title: Synthesis of a non-cationic, water-soluble perylenetetracarboxylic diimide and its interactions with G-quadruplex-forming DNA.
abstract: A number of N,N'-disubstituted perylenetetracarboxylic diimides have been reported to bind effectively to DNA that adopts G-quadruplex motifs. In some cases, this binding may actively drive the transition from single-strand DNA to the quadruplex form. The perylenediimides in the reported cases all have amine-containing side chains, which are thought to interact with the grooves of the quadruplex and help dictate the selectivity of these compounds for quadruplex versus duplex DNA. We synthesized a polyethyleneglycol-swallowtailed (PEG-tailed) perylenediimide that is water-soluble even though it is uncharged. Binding to duplex and quadruplex DNA of this perylenediimide was studied by fluorescence quenching titrations under a variety of salt conditions, and the compound's effect on quadruplex formation was studied by non-denaturing gel electrophoresis. Our results indicate that while the molecule binds to single-stranded DNA quite effectively and with selectivity, it does not drive the transition of the DNA to the tetrameric quadruplex structure, supporting the idea that charge neutralization is a key component of perylene compounds that stabilize tetrameric quadruplexes.
authors.affiliation: Department of Chemistry and Biochemistry, Box 1848, University of Mississippi University, MS 38677, USA.
authors.forename: Ramakrishna
authors.initials: R
authors.lastname: Samudrala
authors.forename: Xu
authors.initials: X
authors.lastname: Zhang
authors.forename: Randy M
authors.initials: RM
authors.lastname: Wadkins
authors.forename: Daniell Lewis
authors.initials: DL
authors.lastname: Mattern
mesh_terms: D004247:DNA / Q000737:chemistry*; D004591:Electrophoresis, Polyacrylamide Gel; D054856:G-Quadruplexes; D007094:Imides / Q000138:chemical synthesis* / Q000737:chemistry*; D015394:Molecular Structure; D010569:Perylene / Q000031:analogs & derivatives* / Q000138:chemical synthesis* / Q000737:chemistry*; D011092:Polyethylene Glycols / Q000737:chemistry; D012680:Sensitivity and Specificity; D012995:Solubility; D013237:Stereoisomerism; D013329:Structure-Activity Relationship; D017186:Titrimetry; D014867:Water / Q000737:chemistry
chemical_list: D007094:Imides; C517085:perylenetetracarboxylic diimide; D014867:Water; D011092:Polyethylene Glycols; D010569:Perylene; D004247:DNA