Rapid compaction during RNA folding

doi:10.1073/pnas.072589599

Rapid compaction during RNA folding

Departments of ^*Biochemistry, ^†Chemistry, and ^**Physics and Applied Physics, Stanford University, Stanford, CA 94305; ^‡Physics Department, ^§School of Applied and Engineering Physics, and ^¶Cornell High Energy Synchrotron Source (CHESS), Cornell University, Ithaca, NY 14853; and ^‖Department of Physics, Yale University, New Haven, CT 06520

Edited by S. Walter Englander, University of Pennsylvania School of Medicine, Swarthmore, PA, and approved January 30, 2002 (received for review November 2, 2001)

Abstract

We have used small angle x-ray scattering and computer simulations with a coarse-grained model to provide a time-resolved picture of the global folding process of the Tetrahymena group I RNA over a time window of more than five orders of magnitude. A substantial phase of compaction is observed on the low millisecond timescale, and the overall compaction and global shape changes are largely complete within one second, earlier than any known tertiary contacts are formed. This finding indicates that the RNA forms a nonspecifically collapsed intermediate and then searches for its tertiary contacts within a highly restricted subset of conformational space. The collapsed intermediate early in folding of this RNA is grossly akin to molten globule intermediates in protein folding.

Footnotes

↵ ‡‡ To whom reprint requests should be addressed. E-mail: lp26{at}cornell.edu.
This paper was submitted directly (Track II) to the PNAS office.
↵ †† Ca²⁺ was used for calibration instead of Mg²⁺ because of the availability of well characterized calcium-sensitive dyes. As the hydrated radii of Ca²⁺ and Mg²⁺ are nearly equal (45), their diffusive mixing times are expected to be similar.
↵ §§ The PDMS layers contain channels that are directly above and below the side channels and the outlet channel of the silicon device, but not above or below the inlet channel. Buffer solutions that do not contain RNA flow through these channels against the top and bottom sealed surfaces of the chip. Thus, the RNA solution in the outlet channel is surrounded by buffer on all sides, minimizing surface effects on the flow profile of the RNA solution.
↵ ¶¶ Additional uncertainty, beyond the reported value obtained from the fit, exists in the time constant for this 140-ms phase. This additional uncertainty arises because of uncertainty in the amplitude of the fast phase under the experimental conditions used to measure the slow phase (25°C for the fast phase vs. 15°C and 37°C for the slower phase). Changes in the amplitude of the fast phase would give changes in the time constant of the slower phase by changing the “starting” point (the y axis value in Fig. 3 B) of the slower transition. This uncertainty does not affect the conclusion that both phases of compaction are completed more rapidly than stable tertiary structure has been shown to form.
Abbreviations:

SAXS,

small angle x-ray scattering;

SVD,

singular value decomposition