RNA Tertiary Interactions Mediate Native Collapse of a Bacterial Group I Ribozyme

Journal Article · Tue Jul 13 04:00:00 EDT 2010 · J. Mol. Biol.

OSTI ID:1008593

Chauhan, Seema; Caliskan, Gokhan; Briber, Robert M; Perez-Salas, Ursula; Rangan, Prashanth; Thirumalai, D; Woodson, Sarah A ^[1]

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1. NIST

Large RNAs collapse into compact intermediates in the presence of counterions before folding to the native state. We previously found that collapse of a bacterial group I ribozyme correlates with the formation of helices within the ribozyme core, but occurs at Mg{sup 2+} concentrations too low to support stable tertiary structure and catalytic activity. Here, using small-angle X-ray scattering, we show that Mg{sup 2+}-induced collapse is a cooperative folding transition that can be fit by a two-state model. The Mg{sup 2+} dependence of collapse is similar to the Mg{sup 2+} dependence of helix assembly measured by partial ribonuclease T{sub 1} digestion and of an unfolding transition measured by UV hypochromicity. The correspondence between multiple probes of RNA structure further supports a two-state model. A mutation that disrupts tertiary contacts between the L9 tetraloop and its helical receptor destabilized the compact state by 0.8 kcal/mol, while mutations in the central triplex were less destabilizing. These results show that native tertiary interactions stabilize the compact folding intermediates under conditions in which the RNA backbone remains accessible to solvent.

• Research Organization: Advanced Photon Source (APS), Argonne National Laboratory (ANL), Argonne, IL (US)
• Sponsoring Organization: USDOE
• OSTI ID: 1008593
• Journal Information: J. Mol. Biol., Journal Name: J. Mol. Biol. Journal Issue: (5) ; 2005 Vol. 353; ISSN JMOBAK; ISSN 0022-2836
• Country of Publication: United States
• Language: ENGLISH

Related Subjects

59 BASIC BIOLOGICAL SCIENCES
60 APPLIED LIFE SCIENCES
DIGESTION
MUTATIONS
PROBES
RNA
RNA-ASE
SCATTERING