A Comparative Docking Analysis of Non-Carcinogenic DNA Staining Dyes to Propose the Best Alternative to Ethidium Bromide

Fluorescent dyes that stain a cell’s DNA are used in live cell imaging as they allow for tracking of cell division, for the visualization and sizing of dsDNA restriction fragments, and for the examination of properties of the isolated DNA molecules. Conventionally, Ethidium bromide (EtBr) is the cationic dye used to visualize DNA after separating the fragments on Agarose Gel Electrophoresis. It is widely used due to the striking fluorescence enhancement it displays upon intercalation into the dsDNA at the minor groove. Although a highly sensitive stain, it is notoriously unsafe, not only is it a very strong mutagen, it may also be a carcinogen or teratogenic. Histopathological changes of Ethidium Bromide treated rats showed little degenerative changes characterized by glomerular and tubulointerstitial injury, nephrosis, synechia, necrotic changes, cirrhosis, and ischemia. Ethidium bromide revealed pronounced degenerative changes in ovarian histoarchitecture. The sequence of atretic changes involved nuclear degeneration, characterized by Chromatolysis, rupture, and dissolution of the nuclear membrane. Granulosa cells associated with degenerating follicle types (bilaminar, Multilaminar and graffian follicle) showed desquamation, cytolysis, and nuclear dissolution. Extensive vacuolation also occurred in these follicles. Only a few follicles reached the maturity. In most of the females, Graffian follicle failed to rupture, which led to failure in ovulation. This resulted in Sterility of the females.Hence need has arisen for now –carcinogenic and nothazardous nucleic acid staining dyes.Our Present study has thus been aimed at finding out the non-carcinogenic DNA staining dyes and to compare their binding efficiency with DNA and find out which is the best DNA staining Dye which has least binding energy score and is non-carcinogenic as well. Hence nowadays safer alternatives to EtBr are being sought after. A comparative docking study of six of such The interaction of EtBr and the six other alternative dyes (Crystal violet, GelRed, Hoechst 33258, Methylene blue, SYBR Green and GelGreen) with the ds-B-DNA were studied, their chemical structures were drawn using ChemSketch and the potential ligands were optimized using ArgusLab. Further, the docking studies of these DNA stains on a dsDNA molecule (1D49) was performed using AutoDock tools and their interaction with the DNA was visualized using Discovery Studio. The binding energies of Hoechst 33258 with the DNA was found to be better (-11.96 Kcal/mol) as compared to the other stains, thus suggesting its use as both a non-carcinogenic and highly sensitive alternative to EtBr.