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Moreover, it is deduced from the simulations that the oligomers have three distinct backbone conformations for neighboring amides. In particular, two of the backbone conformations have a closed and compact structure, while in the third, the backbone is open and elongated. The bottom-up approach allowed us to infer that such backbone conformations exist in PNIPAM as well. Consequently, the two major amide I transitions of the polymer are also assigned to split amide I transitions resulting from the vibrationally coupled nearest-neighboring amides. In contrast, the additional minor transition observed in PNIPAM is assigned to unsolvated amide units of the polymer. The proposed molecular model successfully describes that PNIPAM amide I band changes with temperature in terms of its molecular structure. PLX4032 inhibitor This new model strongly suggests that PNIPAM does not have a completely random backbone structure, but has distinct backbone conformers between neighboring amides.Xenobiotic nucleic acids (XNAs) are chemically modified nucleic acid analogues with potential applications in nucleic acid-based therapeutics including nucleic acid aptamers, ribozymes, small interfering RNAs, and antisense oligonucleotides. We have developed a promising XNA for therapeutic uses, 2',4'-bridged nucleic acid (2',4'-BNA), also known as locked nucleic acid (LNA). Unlike the rational design of small interfering and antisense oligonucleotides, the development of LNA aptamers and catalysts requires genetically engineered polymerases that enable the synthesis of LNA from DNA and the converse reverse transcription. However, no LNA decoders or encoders with sufficient performance have been developed. In this study, we developed variants of KOD DNA polymerase, a family B DNA polymerase derived from Thermococcus kodakarensis KOD1, which are effective LNA decoders and encoders, via structural analyses. KOD DGLNK (KOD N210D/Y409G/A485L/D614N/E664K) enabled LNA synthesis from DNA (DNA → LNA), and KOD DLK (KOD N210D/A485L/E664K) enabled LNA reverse transcription to DNA (LNA → DNA). Both variants exhibited greatly improved efficiency and accuracy. Notably, we synthesized LNAs longer than one kilobase using KOD DGLNK. We also showed that these variants can accept 2'-O-methyl (2'-OMe), a common modification for therapeutic uses. Here, we also show that LNA and 2'-OMe mix aptamer can be practically obtained via SELEX. The variants can be used as powerful tools for creating XNA aptamers and catalysts to completely eliminate the natural species, DNA and RNA.The metalloenzymes from the alkaline phosphatase (AP) superfamily catalyze the hydrolysis and transphosphorylation of phosphate monoesters. The role of several amino acids highly conserved in the active site of this family of enzymes was examined, using human placental AP (PLAP) as a model protein. By employing an active-site model based on the X-ray crystal structure of PLAP, mutations of several key residues were modeled by quantum mechanical methods in order to determine their impact on the catalytic activity. Kinetic and thermodynamic estimations were achieved for each reaction step of the catalytic mechanism by characterization of the intermediates and transition states on the reaction pathway, and the effects of mutations on the activation barriers were analyzed. A good accordance was observed between the present computational results and experimental measurements reported in the literature.Insertion of a tricoordinate phosphorus ligand into late metal-carbon bonds is reported. Metalation of a P^P-chelating ligand (L1), composed of a nontrigonal phosphorous (i.e., P(III)) triamide moiety, P(N(o-N(Ar)C6H4)2, tethered by a phenylene linker to a -P i Pr2 anchor, with group 10 complexes L2M(Me)Cl (M = Ni, Pd) results in insertion of the nontrigonal phosphorus site into the metal-methyl bond. The stable methylmetallophosphorane compounds thus formed are characterized spectroscopically and crystallographically. Metalation of L1 with (cod)PtII(Me)(Cl) does not lead to a metallophosphorane but rather to the standard bisphosphine chelate (κ2-L1)Pt(Me)(Cl). These divergent reactivities within group 10 are rationalized by reference to periodic variation in M-C bond enthalpies.Interactions between metal-organic frameworks (MOFs) and nucleic acids are of great importance in molecular assembly. However, current MOF-nucleic acid interactions lack diversity and are normally realized in an uncontrollable manner. Herein, the interaction of zirconium-based MOFs (Zr-MOFs) with nucleic acids is enabled by the formation of Zr-O-P bonds and further manipulated by a phosphate-induced site-occupying effect. Covering Zr ions in clusters of MOFs with phosphates impedes the formation of Zr-O-P bonds with nucleic acids, rendering the MOF-nucleic acid interaction tunable and stimulus-responsive. Notably, the experimental results demonstrate that various phosphates, Zr-MOFs, and nucleic acids can all be adopted in the tunable interaction. On the basis of these findings, fluorescent DNA and typical Zr-MOFs are proposed as functional probe-quencher pairs to establish molecular sensing and logic systems. Accordingly, alkaline phosphatase and inorganic pyrophosphatase can be quantified simultaneously, and the overall relation of different phosphates and phosphatases is facilely displayed. The work provides a general strategy for modulating MOF-nucleic acid interactions, which is conducive to the development of molecular intelligent systems.We report the self-assembly of amphiphilic polystyrene-block-poly(ethylene oxide) (PS-b-PEO) brush block copolymers (BBCPs) into spherical micelles in an ethanol/water mixture as an efficient templating approach to fabricate mesoporous carbon spheres using polydopamine as a carbon source. Mesopore sizes of up to 25 nm are well controlled and are dependent on the molecular weight (Mw) of the BBCP. Such large pores are difficult to obtain using traditional linear block copolymers templates. Furthermore, bimodal mesoporous carbon spheres with two populations of pore sizes (24.5 and 6.5 nm) are obtained using a BBCP coassembled with a small molecule surfactant (Pluronic F127). An oxygen reduction reaction is used to demonstrate that electrocatalytic performance can be tuned by controlling the carbon sphere morphologies. This work provides a novel and versatile method to fabricate carbon spheres with broadly tunable bimodal pore sizes for potential applications in catalysis, separations, and energy storage.