title: Benzoquinoquinoxaline derivatives stabilize and cleave H-DNA and repress transcription downstream of a triplex-forming sequence.
abstract: Oligopyrimidine*oligopurine sequences with potential to form intramolecular triple helix structures (H-DNA) have been found mainly in high eukaryote genomes. However, the natural occurrence and function of H-DNA remains elusive largely because we lack appropriate reagents to demonstrate the formation of these structures in cells. We examined whether a triple-helix specific stabilizing compound, benzoquinoquinoxaline (BQQ), and its 1,10-phenanthroline derivative can be efficiently utilized to study the formation and stabilization of an intramolecular triple-helical DNA structure in growing Escherichia coli cells and in vitro. Cell uptake of BQQ was confirmed by fluorescence microscopy. A plasmid carrying an H-DNA forming sequence upstream of a reporter gene was used to assess the effects of H-DNA formation and stabilization in growing cells. The presence of the H-DNA forming sequence dramatically repressed beta-lactamase expression, and sub-growth-inhibitory doses of BQQ caused a further 40% reduction. Most importantly, repression was dependent on the triple-helix forming sequence and correlated with the addition of BQQ. As the abundance of the H-DNA forming plasmid was not affected by the addition of BQQ, the dose-dependent reduction at the protein level observed here is likely caused by repression of transcription. Finally, the triple-helix specific interaction of BQQ with the target DNA sequence was demonstrated using a triple-helix directed cleavage assay by BQQ-1,10-phenanthroline conjugate in vitro.
authors.affiliation: Department of Molecular Biology and Functional Genomics, Stockholm University, S-10691 Stockholm, Sweden.
authors.forename: Haleh
authors.initials: H
authors.lastname: Amiri
authors.forename: Natalia
authors.initials: N
authors.lastname: Nekhotiaeva
authors.forename: Jian-Sheng
authors.initials: JS
authors.lastname: Sun
authors.forename: Chi-Hung
authors.initials: CH
authors.lastname: Nguyen
authors.forename: David S
authors.initials: DS
authors.lastname: Grierson
authors.forename: Liam
authors.initials: L
authors.lastname: Good
authors.forename: Rula
authors.initials: R
authors.lastname: Zain
mesh_terms: D001483:Base Sequence; D004247:DNA / Q000737:chemistry* / Q000187:drug effects* / Q000235:genetics; D004269:DNA, Bacterial / Q000737:chemistry / Q000187:drug effects / Q000235:genetics; D004355:Drug Stability; D004926:Escherichia coli / Q000187:drug effects / Q000235:genetics / Q000378:metabolism; D015870:Gene Expression / Q000187:drug effects; D009690:Nucleic Acid Conformation; D010957:Plasmids / Q000235:genetics / Q000378:metabolism; D011810:Quinoxalines / Q000378:metabolism / Q000494:pharmacology*; D014158:Transcription, Genetic / Q000187:drug effects
chemical_list: D004269:DNA, Bacterial; D011810:Quinoxalines; C051802:triplex DNA; D004247:DNA