Ionic Effects on VEGF G-Quadruplex Stability

Abstract

In a potassium solution, a modified 22-meric DNA sequence Pu22-T12T13 from a region proximal to the transcription initiation site of the human VEGF gene adopts a single parallel-stranded G-quadruplex conformation with a 1:4:1 loop-size arrangement. We measured the thermal stability, TM, of the K(+)-stabilized Pu22-T12T13 G-quadruplex as a function of stabilizing K(+) ions and nonstabilizing Cs(+) and TMA(+) ions. The thermal stability, TM, of the Pu22-T12T13 G-quadruplex increases with the concentration of the stabilizing potassium ions, while it sharply decreases upon the addition of the nonstabilizing cations. We interpret these results as underscoring the opposing effects of internal binding and counterion condensation on the stability of the Pu22-T12T13 G-quadruplex. While centrally bound ions stabilize the G-quadruplex conformation, counterion condensation destabilizes it, favoring the coil conformation. From the initial slopes of the dependences of TM on the concentration of Cs(+) and TMA(+) cations, we estimate that the deleterious effect of counterion condensation stems from roughly one extra counterion associated with the coil relative to the G-quadruplex state of Pu22-T12T13. The reduced accumulation of counterions around the G-quadruplex state of Pu22-T12T13 relative to its coil state is due to the low surface charge density of the G-quadruplex reflecting its structural characteristics. On the basis of the analysis of our data along with the results of a previous study, we propose that the differential effect of internally (stabilizing) and externally (destabilizing) bound cations may be a general feature of parallel intramolecular G-quadruplexes.

G-quadruplex prediction in E.coli genome reveals a conserved putative G-quadruplex-Hairpin-Duplex switch

“…It is well-established that K + has a strong stabilizing effect on G-quadruplexes (53)(54)(55). Considering the high K + content in the E.coli cytosol, up to 200 mM (56), together with previous studies indicating a role of G-quadruplexes with Table 2 in the presence of K + and Li + according to the change at 260 nm using CD spectrophotometer indicates similar melting temperatures for both structures (73 • C and 71 • C, respectively).…”

The Design and Characterization of Multifunctional Aptamer Nanopore Sensors

“…Our measurements and modelling show that the charge density of G-quadruplex is lower compared to the charge of unfolded DNA; the lowering of the charge density is attributed to the specific binding of stabilizing cations, including K + and divalent ions. 40,41 We also present simulations for signal strength when the aptamer length and relative location of the tertiary structure and flanking nonbinding ssDNA to the surface of the SPB are changed. This insight gives a basis to understand how to design and predict the behaviour of future RPS aptamer assays.…”

Electronic structure and optical properties of isolated and TiO2‐grafted free base porphyrins for water oxidation: A challenging test case for DFT and TD‐DFT

“…The design of efficient metal-free organic dyes is, thus, of primary interest, in virtue of raw materials abundance, generally high synthetic yields and easy tunabilty of their optical and redox properties. While the utilization of full organic sensitizers has been extensively studied and optimized in conventional DSSCs, [34][35][36][37][38][39][40] only limited interesting applications have been reported in water oxidation devices. [26,41] In this context, promising porphyrin and phthalocyanine derivatives have been reported in combination with different WOCs.…”