Mechanical diversity and folding intermediates of parallel-stranded G-quadruplexes with a bulge

• Published in: Nucleic acids research Vol. 49; no. 12; pp. 7179 - 7188
• Main Authors: Zhang, Yashuo, Cheng, Yuanlei, Chen, Juannan, Zheng, Kewei, You, Huijuan
• Format: Journal Article
• Language: English
• Published: Oxford University Press 09.07.2021
• Subjects: Structural Biology
• ISSN: 0305-1048; 1362-4962
• DOI: 10.1093/nar/gkab531

Abstract A significant number of sequences in the human genome form noncanonical G-quadruplexes (G4s) with bulges or a guanine vacancy. Here, we systematically characterized the mechanical stability of parallel-stranded G4s with a one to seven nucleotides bulge at various positions. Our results show that G4-forming sequences with a bulge form multiple conformations, including fully-folded G4 with high mechanical stability (unfolding forces > 40 pN), partially-folded intermediates (unfolding forces < 40 pN). The folding probability and folded populations strongly depend on the positions and lengths of the bulge. By combining a single-molecule unfolding assay, dimethyl sulfate (DMS) footprinting, and a guanine-peptide conjugate that selectively stabilizes guanine-vacancy-bearing G-quadruplexes (GVBQs), we identified that GVBQs are the major intermediates of G4s with a bulge near the 5′ or 3′ ends. The existence of multiple structures may induce different regulatory functions in many biological processes. This study also demonstrates a new strategy for selectively stabilizing the intermediates of bulged G4s to modulate their functions.