title: The expanding repertoire of G4 DNA structures.
abstract: The definition of DNA and RNA G-quadruplexes (G4s) has recently been broadened to include structures with certain defects: bulges, G-vacancies or mismatches. Despite the striking progress in computational methods for assessing G4 folding propensity, predicting G4s with defects remains problematic, reflecting the enhanced sequential diversity of these motifs. "Imperfect" G4 motifs, i.e., those containing interrupted or truncated G-runs, are typically omitted from genomic analyses. We report here studies of G4s with defects and compare these structures with classical ("perfect") quadruplexes. Thermal stabilities and ligand interactions are also discussed. We exploited a simple in-house computational tool for mining putative G4s with defects in the human genome. The obtained profiles of the genomic distribution of imperfect G4 motifs were analyzed. Collectively, our findings suggest that, similar to classical G4s, imperfect G4s could be considered as potential regulatory elements, pathology biomarkers and therapeutic targets.
authors.affiliation: Research and Clinical Center for Physical Chemical Medicine, 119435 Moscow, Russia; Engenlhardt Institute of Molecular Biology, 119991 Moscow, Russia.
authors.forename: Anna
authors.initials: A
authors.lastname: Varizhuk
authors.affiliation: Research and Clinical Center for Physical Chemical Medicine, 119435 Moscow, Russia; Moscow Institute of Physics and Technology (State University), 117303 Moscow, Russia.
authors.forename: Dmitry
authors.initials: D
authors.lastname: Ischenko
authors.affiliation: Research and Clinical Center for Physical Chemical Medicine, 119435 Moscow, Russia; Department of Molecular Virology, FSBI Research Institute of Influenza, Ministry of Health of the Russian Federation, Saint Petersburg, Russia.
authors.forename: Vladimir
authors.initials: V
authors.lastname: Tsvetkov
authors.affiliation: Engenlhardt Institute of Molecular Biology, 119991 Moscow, Russia; N.D. Zelinsky Institute of Organic Chemistry, Moscow 119991, Russia.
authors.forename: Roman
authors.initials: R
authors.lastname: Novikov
authors.affiliation: Research and Clinical Center for Physical Chemical Medicine, 119435 Moscow, Russia; Moscow Institute of Physics and Technology (State University), 117303 Moscow, Russia.
authors.forename: Nikolay
authors.initials: N
authors.lastname: Kulemin
authors.affiliation: Engenlhardt Institute of Molecular Biology, 119991 Moscow, Russia.
authors.forename: Dmitry
authors.initials: D
authors.lastname: Kaluzhny
authors.affiliation: Research and Clinical Center for Physical Chemical Medicine, 119435 Moscow, Russia; Moscow Institute of Physics and Technology (State University), 117303 Moscow, Russia.
authors.forename: Maria
authors.initials: M
authors.lastname: Vlasenok
authors.affiliation: Research and Clinical Center for Physical Chemical Medicine, 119435 Moscow, Russia.
authors.forename: Vladimir
authors.initials: V
authors.lastname: Naumov
authors.affiliation: Research and Clinical Center for Physical Chemical Medicine, 119435 Moscow, Russia.
authors.forename: Igor
authors.initials: I
authors.lastname: Smirnov
authors.affiliation: Research and Clinical Center for Physical Chemical Medicine, 119435 Moscow, Russia. Electronic address: pozmogova@niifhm.ru.
authors.forename: Galina
authors.initials: G
authors.lastname: Pozmogova
mesh_terms: D004247:DNA / Q000737:chemistry*; D054856:G-Quadruplexes; D015894:Genome, Human / Q000235:genetics; D023281:Genomics; D006801:Humans
chemical_list: D004247:DNA
keywords: G-quadruplexes; G4 ligands; Genomic analysis; Noncanonical DNA structures