Computational detection and analysis of sequences with duplex-derived interstrand G-quadruplex forming potential.
Bioinformatic approaches to the identification of genomic sequences having G-quadruplex forming potential (QFP) has enabled important tests of the structure of these sequences in vitro and of their behavior under conditions where the formation or function of G-quadruplexes is modulated in vivo. Several similar approaches to identifying intramolecular QFP (i.e. forming among G-runs on one strand of DNA) have been developed previously, but none appears to perfectly predict G-quadruplex formation. Here we describe a new approach, which complements and differs from prior approaches in that it identifies motifs containing G-runs on both strands of duplex DNA that could contribute to G-quadruplex structures. We call these motifs duplex-derived interstrand QFP (ddiQFP), and illustrate their potential applications by describing their genomic distribution and an example of their correspondence to loci targeted by a G-quadruplex-unwinding DNA helicase in yeast.
Department of Cell and Molecular Biology, University of Pennsylvania School of Medicine, Philadelphia, PA, USA.
Kajia
K
Cao
Paul
P
Ryvkin
F Brad
FB
Johnson
D002942:Circular Dichroism; D019295:Computational Biology / Q000379:methods; D004247:DNA / Q000737:chemistry*; D004265:DNA Helicases / Q000737:chemistry*; D054856:G-Quadruplexes; D023281:Genomics; D006147:Guanine / Q000737:chemistry; D009690:Nucleic Acid Conformation; D016615:Telomere / Q000737:chemistry
D006147:Guanine; D004247:DNA; D004265:DNA Helicases