Binding interaction of spherical silver nanoparticles and calf thymus DNA: Comprehensive multispectroscopic, molecular docking, and RAPD PCR studies

Abstract

It is well established that silver nanoparticles (AgNPs) can interact with deoxyribonucleic acid (DNA), inducing different DNA damages. Here, absorption spectra, fluorescence and synchronous fluorescence spectra, analysis of melting temperature curves, transmission electron microscopy (TEM), molecular docking, and random amplification of polymorphic DNA (RAPD) experiments were used to study the interaction of double-stranded calf thymus DNA (dsCT-DNA) with 5 nm bare spherical silver nanoparticles. The association constant (Kapp) of AgNPs with DNA from UV–Vis study was found to be 1.6 (±0.2) × 104 L mol−1 which is comparable to Kapp of groove binders. Moreover, the interaction strength of the DNA bases with AgNPs has been explored through absorbance measurements based on the values of their binding constants in the order G > C > A ≫ T. The quenching data were analyzed using Stern-Volmer and Hill equations. The Stern-Volmer analyzed data demonstrated that the DNA-AgNPs quenching process is static in nature. The calculated binding constant of AgNPs in the DNA environment (<105 L mol−1) indicates the groove binding. The Hill coefficients < 1 indicated the existence of the negative cooperative interactions. The synchronous fluorescence, molecular docking, and RAPD PCR studies as well as the TEM analysis of DNA in the absence and presence of AgNPs suggest the complex formation between DNA and AgNPs. The change in melting temperature also supported the groove binding between DNA and AgNPs.