Primary Citation PubMed: 8251479
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Thermodynamic characterization of tandem mismatches found in naturally occurring RNA.
(2009) Nucleic Acids Res 37
PubMed: 19509311 | PubMedCentral: PMC2724281 | DOI: 10.1093/nar/gkp465
In both PDB ID 1S72 and 1YFV, the GA pairs are also in a sugar-edge/Hoogsteen conformation; however, both pairs in both structures have two base–base hydrogen bonds, a G amino proton to A N7 a... d an A amino proton to G N3 (see Supplementary Figure S3 ).
Hydrogen bonding of this tandem mismatch was investigated in three different PDB structures, the PDB structure (1NKW) of the Deinococcus radiodurans large ribosomal subunit from the Yonath laboratory ( 47 ), the PDB structure (1S72) of the H. marismortui large ribosomal subunit from the Moore and Steitz laboratories ( 48 ) and the PDB structure (1YFV) of a synthetic RNA from the Turner laboratory ( 49 ).
Publication Year: 2009
Effects of Restrained Sampling Space and Nonplanar Amino Groups on Free-Energy Predictions for RNA with Imino and Sheared Tandem GA Base Pairs Flanked by GC, CG, iGiC or iCiG Base Pairs.
(2009) J Chem Theory Comput 5
PubMed: 20090924 | PubMedCentral: PMC2807739 | DOI: 10.1021/ct800540c
Colored nucleotides in a−d are the loop regions of NMR structures of 2O81 , 1MIS , 2O83 , and 1YFV , respectively, from the PDB.
PDB IDs of (5′GGC GA GCC3′) 2 and (5′GGiC GA iGCC3′) 2 are 1YFV and 2O83 , respectively.
Modified Amber Force Field Correctly Models the Conformational Preference for Tandem GA pairs in RNA.
(2014) J Chem Theory Comput 10
PubMed: 24803859 | PubMedCentral: PMC3985902 | DOI: 10.1021/ct400861g
38 They used four solution structures (PDB numbers 1MIS, 2O83, 2O81, and 1YFV), 22 , 44 , 45 and they used thermodynamic integration to calculate free energy differences.
Publication Year: 2014
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