ABSTRACT

Hoechst 33258 is a well-known nucleic acid dye which is noted for its affinity to B-DNA. Prior drug discovery research has investigated two fragments that attach at a target site and are connected via combinations of linkers to observe activity between the two. Yet, the effects of linkers on an individual fragment itself has not been fully understood. The objective of this study was to observe the impact of linker length and composition with Hoechst 33258 binding to B-DNA. After using multiple experimentation methods such as UV thermal denaturation and fluorescence microscopy studies, the results showed that shorter linkers localized in the DNA nucleus while longer linkers interacted with extranuclear organelles. The composition of the linker also played a role in its stabilization to the binding site, particularly when referring to the number of oxygen atoms increasing the compound’s stability. Using these results, we are better able to see the applications of Hoechst 33258 and future linker research in drug developments.