Nucleic acid clamp-mediated recognition and stabilization of the physiologically relevant MYC promoter G-quadruplex

Abstract

The MYC proto-oncogene is upregulated, often at the transcriptional level, in ∼80% of all cancers. MYC's promoter is governed by a higher order G-quadruplex (G4) structure in the NHE III1 region. Under a variety of conditions, multiple isoforms have been described to form from the first four continuous guanine runs (G41–4) predominating under the physiologically relevant supercoiled conditions. In the current study, short oligonucleotides complementing the 5′- and 3′-regions flanking the G4 have been connected by an abasic linker to form G4 clamps, varying both linker length and G4 isoform being targeted. Clamp A with an 18 Å linker was found to have marked affinity for its target isomer (G41–4) over the other major structures (G42–5 and G41–5, recognized by clamps B and C, respectively), and to be able to shift equilibrating DNA to foster greater G4 formation. In addition, clamp A, but not B or C, is able to modulate MYC promoter activity with a significant and dose-dependent effect on transcription driven by the Del4 plasmid. This linked clamp-mediated approach to G4 recognition represents a novel therapeutic mechanism with specificity for an individual promoter structure, amenable to a large array of promoters.

Cysteine‐rich protein 61 regulates the chemosensitivity of chronic myeloid leukemia to imatinib mesylate through the nuclear factor kappa B/Bcl‐2 pathway

“…In addition, it has been reported that a secondary structure, called the G‐quadruplex (G4) structure, can form on the 3′‐untranslated region of Cyr61 mRNA, potentially modulating its translation . For example, therapeutic strategies using either G4 stabilizing small molecules or a nucleic acid clamp approach could possibly be used to modulate the stability of this mRNA G4 structure, and thus the translation of Cyr61 . In conclusion, Cyr61 plays important roles in the survival of CML cells and could potentially serve as a molecular target for the treatment of CML.…”

Time-Dependent Effects of POT1 Knockdown on Proliferation, Tumorigenicity, and HDACi Response of SK-OV3 Ovarian Cancer Cells

“…These changes were consistent with those noted in a study by Veldman et al [ 29 ]. The POT1 protein can bind to 3′-overhangs in the form of a quadruplex [ 28 , 30 ], which has been observed in the promoter region of c-Myc [ 31 ]. The knockdown of POT1 gene expression changed the spatial conformation of the quadruplex and thus affected the function of the c-Myc promoter, which directly resulted in the downregulation of c-Myc mRNA expression [ 28 , 30 , 31 ].…”

“…The POT1 protein can bind to 3′-overhangs in the form of a quadruplex [ 28 , 30 ], which has been observed in the promoter region of c-Myc [ 31 ]. The knockdown of POT1 gene expression changed the spatial conformation of the quadruplex and thus affected the function of the c-Myc promoter, which directly resulted in the downregulation of c-Myc mRNA expression [ 28 , 30 , 31 ]. Subsequently, the transcription of hTERT, a downstream gene of c-Myc [ 9 , 10 ], was also decreased.…”

The role of RNA G‐quadruplexes in human diseases and therapeutic strategies

“…This therapeutic strategy to maintain GQ formation displayed effected dose-dependent treatment in tumorigenic nonsmall cell lung carcinoma cells inducing an increase in PTEN expression and a decrease in cancer cell proliferation. Hao, Gaerig, and Brooks (2016) used a clamp approach for targeting a DNA GQ in the c-MYC promoter regions. In a similar fashion as the previous report, the therapeutic was designed with nucleic acids to harness the specific complementary binding ability to the flanking regions around a specific GQ structure, while being connected by a conjugated polyethylene glycol linker.…”