Nucleic Acids Research, Vol 26, Issue 4 980-987, Copyright © 1998 by Oxford University Press
SR Lynch and I Tinoco Jr
The structure of the L3 central hairpin loop isolated from the antigenomic
sequence of the hepatitis delta virus ribozyme with the P2 and P3 stems
from the ribozyme stacked on top of the loop has been determined by NMR
spectroscopy. The 26 nt stem-loop structure contains nine base pairs and a
7 nt loop (5'-UCCUCGC-3'). This hairpin loop is critical for efficient
catalysis in the intact ribozyme. The structure was determined using
homonuclear and heteronuclear NMR techniques on non-labeled and15N-labeled
RNA oligonucleotides. The overall root mean square deviation for the
structure was 1.15 A (+/- 0.28 A) for the loop and the closing C.G base
pair and 0.90 A (+/- 0.18 A) for the loop and the closing C.G base pair but
without the lone purine in the loop, which is not well defined in the
structure. The structure indicates a U.C base pair between the nucleotides
on the 5'- and 3'-ends of the loop. This base pair is formed with a single
hydrogen bond involving the cytosine exocyclic amino proton and the
carbonyl O4 of the uracil. The most unexpected finding in the loop is a syn
cytidine. While not unprecedented, syn pyrimidines are highly unusual. This
one can be confidently established by intranucleotide distances between the
ribose and the base determined by NMR spectroscopy. A similar study of the
structure of this loop showed a somewhat different three-dimensional
structure. A discussion of differences in the two structures, as well as
possible sites of interaction with the cleavage site, will be presented.
ARTICLES
The structure of the L3 loop from the hepatitis delta virus ribozyme: a syn cytidine
Department of Chemistry, University of California and Structural Biology Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720-1460, USA.
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