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Structure of the 3′‐hairpin of the TYMV pseudoknot: preformation in RNA folding
Author(s) -
Kolk Michaél H.,
van der Graaf Marinette,
Fransen Carel T.M.,
Wijmenga Sybren S.,
Pleij Cornelis W.A.,
Heus Hans A.,
Hilbers Cornelis W.
Publication year - 1998
Publication title -
the embo journal
Language(s) - English
Resource type - Journals
SCImago Journal Rank - 7.484
H-Index - 392
eISSN - 1460-2075
pISSN - 0261-4189
DOI - 10.1093/emboj/17.24.7498
Subject(s) - pseudoknot , biology , rna , folding (dsp implementation) , computational biology , nucleic acid structure , protein folding , genetics , microbiology and biotechnology , gene , electrical engineering , engineering
The solution structure of an RNA‐hairpin present in the pseudoknot, which is found at the 3′‐terminus of turnip yellow mosaic virus genomic RNA, has been solved by nuclear magnetic resonance spectroscopy. The loop, which contains the sequence 5′‐GGGUCA‐3′, was found to be highly structured and, contrary to expectations, does not attain its stability through GA or GC base pair formation but by triple interactions between the tilted adenosine and the minor groove sides of the first two guanosines. Interestingly, a very similar conformation was found for the cognate pseudoknot, implying that the 3′‐hairpin is preformed for folding into a pseudoknotted structure. These findings suggest a mechanism of ‘predetermined‐fit’ as a principle in RNA folding.