title: A parallel quadruplex DNA is bound tightly but unfolded slowly by pif1 helicase.
abstract: DNA sequences that can form intramolecular quadruplex structures are found in promoters of proto-oncogenes. Many of these sequences readily fold into parallel quadruplexes. Here we characterize the ability of yeast Pif1 to bind and unfold a parallel quadruplex DNA substrate. We found that Pif1 binds more tightly to the parallel quadruplex DNA than single-stranded DNA or tailed duplexes. However, Pif1 unwinding of duplexes occurs at a much faster rate than unfolding of a parallel intramolecular quadruplex. Pif1 readily unfolds a parallel quadruplex DNA substrate in a multiturnover reaction and also generates some product under single cycle conditions. The rate of ATP hydrolysis by Pif1 is reduced when bound to a parallel quadruplex compared with single-stranded DNA. ATP hydrolysis occurs at a faster rate than quadruplex unfolding, indicating that some ATP hydrolysis events are non-productive during unfolding of intramolecular parallel quadruplex DNA. However, product eventually accumulates at a slow rate.
authors.affiliation: From the Department of Biochemistry and Molecular Biology, University of Arkansas for Medical Sciences, Little Rock, Arkansas 72205.
authors.forename: Alicia K
authors.initials: AK
authors.lastname: Byrd
authors.affiliation: From the Department of Biochemistry and Molecular Biology, University of Arkansas for Medical Sciences, Little Rock, Arkansas 72205 raneykevind@uams.edu.
authors.forename: Kevin D
authors.initials: KD
authors.lastname: Raney
mesh_terms: D000255:Adenosine Triphosphate / Q000737:chemistry; D018360:Crystallography, X-Ray; D004265:DNA Helicases / Q000737:chemistry* / Q000235:genetics / Q000378:metabolism; D004277:DNA, Single-Stranded / Q000737:chemistry / Q000235:genetics; D054856:G-Quadruplexes; D042822:Genomic Instability; D011485:Protein Binding; D012441:Saccharomyces cerevisiae / Q000235:genetics; D029701:Saccharomyces cerevisiae Proteins / Q000737:chemistry / Q000235:genetics* / Q000378:metabolism; D016615:Telomere / Q000235:genetics
chemical_list: D004277:DNA, Single-Stranded; D029701:Saccharomyces cerevisiae Proteins; D000255:Adenosine Triphosphate; C085463:PIF1 protein, S cerevisiae; D004265:DNA Helicases
keywords: DNA Helicase; Enzyme Kinetics; Fluorescence Resonance Energy Transfer (FRET); G-quadruplex; Protein-DNA Interaction