The recent report of a hydrophobic unnatural base pair (UBP), d5SICS-dNaM, which replicated in DNA PCR and also sustained and synthesized a plasmid inside E. coli genome by Romesberg and coworkers, is intriguing. Quantum chemical calculations show that the UBPs prefer a slipped parallel configuration to facilitate weak dispersion interactions somewhat similar to the so-called π-stacking interaction. Nevertheless, within a natural DNA tract, classical molecular dynamics simulations show that the backbone and neighboring stacked bases together reorient the UBPs in natural base pair like planar environment. Our computed structure with an average end-end distance, dC1'-C1' = 10.7 Å for d5SICS-dNaM is in excellent agreement with available crystal structure (PDB ID: 3SV3 , planar UBP with dC1'-C1'(crystal) = 11.0 Å). Quantum mechanical calculations for the UBP flanked by two natural base-pairs (A-T) on top and on bottom on equilibrated MD structure found large binding energy (ΔE = -74.0 kcal/mol). The present calculations therefore establish the fact that the hydrophobic UBPs can be stabilized by dispersion interactions with other base pairs in the DNA tract even in the absence of any hydrogen bonding between the UBPs themselves.
Recent reports of the successful incorporation of unnatural base pairs (UBPs), such as d5SICS–dNaM, in the gene sequence and replication with DNA is an important milestone in synthetic biology. Followed by this, several other UBPs, such as dTPT3–dNaM, dTPT3–dFIMO, dTPT3–IMO, dTPT3–FEMO, FTPT3–NaM, FTPT3–FIMO, FTPT3–IMO, and FTPT3–FEMO, have demonstrated similar or better retention and fidelity inside cells. Of these base pairs, dNaM–dTPT3 has been optimized to be a better fit inside a pAIO plasmid. Based on both implicit and explicit dispersion‐corrected density functional theory (DFT) calculations, we show that although this set of UBPs is significantly diverse in elemental and structural configuration, the members do share a common trait of favoring a slipped parallel stacked dimer arrangement. Unlike the natural bases (A, T, G, C, and U), this set of UBPs has a negligible affinity for a Watson–Crick (WC)‐type planar structure because they are invariably more stable within slipped parallel stacked orientations. We also observed that all the UBPs have either similar or higher binding energies with the natural bases in similar stacked orientations. When arranged between two natural base pairs, the UBPs exhibited a binding energy similar to that of three‐base sequences of natural bases. Our computational data show that the most promising base pairs are 5SICS–NaM, TPT3–NaM, and TPT3–FEMO. These results are consistent with recent progress on experimental research into UBPs along with our previous calculations on the d5SICS–dNaM pair and, therefore, strengthen the hypothesis that hydrogen bonding might not be absolutely essential and that interbase stacking dispersion interactions play a key role in the stabilization of genetic materials.
Two new mixed ligand metal-organic frameworks of Zn(II) with disodium 5hydroxyisophthalate and 4,4′-azobispyridine (azbpy) ligands, {[Zn(azbpy)(HO-1,3bdc)(H 2 O)].(azbpy)} n (1) and {[Zn(azbpy) 0.5 (HO-1,3-bdc)(C 2 H 5 OH)].(H 2 O)} n (2) have been synthesized by changing the reaction medium (methanol to ethanol) and structurally characterized by elemental analyses, IR, PXRD, TG and single crystal X-ray diffraction.Compound 1 exhibits 2D sheet network structure with free azbpy ligands in their void space; which has been stabilized by π-π and C-H···π interactions whereas 2 has a 2D layered architecture with lattice water molecules in their void space. Compound 2 has a flexible structure and shows gated adsorption (gas and solvent) behavior, while framework 1 is nonporous. These two MOFs exhibit remarkable electrical conductivity values at room temperature and their comparison has been discussed carefully. Theoretical calculations suggest that both the compounds are p-type semiconductor and correlate the structure property relationship. Schottky barrier diode electronic devices have been fabricated by using these two semiconductor materials with aluminium (Al) and indium tin oxide (ITO) in sandwich configuration as, ITO/MOF-1 or Fig. 6 Electronic band structure of 1 and 2 keeping the Fermi energy at 0 eV.Fig. 7 Current -Voltage characteristics of the devices.Fig. 8 log (I) vs log (V) plot.Fig. 9Solid-state emission spectra for free azbpy ligand and complexes 1-2 at room temperature.
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