The 3′-end region of the human PDGFR-β core promoter nuclease hypersensitive element forms a mixture of two unique end-insertion G-quadruplexes

• Published in: Biochimica et biophysica acta. General subjects Vol. 1862; no. 4; pp. 846 - 854
• Main Authors: Onel, Buket, Carver, Megan, Agrawal, Prashansa, Hurley, Laurence H., Yang, Danzhou
• Format: Journal Article
• Language: English
• Published: Netherlands Elsevier B.V 01.04.2018
• Subjects: Base Sequence; Circular Dichroism; circular dichroism spectroscopy; DNA - chemistry; DNA - genetics; Drug target; electrophoresis; End-insertion G-quadruplexes; G-quadruplex; G-Quadruplexes; guanine; Guanine - chemistry; Humans; nuclear magnetic resonance spectroscopy; Nucleic Acid Denaturation; PDGFR-β gene downregulation; platelet-derived growth factor receptor beta; promoter regions; Promoter Regions, Genetic - genetics; Receptor, Platelet-Derived Growth Factor beta - genetics; repressor proteins; Sequence Homology, Nucleic Acid; thermal stability; Transition Temperature; Drug target; PDGFR-β gene downregulation; End-insertion G-quadruplexes; G-quadruplex
• ISSN: 0304-4165; 1872-8006
• DOI: 10.1016/j.bbagen.2017.12.011

While the most stable G-quadruplex formed in the human PDGFR-β promoter nuclease hypersensitive element (NHE) is the 5′-mid G-quadruplex, the 3′-end sequence that contains a 3′-GGA run forms a less stable G-quadruplex. Recently, the 3′-end G-quadruplex was found to be a transcriptional repressor and can be selectively targeted by a small molecule for PDGFR-β downregulation. We use 1D and 2D high-field NMR, in combination with Dimethylsulfate Footprinting, Circular Dichroism Spectroscopy, and Electrophoretic Mobility Shift Assay. We determine that the PDGFR-β extended 3′-end NHE sequence forms two novel end-insertion intramolecular G-quadruplexes that co-exist in equilibrium under physiological salt conditions. One G-quadruplex has a 3′-non-adjacent flanking guanine inserted into the 3′-external tetrad (3′-insertion-G4), and another has a 5′-non-adjacent flanking guanine inserted into the 5′-external tetrad (5′-insertion-G4). The two guanines in the GGA-run move up or down within the G-quadruplex to accommodate the inserted guanine. Each end-insertion G-quadruplex has a low thermal stability as compared to the 5′-mid G-quadruplex, but the selective stabilization of GSA1129 shifts the equilibrium toward the 3′-end G-quadruplex in the PDGFR-β NHE. An equilibrium mixture of two unique end-insertion intramolecular G-quadruplexes forms in the PDGFR-β NHE 3′-end sequence that contains a GGA-run and non-adjacent guanines in both the 3′- and 5′- flanking segments; the novel end-insertion structures of the 3′-end G-quadruplex are selectively stabilized by GSA1129. We show for the first time that an equilibrium mixture of two unusual end-insertion G-quadruplexes forms in a native promoter sequence and appears to be the molecular recognition for PDGFR-β downregulation. •The PDGFR-β 3′-end NHE sequence forms two novel end-insertion intramolecular G-quadruplexes.•The two G-quadruplexes co-exist in equilibrium under physiological salt conditions.•PDGFR-β NHE 3′-end sequence contains a GGA-run and non-adjacent guanines in both the 3′- and 5′- flanking segments.•The dynamic equilibrium of the two G-quadruplexes provides a potential means for PDGFR-β transcriptional regulation.•GSA1129 selectively stabilizes the less stable 3′-end G-quadruplex to shift the equilibriumin the PDGFR-β NHE.