Biophysical Characterization of Nucleolin Domains Crucial for Interaction with Telomeric and TERRA G-Quadruplexes

Nucleolin (NCL) is a well-characterized nucleic acid-binding protein; it binds to various canonical and non canonical structures including single-and double-stranded DNA and RNA, hairpin, loops, and G-quadruplex structures. Gquadruplex structures are majorly formed in promoter, telomeric, and untranslated regions of the genome and affect the process of replication, transcription, and translation. One of the widely studied G-quadruplex-forming regions are telomeres, as these are sites for the recruitment for various proteins providing stability or having an effect on the telomerase activity. NCL is known to bind to both single-and double-stranded telomeric regions and its transcribed telomeric RNA (TERRA). In our study, we show that the 21nt G-quadruplex-forming region of telomeric DNA and TERRA RNA binds to NCL and the domains RRM1234 destabilize the telomeric G-quadruplex structure. We also show the preferential binding of the RNA G-quadruplex over the DNA G-quadruplex by two NCL domains, RRM3 and RRM4. Our findings provide insights into the binding preferences of RRM domains toward G-quadruplex structures and their subsequent effect on the quadruplex stability.

Automated summary

Nucleolin (NCL) is a nucleic acid-binding protein that can bind to various DNA and RNA structures, including single-stranded and double-stranded DNA/RNA, hairpin, loops, and G-quadruplex structures. G-quadruplex structures are mainly formed in promoter, telomeric, and untranslated regions of the genome, and affect replication, transcription, and translation processes. Our study demonstrates that the 21nt G-quadruplex-forming region of telomeric DNA and TERRA RNA can bind to NCL, and the RRM1234 domains destabilize the telomeric G-quadruplex structure. We also find that the RNA G-quadruplex preferentially binds to the RRM3 and RRM4 domains. Our findings provide insights into the binding preferences of RRM domains towards G-quadruplex structures and their subsequent effect on stability.