Facile preparation of near-monodisperse oligocellulose and its elastomeric derivatives with tunable mechanical properties

Oligocellulose (OC) with low polydispersity indices has been produced in large quantities using an improved method of acid-assisted hydrolysis, in which long cellulose chains disintegrate in concentrated phosphoric acid at moderately elevated temperatures. The hydrolysis time has been reduced by three orders of magnitude without compromising the overall yield of the process or the quality of OC products. The efficient production of high-quality OCs in large quantities allows for developing OC-derived elastomeric materials. A series of OC-graft-poly(isobornyl methacrylate-random-n-butyl acrylate) [OC-g-P(IBOMA-r-BA)] elastomers have been synthesized via activators regenerated by electron transfer for atom transfer radical polymerization (ARGET ATRP). OC-g-P(IBOMA-r-BA) elastomers have tunable molecular architectures and phase morphologies toward desirable mechanical properties and thermal stability suitable for various applications. The methodologies of the OC production and the graft-polymers synthesis in this study would help advance technologies for broader applications of bio-based elastomers.

Highly stable, antiviral, antibacterial cotton textiles via molecular engineering

Cotton textiles are ubiquitous in daily life and are also one of the primary mediums for transmitting viruses and bacteria. Conventional approaches to fabricating antiviral and antibacterial textiles generally load functional additives onto the surface of the fabric and/or their microfibres. However, such modifications are susceptible to deterioration after long-term use due to leaching of the additives. Here we show a different method to impregnate copper ions into the cellulose matrix to form a copper ion-textile (Cu-IT), in which the copper ions strongly coordinate with the oxygen-containing polar functional groups (for example, hydroxyl) of the cellulose chains. The Cu-IT displays high antiviral and antibacterial performance against tobacco mosaic virus and influenza A virus, and Escherichia coli, Salmonella typhimurium, Pseudomonas aeruginosa and Bacillus subtilis bacteria due to the antimicrobial properties of copper. Furthermore, the strong coordination bonding of copper ions with the hydroxyl functionalities endows the Cu-IT with excellent air/water retainability and superior mechanical stability, which can meet daily use and resist repeated washing. This method to fabricate Cu-IT is cost-effective, ecofriendly and highly scalable, and this textile appears very promising for use in household products, public facilities and medical settings.

A cellulose-derived supramolecule for fast ion transport

Supramolecular frameworks have been widely synthesized for ion transport applications. However, conventional approaches of constructing ion transport pathways in supramolecular frameworks typically require complex processes and display poor scalability, high cost, and limited sustainability. Here, we report the scalable and cost-effective synthesis of an ion-conducting (e.g., Na+) cellulose-derived supramolecule (Na-CS) that features a three-dimensional, hierarchical, and crystalline structure composed of massively aligned, one-dimensional, and ångström-scale open channels. Using wood-based Na-CS as a model material, we achieve high ionic conductivities (e.g., 0.23 S/cm in 20 wt% NaOH at 25 °C) even with a highly dense microstructure, in stark contrast to conventional membranes that typically rely on large pores (e.g., submicrometers to a few micrometers) to obtain comparable ionic conductivities. This synthesis approach can be universally applied to a variety of cellulose materials beyond wood, including cotton textiles, fibers, paper, and ink, which suggests excellent potential for a number of applications such as ion-conductive membranes, ionic cables, and ionotronic devices.

A high-performance hydroxide exchange membrane enabled by Cu2+-crosslinked chitosan

