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Hydrophobic Groups Stabilize the Hydration Shell of 2′‐ O ‐Methylated RNA Duplexes
Author(s) -
Auffinger Pascal,
Westhof Eric
Publication year - 2001
Publication title -
angewandte chemie international edition
Language(s) - English
Resource type - Journals
SCImago Journal Rank - 5.831
H-Index - 550
eISSN - 1521-3773
pISSN - 1433-7851
DOI - 10.1002/1521-3773(20011217)40:24<4648::aid-anie4648>3.0.co;2-u
Subject(s) - hydrogen bond , chemistry , guanine , molecule , crystallography , cytosine , rna , base pair , molecular dynamics , stereochemistry , dna , computational chemistry , nucleotide , organic chemistry , biochemistry , gene
The simple replacement of 2′‐OH by 2′‐OMe groups leads, in certain RNA structures, to a significant strengthening of important solute–solvent interactions. Molecular dynamics simulations uncover the complexity of effects associated with the insertion of hydrophobic groups into hydrophilic systems (the arrow indicates a long‐lived bridging water molecule located in the shallow groove of a 2′‐OMe(GpC) base pair step). Green=skeleton of cytosine, black=skeleton of guanine, red=oxygen atoms of water and of shallow groove carbonyl groups, blue=shallow groove nitrogen atoms, cyan=hydrogen atoms of OMe groups.