Exploring the Parallel G-Quadruplex Nucleic Acid World: A Spectroscopic and Computational Investigation on the Binding of the c-myc Oncogene NHE III1 Region by the Phytochemical Polydatin

Abstract

Trans-polydatin (tPD), the 3-β-D-glucoside of the well-known nutraceutical trans-resveratrol, is a natural polyphenol with documented anti-cancer, anti-inflammatory, cardioprotective, and immunoregulatory effects. Considering the anticancer activity of tPD, in this work, we aimed to explore the binding properties of this natural compound with the G-quadruplex (G4) structure formed by the Pu22 [d(TGAGGGTGGGTAGGGTGGGTAA)] DNA sequence by exploiting CD spectroscopy and molecular docking simulations. Pu22 is a mutated and shorter analog of the G4-forming sequence known as Pu27 located in the promoter of the c-myc oncogene, whose overexpression triggers the metabolic changes responsible for cancer cells transformation. The binding of tPD with the parallel Pu22 G4 was confirmed by CD spectroscopy, which showed significant changes in the CD spectrum of the DNA and a slight thermal stabilization of the G4 structure. To gain a deeper insight into the structural features of the tPD-Pu22 complex, we performed an in silico molecular docking study, which indicated that the interaction of tPD with Pu22 G4 may involve partial end-stacking to the terminal G-quartet and H-bonding interactions between the sugar moiety of the ligand and deoxynucleotides not included in the G-tetrads. Finally, we compared the experimental CD profiles of Pu22 G4 with the corresponding theoretical output obtained using DichroCalc, a web-based server normally used for the prediction of proteins’ CD spectra starting from their “.pdb” file. The results indicated a good agreement between the predicted and the experimental CD spectra in terms of the spectral bands’ profile even if with a slight bathochromic shift in the positive band, suggesting the utility of this predictive tool for G4 DNA CD investigations.

New Cu(i) square grid-type and Ni(ii) triangle-type complexes: synthesis and characterization of effective binders of DNA and serum albumins

“…Stabilization of GQ forming sequences to prevent its disassembly is a target of many studies 30,46,47 therefore, taking advantage of the multivalency of metallosupramolecular complexes, we performed preliminary GQ binding (Fig. S10‡) and induction (induced circular dichroism, ICD) experiments (Fig.…”

“…In our case the stiffened cyclohexane could also, potentially, interact on the surface of the helix and, moreover, the metal ions incorporated in the scaffold can induce the electrostatic interactions. 45 Stabilization of GQ forming sequences to prevent its disassembly is a target of many studies 30,46,47 therefore, taking advantage of the multivalency of metallosupramolecular complexes, we performed preliminary GQ binding (Fig. S10 ‡) and induction (induced circular dichroism, ICD) experiments (Fig.…”

CD, UV, and In Silico Insights on the Effect of 1,3-Bis(1′-uracilyl)-2-propanone on Serum Albumin Structure

“…Circular dichroism (CD) spectra were recorded on a Jasco J-715 spectropolarimeter equipped with a Jasco Peltier PTC-423S/15 temperature controller (Jasco Europe S.r.l, Cremella, Italy) using a Hellma-238-QS tandem quartz cell (2 × 0.4375 cm from Hellma Italia S.r.l., Milano, Italy) according to the previous literature experiments [ 50 , 51 , 52 , 53 , 54 , 55 , 56 , 57 , 58 , 59 ] with a response time of 1 s, a scanning speed of 100 nm min −1 , and a bandwidth of 2.0 nm in the 205–260 nm wavelength range. All the spectra were averaged over three scans.…”

Structural insights and shedding light on preferential interactions of dietary flavonoids with G-quadruplex DNA structures: A new horizon

“…In most of these circumstances, the G-quadruplex forming sequences works as a transcriptional repressor, retaining a threshold amount of gene transcript. According to research, stability of the G-quadruplex architecture in NHEIII1 leads to a reduction in c-MYC transcription [ 25 ]. Likewise, the guanine rich strands on the VEGF gene's proximal promoter region governs its production.…”