Protein-DNA/RNA Interactions: An Overview of Investigation Methods in the -Omics Era

The fields of application of functional proteomics are not limited to the study of protein-protein interactions; they also extend to those involving protein complexes that bind DNA or RNA. These interactions affect fundamental processes such as replication, transcription, and repair in the case of DNA, as well as transport, translation, splicing, and silencing in the case of RNA. Analytical or preparative experimental approaches, both in vivo and in vitro, have been developed to isolate and identify DNA/RNA binding proteins by exploiting the advantage of the affinity shown by these proteins toward a specific oligonucleotide sequence. The present review proposes an overview of the approaches most commonly employed in proteomics applications for the identification of nucleic acid-binding proteins, such as affinity purification (AP) protocols, EMSA, chromatin purification methods, and CRISPR-based chromatin affinity purification, which are generally associated with mass spectrometry methodologies for the unbiased protein identification.

Automated summary

Functional proteomics applications extend beyond protein-protein interactions to include protein complexes binding DNA or RNA, which impact crucial processes. Various experimental methods have been developed to identify nucleic acid binding proteins, leveraging the affinity of these proteins towards specific nucleotide sequences. Affinity purification protocols, EMSA, chromatin purification methods, and CRISPR-based chromatin affinity purification are commonly used approaches associated with mass spectrometry for unbiased protein identification.