Optical tweezers experiments reveal anticancer drug BI-3802 binds DNA in the micromolar range.

Abstract

B-cell lymphoma is a common form of cancer associated with the lymphatic system. A recently developed anticancer drug BI-3802 is known to target B-cell lymphoma by binding to transcription repressor BCL6 in order to kill cancerous cells. Many small molecule drugs like BI-3802 that are dissolved in DMSO have been a challenge to study with optical tweezers since DMSO changes the refractive index of the medium. Here we have carefully conducted control experiments to estimate the concentration limits of DMSO to study these drugs. Staying within these limits (1:400 volume ratio of DMSO to Buffer), we use optical tweezers to trap a single DNA molecule to explore the binding of BI-3802 with DNA. Once we trap a single DNA molecule, we stretch the DNA and measure the tension in the DNA as a function of extension. During this process, the DNA undergoes a phase transition from double-stranded DNA (dsDNA) to single-stranded DNA (ssDNA) at a certain force which is commonly referred to as the overstretching transition. Based on its structure we believed that this small molecule drug would bind to DNA through intercalation. However, our results suggest that the force where the phase transition from dsDNA to ssDNA occurs is decreased as the concentration of BI-3802 is increased. This indicates that this drug destabilizes the naturally occurring double-stranded form of DNA, which is the opposite effect of intercalating drugs. These effects were observed only at micromolar concentrations of BI-3802, whereas it is used in nanomolar concentrations in targeting BCL6. Even though this is weak DNA binding, the outcome of these experiments may help us better understand BI-3802 interactions at the molecular level and help develop new therapeutics.