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Solution Structure of a RNA Decamer Duplex, Containing 9‐[2‐ O ‐( β ‐ D ‐ribofuranosyl)‐ β ‐ D ‐ribofuranosyl]adenine, a Special Residue in Lower Eukaryotic Initiator tRNAs
Author(s) -
Luyten Ingrid,
Esnouf Robert M.,
Mikhailov Sergey N.,
Efimtseva Ekaterina V.,
Michiels Paul,
Heus Hans A.,
Hilbers Cees W.,
Herdewijn Piet
Publication year - 2000
Publication title -
helvetica chimica acta
Language(s) - English
Resource type - Journals
SCImago Journal Rank - 0.74
H-Index - 82
eISSN - 1522-2675
pISSN - 0018-019X
DOI - 10.1002/1522-2675(20000607)83:6<1278::aid-hlca1278>3.0.co;2-q
Subject(s) - chemistry , moiety , ribonucleotide , stereochemistry , ribose , duplex (building) , nucleotide , molecule , nuclear magnetic resonance spectroscopy , rna , crystallography , dna , biochemistry , organic chemistry , gene , enzyme
The solution structure of the self‐complementary deca‐ribonucleotide 5′‐r(GCGA*AUUCGC)‐3′ containing 9‐[2‐ O ‐( β ‐ D ‐ribofuranosyl)‐ β ‐ D ‐ribofuranosyl]adenine (A*), a modified nucleotide that occurs in lower eukaryotic methionine initiator tRNAs (tRNAs i Met ), was determined by NMR spectroscopy. Unexpectedly, the modification has no effect on the thermal stability of the duplex. However, the extra ribose moiety is in the C(3′)‐ endo conformation and takes up a well‐defined position in the minor groove, which is in agreement with its position in tRNAs i Met as determined by X‐ray crystallography. Molecular‐dynamics simulations on the RNA duplex in H 2 O show that the position of the extra ribofuranose moiety seems to be stabilized by bridged H‐bonds (mediated by two H 2 O molecules) to the backbone of the complementary chain.