Interactions of Novel Sets of Naphthalene Diimides with G – Quadruplex Structures in Human DNA

The discovery of naphthalene diimide derivatives ability to intercalate DNA and stabilize G – quadruplex structures have drawn interest for investigations. Binding affinities of different NDI derivatives to these DNA assemblies depend on various parameters including the planar structure of ligand and attractive molecule. Here we present the interaction of N,N’-bis(4-sulfophenyl)-1,4,5,8-naphthalene diimide with G – quadruplex DNAs such as telomeric DNA (a-coreTT) & non – telomeric DNA (c-myc). The interactions of the ligand with different types of oligonucleotides were measured by UV – Vis spectroscopy & emission spectroscopy. Additionally, a polymerase chain reaction amplified region of the human beta globin gene was used to confirm the formation of G – quadruplex structures within human DNA via gel electrophoresis method. Absorption and emission spectroscopy measurements have indicated notable variations between pure compound and the complexes of compound & oligonucleotide. Moreover, gel electrophoresis results have displayed significant difference between the PCR amplified product alone and PCR amplified product with the ligand where the complex migrated slower. Therefore, the examined S-NDI is a promising DNA – binding ligand within the human genome which requires further investigations to understand the reliability and stability of this particular NDI derivative as DNA – binding ligand. Keywords: Naphthalene diimide derivative, G – quadruplex, human beta globin gene, telomeric region, non – telomeric region