Profiling the nucleobase and structure selectivity of anticancer drugs and other DNA alkylating agents by RNA-Seq

Drugs that covalently modify DNA are components of most chemotherapy regimens, often serving as first-line treatments. Classically the chemical reactivity of DNA alkylators has been determined in vitro with short oligonucleotides. Here University of Basel chemists use next generation RNA sequencing to report on the chemoselectivity of alkylating agents. They develop the method with the well-known clinically used DNA modifiying drugs streptozotocin and temozolomide, and then apply the technique to profile RNA modification with uncharacterized alkylation reactions such as with powerful electrophiles like trimethylsilyldiazomethane. The multiplexed and massively parallel format of NGS offers analyses of chemical reactivity in nucleic acids to be accomplished in less time with greater statistical power.

HPLC traces for single RNA nucleosides alkylated with DMS

The red line is a control injection of a mixture of A C G and U, the peaks elute as C, U, A and G. Letters prefixed with r are intact ribonucleosides. Letters without are the result of depurination