Short Tandem Repeats of Single-Stranded (ATTCC)n in Neutrophil Extracellular Traps Bind Thrombin

DNA-protein interactions play a pivotal role in a variety of cellular processes. Despite the considerable research dedicated to understanding these interactions, the specific role of single-stranded DNA (ssDNA) remains largely unexplored. Our study aimed to uncover the role of ssDNA in the interplay between neutrophil extracellular traps (NETs) and thrombin, a crucial enzyme involved in both blood clot formation and immune response. Using chromatin immunoprecipitation sequencing (ChIP-seq) and kethoxal-assisted ssDNA sequencing, we identified a specific short tandem repeat (STR) sequence, ss(ATTCC)n, that is highly enriched and forms an iI-motif structure crucial for its interaction with thrombin. We further observed that the binding affinity between ss(ATTCC)n and thrombin is increased under acidic conditions, a condition frequently linked to diseases such as cancer. Our findings not only shed light on the unexplored area of sequence-dependent ssDNA-protein interactions but also pave the way for targeted interventions in thrombosis and coagulation disorders. Overall design: Pull down thrombin binding DNA and do DNA seq to reveal the binding sites in 4 replicates. Do KAS-seq to reveal all single stranded DNA as a comparison.