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Halogen bonds in biological molecules.
The present survey of protein and nucleic acid structures reveals similar halogen bonds as potentially stabilizing inter- and intramolecular interactions that can affect ligand binding and molecular folding that offer new and versatile tools for the design of ligands as drugs and materials in nanotechnology. Expand
Anion binding to nucleic acids.
It is shown that the nucleotide electropositive edges involving mainly amino, imino, and hydroxyl groups can cast specific anion binding sites that constitute also good locations for the binding of the negatively charged groups of the Asp and Glu residues or the nucleic acid phosphate groups. Expand
Rules governing the orientation of the 2'-hydroxyl group in RNA.
The fact that the 2'-hydroxyl group is not monopolised by axial stabilization, together with its water-like behaviour, facilitates complex formation involving RNA helical regions. Expand
RNA hydration: three nanoseconds of multiple molecular dynamics simulations of the solvated tRNA(Asp) anticodon hairpin.
Simulation results confirm the conclusion reached from an analysis of X-ray crystal structures according to which water molecules form an integral part of nucleic acid structure and suggest that RNA and water together constitute the biologically relevant functional entity. Expand
Molecular dynamics simulations of solvated yeast tRNA(Asp).
The present molecular dynamics simulation of a complex and highly charged nucleic acid molecule attests to the fact that simulation methods are now able to investigate not only the dynamics of proteins, but also that of large RNA molecules. Expand
SwS: a solvation web service for nucleic acids
UNLABELLED SwS, based on a statistical analysis of crystallographic structures deposited in the NDB, is designed to provide an exhaustive overview of the solvation of nucleic acid structural elementsExpand
Water and ion binding around RNA and DNA (C,G) oligomers.
The dynamics, hydration, and ion-binding features of two duplexes, the A(r(CG)(12)) and the B(d( CG)(12)), in a neutralizing aqueous environment with 0.25 M added KCl have been investigated by molecular dynamics simulations and may be of importance for understanding various sequence-dependent binding affinities. Expand
Singly and bifurcated hydrogen-bonded base-pairs in tRNA anticodon hairpins and ribozymes.
The data demonstrate the conservation of a bifurcated hydrogen bond interaction between residues 32 and 38, located at the stem/loop junction, which leads to the formation of a non-canonical base-pair which is preserved in the known crystal structures of tRNA/synthetase complexes. Expand
Nucleic acid solvation: from outside to insight.
Recent experimental and theoretical reports demonstrate that water molecules within complex nucleic acid structures can display very long residency times, and assist drug binding and catalytic reactions, and anions can also bind to these polyanionic systems. Expand
Metal ion binding to RNA.
The ions that are observed bound to RNA, their coordination properties, and the roles they play in RNA structural studies are discussed. Expand