Ion exchange membranes are widely used to selectively transport ions in various electrochemical devices. Hydroxide exchange membranes (HEMs) are promising to couple with lower cost platinum-free electrocatalysts used in alkaline conditions, but are not stable enough in strong alkaline solutions. Herein, we present a Cu²⁺-crosslinked chitosan (chitosan-Cu) material as a stable and high-performance HEM. The Cu²⁺ ions are coordinated with the amino and hydroxyl groups of chitosan to crosslink the chitosan chains, forming hexagonal nanochannels (~1 nm in diameter) that can accommodate water diffusion and facilitate fast ion transport, with a high hydroxide conductivity of 67 mS cm^-1 at room temperature. The Cu²⁺ coordination also enhances the mechanical strength of the membrane, reduces its permeability and, most importantly, improves its stability in alkaline solution (only 5% conductivity loss at 80 °C after 1,000 h). These advantages make chitosan-Cu an outstanding HEM, which we demonstrate in a direct methanol fuel cell that exhibits a high power density of 305 mW cm^-2. The design principle of the chitosan-Cu HEM, in which ion transport channels are generated in the polymer through metal-crosslinking of polar functional groups, could inspire the synthesis of many ion exchange membranes for ion transport, ion sieving, ion filtration and more.

Efficient production of oligomeric chitin with narrow distributions of degree of polymerization using sonication-assisted phosphoric acid hydrolysis

A method of producing oligomeric chitin using sonication-assisted phosphoric acid hydrolysis was introduced. The processing was continuous and scalable. Oligomeric chitin fractions with narrow distributions of degree of polymerization were obtained by differential precipitation using ethanol as precipitating agent at different ethanol-to-phosphoric-acid-solution volume ratios. The yield of oligomeric chitin with degree of polymerization between 4 and 10 was ≈30% (mass fraction). The content of each fraction was characterized by matrix-assisted laser desorption/ionization time-of-flight mass spectroscopy (MALDI TOF MS). Changes in chemical composition of oligomeric chitin were negligible, as verified by MALDI TOF MS, Fourier-transform infrared, and nuclear magnetic resonance spectroscopy. This new method for producing oligomeric chitin molecules is rapid, cost-effective, and safe.

Solvent-Assisted Fractionation of Oligomeric Cellulose and Reversible Transformation of Cellulose II and IV

Oligomeric cellulose with an average degree of polymerization of 7.68 and a polydispersity of 1.04 has been fractionated using solution processes. Three fractions have been obtained through initial dissolution, subsequent crystallization, and solvent precipitation, respectively. The resulting oligocellulose fraction has an average degree of polymerization of 7.70 and a polydispersity of 1.01, respectively. Cellulose IV₂ crystals form in the oligocellulose fraction, and reversibly transform to II and back to IV using simple solvents.

Effect of Carbon Chain Length, Ionic Strength, and pH on the In Vitro Release Kinetics of Cationic Drugs from Fatty-Acid-Loaded Contact Lenses

This paper explores the use of fatty acids in silicone hydrogel contact lenses for extending the release duration of cationic drugs. Drug release kinetics was dependent on the carbon chain length of the fatty acid loaded in the lens, with 12-, 14- and 18-carbon chain length fatty acids increasing the uptake and the release duration of ketotifen fumarate (KTF) and tetracaine hydrochloride (THCL). Drug release kinetics from oleic acid-loaded lenses was evaluated in phosphate buffer saline (PBS) at different ionic strengths (I = 167, 500, 1665 mM); the release duration of KTF and THCL was decreased with increasing ionic strength of the release medium. Furthermore, the release of KTF and THCL in deionized water did not show a burst and was significantly slower compared to that in PBS. The release kinetics of KTF and THCL was significantly faster when the pH of the release medium was decreased from 7.4 towards 5.5 because of the decrease in the relative amounts of oleate anions in the lens mostly populated at the polymer–pore interfaces. The use of boundary charges at the polymer–pore interfaces of a contact lens to enhance drug partition and extend its release is further confirmed by loading cationic phytosphingosine in contact lenses to attract an anionic drug.

Molecular partitioning in ternary solutions of cellulose

Neutron scattering measurements on the structure and dynamics of ternary solutions of microcrystalline cellulose (MC) in mixtures of an ionic liquid (IL) 1-ethyl-3-methylimidazolium acetate and a polar organic solvent dimethylformamide (DMF) have shown that MC can be fully dissolved in solvent mixtures. Data also show the molecular partitioning of IL into coexisting states. The structure partitioning is manifested as IL adsorbed to cellulose molecules with additional IL self-assembled to form clusters in solution, while the dynamics partitioning shows dynamical heterogeneities of the IL with slow dynamics resembling neat IL and fast dynamics being coupled with the solvent. The composition dependence of the molecular partitioning results in a solubility gap in dilute cellulose solutions and a phase boundary criterion of the molar ratio of IL / MC ∼ 3 in more concentrated regimes. The two characteristics together define the main features of the dissolution phase diagram of ternary cellulose mixtures of MC / IL / DMF at the room temperature.

