap1-interacting factor 1 (Rif1) from fission yeast (Schizosaccharomyces pombe), binds to Rif1-binding sequence (Rif1BS) and regulates DNA replication timing. Rif1BS is characterized by the presence of multiple G-tracts, often on both strands, and their unusual spacing. Although previous studies have suggested generation of G4-like structures on duplex Rif1BS, its precise molecular architecture remains unknown. Using gel-shift DNA binding assays and DNA footprinting with various nuclease probes, we show here that both of the Rif1BS strands adopt specific higher-order structures upon heat denaturation. We observed that the structure generated on the G-strand is consistent with a G4 having unusually long loop segments and that the structure on the complementary C-strand does not have an intercalated motif (i-motif). Instead, we found that the formation of the C-strand structure depends on the G4 formation on the G-strand. Thus, the higher-order structure generated at Rif1BS involved both DNA strands, and in some cases, G4s ...Continue Reading

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Citations

Dec 19, 2019·Chromosome Research : an International Journal on the Molecular, Supramolecular and Evolutionary Aspects of Chromosome Biology·Michelle L HulkeAmnon Koren
Jul 28, 2020·Trends in Genetics : TIG·Patroula NathanailidouZoi Lygerou
Nov 11, 2020·Journal of Biochemistry·Sana AlaviHisao Masai
Aug 23, 2020·Biochemical and Biophysical Research Communications·Hisao Masai, Taku Tanaka

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