Persistence Length Changes Dramatically as RNA Folds

Abstract

We determine the persistence length, lp, for a bacterial group I ribozyme as a function of concentration of monovalent and divalent cations by fitting the distance distribution functions P (r) obtained from small angle X-ray scattering intensity data to the asymptotic form of the calculated PW LC (r) for a worm-like chain (WLC). The lp values change dramatically over a narrow range of Mg 2+ concentration from ∼21Å in the unfolded state (U) to ∼10Å in the compact (IC) and native states. Variations in lp with increasing Na + concentration are more gradual. In accord with the predictions of polyelectrolyte theory we find lp ∝ 1/κ 2 where κ is the inverse Debye-screening length.Elucidating the mechanisms by which RNA molecules self-assemble to form three dimensional structures is a challenging problem [1,2,3,4]. Because the native state (N) cannot form without significantly neutralizing the negative charge on [5,6] the phosphate group, RNA folding is sensitive to the valence, size, and shape of the counterions. At low counterion concentrations (C) RNA is unfolded (U) in the sense that it contains isolated stretches of base-paired stem loops that have large dynamical fluctuations. When C > C m , the midpoint of the transition from U to the N, RNA becomes compact as a result of formation of tertiary contacts. For many RNA molecules, such as the Tetrahymena ribozyme and RNase P, folding to the native state is preceded by the formation of multiple metastable kinetic intermediates (I) [1,2,7].The large dynamic conformational fluctuations in the U and I states make it difficult to characterize their structures. However, small angle scattering experiments can be used to determine the shape of RNA as it folds. The conformation of RNA in the U, N, and the I states is characterized by R g , the radius of gyration, and l p , the persistence length. Small Angle X-ray Scattering (SAXS) [2,8,9,10,11] and Small Angle Neutron Scattering (SANS) [12] experiments have been used to obtain R g as a function of counterions for a number of RNA molecules. In contrast, l p , which is a function of C and valence and shape of counterions, is more difficult to obtain.In this letter, we use SAXS data and theoretical results for the worm-like chain (WLC) to obtain l p for a 195 nucleotide group I ribozyme from pre-tRNA(Ile) of the Azoarcus bacterium as a function of C for monovalent and divalent counterions. The major conclusions of the present study are: (i) The experimentally determined distance distribution functions P (r) can be accurately fit using the theoretical results for wormlike chains for r/R g > 1 where R g is the radius of gyration of RNA. The l p values, which were calculated by fitting P (r) to P W LC (r) for r > R g , change dramatically from l p ≃ 21Å in the U state to l p ≃ 10 A in the compact conformation. (ii) The large reduction in l p occurs abruptly over a narrow concentration range in Mg 2+ whereas the decrease of l p in Na + is gradual. This result suggests that the compaction of RNA resembles a first order transition i...

Coil–globule transition in the denatured state of a small protein

“…Because the persistence length is a measure of local chain rigidity, this finding is another indication for the role of denaturant-protein backbone interaction. Changes in persistence length could perhaps be directly measured by force spectroscopy of denatured proteins or by fitting distancedistribution functions obtained from SAXS experiments (43).…”

π-conjugation and conformation in a semiconducting polymer: small angle x-ray scattering study

“…For example, the absorption peak shows a red-shift as the conjugation length increases; also the PL drifts to longer conjugation lengths before the radiative relaxation decay [23,24]. Interestingly, a similar decrease in l p has been reported in a biopolymer due to the compact conformation [25]. These results are quite relevant and should be taken into account in device fabrication, since the interchain interactions and aggregation depends on the choice of solvent, and the chain conformation in the solution phase tunes the charge-transfer process in the solid films [26].…”

3 Importance of Diffuse Metal Ion Binding to RNA

“…In the past decades, extensive experiments have been performed to investigate how metal ions promote RNA tertiary structural folding and stabilize tertiary structures; see Table 3 [16,19,32,[46][47][48][49][50][51][52][53][54][55][56][57][58][59][60]. These experiments have revealed several important roles of metal ions, especially Mg 2+ , in tertiary structural folding as shown below:…”