Related Experiment Video
Updated: Jul 19, 2026

In Vitro Chemical Mapping of G-Quadruplex DNA Structures by Bis-3-Chloropiperidines
Published on: May 12, 2023
Synthesis of a non-cationic, water-soluble perylenetetracarboxylic diimide and its interactions with
Ramakrishna Samudrala1, Xu Zhang, Randy M Wadkins
1Department of Chemistry and Biochemistry, Box 1848, University of Mississippi University, MS 38677, USA.
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.
Related Concept Videos
Inhibitors of Bacterial DNA Synthesis
DNA Base Pairing
Maxam-Gilbert Sequencing
Challenges of the Maxam-Gilbert Method
The...
Aromatic Hydrocarbon Cations: Structural Overview
Removing one hydrogen from the intervening CH2 group with both...
Single-Strand DNA Binding Proteins

