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

Buket Onel, Megan Carver, Prashansa Agrawal, Laurence Hurley, Danzhou Yang

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2 Citations (Scopus)

Abstract

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.

Original languageEnglish (US)
Pages (from-to)846-854
Number of pages9
JournalBiochimica et Biophysica Acta - General Subjects
Volume1862
Issue number4
DOIs
StatePublished - Apr 1 2018

Fingerprint

G-Quadruplexes
Guanine
Circular dichroism spectroscopy
Molecular recognition
Electrophoretic mobility
3'-nucleotidase
Assays
Thermodynamic stability
Stabilization
Salts
Nuclear magnetic resonance
Down-Regulation
Molecules
Electrophoretic Mobility Shift Assay
Circular Dichroism

Keywords

  • Drug target
  • End-insertion G-quadruplexes
  • G-quadruplex
  • PDGFR-β gene downregulation

ASJC Scopus subject areas

  • Biophysics
  • Biochemistry
  • Molecular Biology

Cite this

@article{e5fae1db9d6343b585c841e3883bee15,
title = "The 3′-end region of the human PDGFR-β core promoter nuclease hypersensitive element forms a mixture of two unique end-insertion G-quadruplexes",
abstract = "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.",
keywords = "Drug target, End-insertion G-quadruplexes, G-quadruplex, PDGFR-β gene downregulation",
author = "Buket Onel and Megan Carver and Prashansa Agrawal and Laurence Hurley and Danzhou Yang",
year = "2018",
month = "4",
day = "1",
doi = "10.1016/j.bbagen.2017.12.011",
language = "English (US)",
volume = "1862",
pages = "846--854",
journal = "Biochimica et Biophysica Acta - General Subjects",
issn = "0304-4165",
publisher = "Elsevier",
number = "4",

}

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

AU - Yang, Danzhou

PY - 2018/4/1

Y1 - 2018/4/1

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

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VL - 1862

SP - 846

EP - 854

JO - Biochimica et Biophysica Acta - General Subjects

JF - Biochimica et Biophysica Acta - General Subjects

SN - 0304-4165

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