Binding polarity of RPA to telomeric sequences and influence of G-quadruplex stability

•hRPA binding is influenced by G4 stability (effect of cations and temperature).•G4 ligands inhibit binding and unfolding of G4 by hRPA.•hRPA binds unfolded G4 with a 5′–3′ spatial polarity in agreement with that reported on an unstructured ssDNA.•only RPA1 and RPA2 bind the 21 mer human telomeric G4.•data are compatible with a 5′ to 3′ binding and unfolding of G4 by hRPA.

Replication protein A (RPA) is a single-stranded DNA binding protein that plays an essential role in telomere maintenance. RPA binds to and unfolds G-quadruplex (G4) structures formed in telomeric DNA, thus facilitating lagging strand DNA replication and telomerase activity. To investigate the effect of G4 stability on the interactions with human RPA (hRPA), we used a combination of biochemical and biophysical approaches. Our data revealed an inverse relationship between G4 stability and ability of hRPA to bind to telomeric DNA; notably small G4 ligands that enhance G4 stability strongly impaired G4 unfolding by hRPA. To gain more insight into the mechanism of binding and unfolding of telomeric G4 structures by RPA, we carried out photo-crosslinking experiments to elucidate the spatial arrangement of the RPA subunits along the DNA strands. Our results showed that RPA1 and RPA2 are arranged from 5′ to 3′ along the unfolded telomeric G4, as already described for unstructured single-stranded DNA, while no contact is possible with RPA3 on this short oligonucleotide. In addition, these data are compatible with a 5′ to 3′ directionality in G4 unfolding by hRPA.