Gj. Narlikar et D. Herschlag, ISOLATION OF A LOCAL TERTIARY FOLDING TRANSITION IN THE CONTEXT OF A GLOBALLY FOLDED RNA, Nature structural biology, 3(8), 1996, pp. 701-710
Binding of the Tetrahymena ribozyme's oligonucleotide substrate repres
ents a local folding event in the context of a globally folded RNA. Su
bstrate binding involves P1 duplex formation with the ribozyme's inter
nal guide sequence to give an 'open complex', followed by docking of t
he P1 duplex into tertiary interactions to give a 'closed complex'. We
have isolated the open complex as a thermodynamically stable species
using a site-specific modification and high Na+ concentrations. This h
as allowed characterization of P1 docking, which represents a folding
transition between local secondary and local tertiary structure. P1 do
cking is entropically driven, possibly accompanied by a release of bou
nd water molecules. Strategies analogous to those described here can b
e used more generally to study local folding events in large structure
d RNAs and to explore the structural and energetic landscape for RNA f
olding.