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• W2023123780 endingPage "11292" @default.
• W2023123780 startingPage "11277" @default.
• W2023123780 abstract "RNA molecules are stabilized by a wide range of noncanonical interactions that are not present in DNA. Among them, the recently classified base–phosphate (BPh) interactions belong to the most important ones. Twelve percent of nucleotides in the ribosomal crystal structures are involved in BPh interactions. BPh interactions are highly conserved and provide major constraints on RNA sequence evolution. Here we provide assessment of the energetics of BPh interactions using MP2 computations extrapolated to the complete basis set of atomic orbitals and corrected for higher-order electron correlation effects. The reference computations are compared with DFT-D and DFT-D3 approaches, the SAPT method, and the molecular mechanics force field. The computations, besides providing the basic benchmark for the BPh interactions, allow some refinements of the original classification, including identification of some potential doubly bonded BPh patterns. The reference computations are followed by analysis of some larger RNA fragments that consider the context of the BPh interactions. The computations demonstrate the complexity of interaction patterns utilizing the BPh interactions in real RNA structures. The BPh interactions are often involved in intricate interaction networks. We studied BPh interactions of protonated adenine that can contribute to catalysis of hairpin ribozyme, the key BPh interaction in the S-turn motif of the sarcin–ricin loop, which may predetermine the S-turn topology and complex BPh patterns from the glmS riboswitch. Finally, the structural stability of BPh interactions in explicit solvent molecular dynamics simulations is assessed. The simulations well preserve key BPh interactions and allow dissection of structurally/functionally important water-meditated BPh bridges, which could not be considered in earlier bioinformatics classification of BPh interactions." @default.
• W2023123780 created "2016-06-24" @default.
• W2023123780 creator A5026399646 @default.
• W2023123780 creator A5041529029 @default.
• W2023123780 creator A5044759740 @default.
• W2023123780 creator A5046741316 @default.
• W2023123780 creator A5069434073 @default.
• W2023123780 creator A5079806827 @default.
• W2023123780 creator A5083895400 @default.
• W2023123780 creator A5085363071 @default.
• W2023123780 date "2011-09-12" @default.
• W2023123780 modified "2023-10-16" @default.
• W2023123780 title "Noncanonical Hydrogen Bonding in Nucleic Acids. Benchmark Evaluation of Key Base–Phosphate Interactions in Folded RNA Molecules Using Quantum-Chemical Calculations and Molecular Dynamics Simulations" @default.
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