Explicit solvent and counterion molecular dynamics simulations have been carried out for a total of >80 ns on the bacterial and spinach chloroplast 5S rRNA Loop E motifs. The Loop E sequences form unique duplex architectures composed of seven consecutive non-Watson-Crick basepairs. The starting structure of spinach chloroplast Loop E was modeled using isostericity principles, and the simulations refined the geometries of the three non-Watson-Crick basepairs that differ from the consensus bacterial sequence. The deep groove of Loop E motifs provides unique sites for cation binding. Binding of Mg(2+) rigidifies Loop E and stabilizes its major groove at an intermediate width. In the absence of Mg(2+), the Loop E motifs show an unprecedented degree of inner-shell binding of monovalent cations that, in contrast to Mg(2+), penetrate into the most negative regions inside the deep groove. The spinach chloroplast Loop E shows a marked tendency to compress its deep groove compared with the bacterial consensus. Structures with a narrow deep groove essentially collapse around a string of Na(+) cations with long coordination times. The Loop E non-Watson-Crick basepairing is complemented by highly specific hydration sites ranging from water bridges to hydration pockets hosting 2 to 3 long-residing waters. The ordered hydration is intimately connected with RNA local conformational variations.

• MeSH
• RNA, Bacterial chemistry   MeSH
• Base Pair Mismatch MeSH
• Nucleic Acid Denaturation MeSH
• Species Specificity MeSH
• Escherichia coli chemistry   MeSH
• Magnesium chemistry   MeSH
• Nucleic Acid Conformation MeSH
• Macromolecular Substances MeSH
• Models, Molecular * MeSH
• Base Pairing * MeSH
• Computer Simulation MeSH
• Motion MeSH
• RNA, Ribosomal, 5S chemistry   MeSH
• RNA, Plant chemistry   MeSH
• Solvents chemistry   MeSH
• Sodium chemistry   MeSH
• Spinacia oleracea chemistry   MeSH
• Binding Sites MeSH
• Water chemistry   MeSH
• Publication type
• Journal Article MeSH
• Evaluation Study MeSH
• Research Support, Non-U.S. Gov't MeSH
• Research Support, U.S. Gov't, Non-P.H.S. MeSH
• Research Support, U.S. Gov't, P.H.S. MeSH
• Comparative Study MeSH
• Validation Study MeSH
• Names of Substances
• RNA, Bacterial MeSH
• Magnesium MeSH
• Macromolecular Substances MeSH
• RNA, Ribosomal, 5S MeSH
• RNA, Plant MeSH
• Solvents MeSH
• Sodium MeSH
• Water MeSH