Effect of Hydrated and Nonhydrated Choline Chloride–Urea Deep Eutectic Solvent (Reline) on Thrombin-Binding G-quadruplex Aptamer (TBA): A Classical Molecular Dynamics Simulation Study

Abstract

Guanine-rich quadruplex nucleic acid (G-DNA) sequence is highly polymorphic. The obtained structure of G-DNA is exquisitely impressible to its sequence and the chemical environment. Due to its controllable different structures, G-DNA has acquired much attention in various research areas such as nanotechnology, medicinal chemistry, and molecular biology. However, the applications of G-DNA are mainly restricted to the aqueous media, although a large number of important chemical reactions, nanodevices, etc. have also been carried out in purely water-free medium. Recently, deep eutectic solvents (DESs) such as choline−urea (1:2) eutectic mixture, namely, reline, has widely been used as a reaction medium and also water-free storage medium for biological systems like different types of nucleic acids. Hence, it is very important to figure out the effect of the deep eutectic solvent with DNA. In this research work, we have discussed the interaction between reline with guanine-rich quadruplex thrombin-binding aptamer (TBA) DNA at 300 K, for different reline concentrations. To understand the conformational behavior of quadruplex TBA in reline DES, we have performed 10 μs all-atom molecular dynamics simulations. Here, we note that the structure of TBA deviates much more from its NMR structure at low reline concentrations. In other way, at high reline concentrations, the quadruplex TBA is much more rigid or less flexible than comparatively lower reline concentrations. Moreover, from the spatial distribution function study, the density of reline is higher near sugar phosphate backbone region than the others. Furthermore, at lower reline concentrations, guanine-8 and thymine-9 of loop-2 stack to each other, which is not noted at higher reline concentrations.

2D‐MA3Sb2I9 Back Surface Field for Efficient and Stable Perovskite Solar Cells

“…The band offset at the interface of MAPbI 3 /MA 3 Sb 2 I 9 is estimated with aid of first‐principles calculation. The layer‐resolved density of states (DOSs) in Figure 3d demonstrate that 2D‐MA 3 Sb 2 I 9 exhibits p‐type conductivity, as its Fermi energy is closer to MA 3 Sb 2 I 9 VBM, which is consistent with the reported results [ 28,40 ] and the UPS measurements in Figure 3a. Hybridized I(5p) and Sb(5s) orbitals contribute MA 3 Sb 2 I 9 VBM, higher than the MAPbI 3 VBM; the calculated MA 3 Sb 2 I 9 CBM is much higher than the CBM of the MAPbI 3 layer.…”

“…2D antimony halide perovskites A 3 Sb 2 I 9 (A = Cs, MA) is reported to process more favorable optoelectronic property than 0D‐A 3 Sb 2 I 9 and bismuth‐based perovskite A 3 Bi 2 I 9 . [ 28–31 ] It is observed that MA 3 Sb 2 I 9 causes a downshift of Fermi energy level to the valence band maximum (VBM), thus changing the MAPbI 3 surface to be more p‐type. SnO 2 /MAPbI 3 /MA 3 Sb 2 I 9 /Spiro‐OMeTAD constructs an n–i–p–p + heterojunction ( Figure a), where MA 3 Sb 2 I 9 serves as BSF to effectively promote hole extraction.…”

“…In XRD plots (Figure 1b), a small diffraction peak at 9.3° emerges in the modified sample (indicated by a red star), which is assigned to (001) crystal plane as compared to the reported XRD of layered structure MA 3 Sb 2 I 9 . [ 28,32,33 ] To clarify that this simple coating method can successfully obtain 2D‐MA 3 Sb 2 I 9 , we also check the XRD of two‐step‐deposited MA 3 Sb 2 I 9 by spin‐coating SbI 3 on both thin and thick MAI films. As shown in Figure S1 (Supporting Information), the main peaks at ≈17°, 25.2°, and 29.5° are (002), (003), and (022) planes of 2D‐MA 3 Sb 2 I 9 , respectively.…”

Nanostructures from protected L/L and D/L amino acid containing dipeptides

“…[71,72] Moreover, the significance of inter-peptide hydrogen bonds is vital with regards to the aggregation of peptides, which leads to the formation of different shapes of the peptides. To find the role of hydrogen bond in these four peptides aggregation, we have calculated the average number of hydrogen bonds using the geometric criteria [73,74] : (a) the distance between donor and acceptor is less than or equal to 3.5 Å, and simultaneously, (b) donor-acceptor-hydrogen lowing previous studies, [75][76][77] although some lower probability has been observed in Q αR region for both isoleucine and valine residue. For peptide 2, the backbone φ/ψ angles have been noticed in mostly Q β quadrant region along with slightly higher probability has been noticed in Q αR region for both the residues that are comparably higher than the peptides, 1 and 3.…”

Deep Eutectic Solvents (DESs) and Their Application in Biosensor Development

“…Mamajanov et al demonstrated that at least four distinct nucleic acid secondary structures can exist in DESs; they also noted that the anhydrous character and capacity to support natively folded DNA and protein structures make DESs appealing for the synthesis of biopolymers [ 52 ]. Pal et al examined the interaction between reline and guanine-rich quadruplex thrombin-binding aptamer (TBA) at 300 K for different reline concentrations [ 53 ]. They studied the conformational behavior of the aptamer in reline using molecular dynamics simulations.…”