Professor Marraffini uses Staphylococcus epidermidis and Streptococcus pyogenes as model systems for studying CRISPR immunity. The clinical isolate S. epidermidis RP62a harbors a CRISPR spacer that matches the nickase gene (nes) that is present in nearly all staphylococcal conjugative plasmids and prevents their spread. Using this system, Marraffini revealed that the CRISPR-Cas machinery targets DNA, rather than RNA, directly. Work in the Marraffini lab also demonstrated that the S. pyogenes crRNA-guided Cas9 DNA nuclease constitute a formidable tool for genetic engineering.
Professor Marraffini’s current research employs molecular genetic and biochemical approaches to analyze the genesis and function of CRISPR-Cas systems. He ultimately hopes to answer fundamental questions about how CRISPR-Cas systems destroy their targets, how the genetic memory is generated, and how CRISPR-Cas immunity affects the evolution of bacteria and archaea.