title: Combining the best in triplex recognition: synthesis and nucleic acid binding of a BQQ-neomycin conjugate.
abstract: Synthesis of a BQQ-neomycin conjugate is reported. The conjugate combines two ligands, one known to intercalate triplexes (BQQ) and another known to bind in the triplex groove (neomycin). The conjugate stabilizes T.A.T, as well as mixed base DNA triplex, better than neomycin, BQQ, or a combination of both. The conjugate selectively stabilizes the triplex (in the presence of physiological salt concentrations), with as little as 4 muM of the ligand leading to a DeltaTm of >60 degrees C. Competition dialysis studies show a clear preference for the drug binding to triplex DNA/RNA over the duplex/single strand structures. Modeling studies suggest a structure of neomycin bound to the larger W-H (Watson-Hoogsteen) groove with BQQ intercalated between the triplex bases.
authors.affiliation: Laboratory of Medicinal Chemistry, Department of Chemistry, Clemson University, Clemson, SC 29634, USA. dparya@clemson.edu
authors.forename: Dev P
authors.initials: DP
authors.lastname: Arya
authors.forename: Liang
authors.initials: L
authors.lastname: Xue
authors.forename: Paul
authors.initials: P
authors.lastname: Tennant
mesh_terms: D000900:Anti-Bacterial Agents / Q000737:chemistry / Q000494:pharmacology; D004247:DNA / Q000737:chemistry* / Q000378:metabolism; D007364:Intercalating Agents / Q000737:chemistry* / Q000378:metabolism; D008958:Models, Molecular; D009355:Neomycin / Q000031:analogs & derivatives* / Q000737:chemistry / Q000378:metabolism; D009692:Nucleic Acid Heteroduplexes / Q000737:chemistry / Q000378:metabolism; D011810:Quinoxalines / Q000737:chemistry* / Q000378:metabolism; D012313:RNA / Q000737:chemistry / Q000378:metabolism
chemical_list: D000900:Anti-Bacterial Agents; D007364:Intercalating Agents; D009692:Nucleic Acid Heteroduplexes; D011810:Quinoxalines; C051802:triplex DNA; D012313:RNA; D004247:DNA; D009355:Neomycin