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Structure of an RNA hairpin loop with a 5'-CGUUUCG-3' loop motif by heteronuclear NMR spectroscopy and distance geometry.

Abstract：

:Structural features of a 19-nucleotide RNA hairpin loop (5'-GGCGUACGUUUCGUACGCC-3'), a loop motif which occurs in eukaryotic 18S rRNA, have been derived using multidimensional heteronuclear NMR spectroscopy in combination with local conformational analysis and torsion angle distance geometry followed by restrained energy minimization. A method to obtain both the 3JC4'P3' and 3JC4'P5' coupling constants from a set of spin-echo difference constant time HSQC spectra is introduced, and it is shown how these couplings can be assigned to the backbone angles beta and epsilon. A total of 280 distance constraints as well as 132 homo- and heteronuclear three-bond scalar coupling constants were derived from the NMR data. The structure which has been determined is a pentaloop rather than a triloop with no base pairing between G8 and C12. G8 is pointed to the minor groove where it forms a base triplet with C7-G13 that is further stabilized by hydrogen bonding to the 2'-hydroxyl group of C7. C12 is directed to the major groove where its conformation is stabilized by hydrogen bonding between O2 and HO2'. The NMR data suggest two possible, interconverting conformations with stacking of bases U10-G8 or U11-C7. Overall, the loop provides a variety of interaction sites for RNA or protein interactions.

journal_name

Biochemistry

journal_title

Biochemistry

authors

Sich C,Ohlenschläger O,Ramachandran R,Görlach M,Brown LR

doi

10.1021/bi971207g

subject

Has Abstract

pub_date

1997-11-18 00:00:00

pages

13989-4002

issue

46

eissn

0006-2960

issn

1520-4995

pii

bi971207g

journal_volume

36

pub_type

杂志文章

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