TY - JOUR
T1 - The 3′-end region of the human PDGFR-β core promoter nuclease hypersensitive element forms a mixture of two unique end-insertion G-quadruplexes
AU - Onel, Buket
AU - Carver, Megan
AU - Agrawal, Prashansa
AU - Hurley, Laurence H.
AU - Yang, Danzhou
N1 - Funding Information:
This research was supported by grants from the National Institutes of Health ( R01CA177585 (DY), R01CA153821 (LHH), and P30CA023168 (DY, Purdue Center for Cancer Research). We thank Kaibo Wang for his help in preparing DNA oligonucleotides and CD measurements. We thank Drs. David Bishop, Clement Lin, and Pradeep Palakshan for proofreading the manuscript.
Publisher Copyright:
© 2017 Elsevier B.V.
Copyright:
Copyright 2018 Elsevier B.V., All rights reserved.
PY - 2018/4
Y1 - 2018/4
N2 - Background 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. Method We use 1D and 2D high-field NMR, in combination with Dimethylsulfate Footprinting, Circular Dichroism Spectroscopy, and Electrophoretic Mobility Shift Assay. Results 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. Conclusion 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. General significance 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.
AB - Background 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. Method We use 1D and 2D high-field NMR, in combination with Dimethylsulfate Footprinting, Circular Dichroism Spectroscopy, and Electrophoretic Mobility Shift Assay. Results 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. Conclusion 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. General significance 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.
KW - Drug target
KW - End-insertion G-quadruplexes
KW - G-quadruplex
KW - PDGFR-β gene downregulation
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U2 - 10.1016/j.bbagen.2017.12.011
DO - 10.1016/j.bbagen.2017.12.011
M3 - Article
C2 - 29288770
AN - SCOPUS:85040665778
VL - 1862
SP - 846
EP - 854
JO - Biochimica et Biophysica Acta - General Subjects
JF - Biochimica et Biophysica Acta - General Subjects
SN - 0304-4165
IS - 4
ER -