Cellulose ionic conductors with high differential thermal voltage for low-grade heat harvesting

Converting low-grade heat into useful electricity requires a technology that is efficient and cost effective. Here, we demonstrate a cellulosic membrane that relies on sub-nanoscale confinement of ions in oxidized and aligned cellulose molecular chains to enhance selective diffusion under a thermal gradient. After infiltrating electrolyte into the cellulosic membrane and applying an axial temperature gradient, the ionic conductor exhibits a thermal gradient ratio (analogous to the Seebeck coefficient in thermoelectrics) of 24 mV K^-1-more than twice the highest value reported until now. We attribute the enhanced thermally generated voltage to effective sodium ion insertion into the charged molecular chains of the cellulosic membrane, which consists of type II cellulose, while this process does not occur in natural wood or type I cellulose. With this material, we demonstrate a flexible and biocompatible heat-to-electricity conversion device via nanoscale engineering based on sustainable materials that can enable large-scale manufacture.

Effects of Preferential Counterion Interactions on the Specificity of RNA Folding

The real-time search for native RNA structure is essential for the operation of regulatory RNAs. We previously reported that a fraction of the Azoarcus ribozyme achieves a compact structure in less than a millisecond. To scrutinize the forces that drive initial folding steps, we used time-resolved SAXS to compare the folding dynamics of this ribozyme in thermodynamically isostable concentrations of different counterions. The results show that the size of the fast-folding population increases with the number of available counterions and correlates with the flexibility of initial RNA structures. Within 1 ms of folding, Mg²⁺ exhibits a smaller preferential interaction coefficient per charge, ΔΓ₊/ Z, than Na⁺ or [Co(NH₃)₆]³⁺. The lower ΔΓ₊/ Z corresponds to a smaller yield of folded RNA, although Mg²⁺ stabilizes native RNA more efficiently than other ions at equilibrium. These results suggest that strong Mg²⁺-RNA interactions impede the search for globally native structure during early folding stages.

Phase Separation and Stack Alignment in Aqueous Cellulose Nanocrystal Suspension under Weak Magnetic Field

Isotropic-nematic (I-N) transitions in cellulose nanocrystal (CNC) suspension and self-assembled structures in the isotropic and nematic phases were investigated using scattering and microscopy methods. A CNC suspension with a mass fraction of 7.4% spontaneously phase separated into an isotropic phase of 6.9% in the top layer and a nematic phase of 7.9% in the bottom layer. In both the phases, the CNC particles formed stacks with an interparticle distance being of ≈37 nm. One-dimensional small-angle neutron scattering (SANS) profiles due to both phases could be fitted using a stacking model considering finite particle sizes. SANS and atomic force microscopy studies indicate that the nematic phase in the bottom layer contains more populations of larger particles. A weak magnetic field of ≈0.5 T was able to induce a preferred orientation of CNC stacks in the nematic phase, with the stack normals being aligned with the field (perpendicular to the long axis of CNC particles). The Hermans orientation parameter, ⟨ P₂⟩, was ≈0.5 for the nematic phase; it remained unchanged during the relaxation process of ≈10 h. The fraction of oriented CNC populations decreased during the relaxation; dramatic decrease occurred in the first 3 h. The top layer remained isotropic in the weak field. Polarized microscopy studies revealed that the nematic phase was chiral. Adjacent particles in a stack form a twisting angle of ≈0.6 °, resulting in a helix pitch distance of ≈22 μm.

Spray-Processed Composites with High Conductivity and Elasticity

Highly conductive elastic composites were constructed using multistep solution-based fabrication methods that included the deposition of a nonwoven polymer fiber mat through solution blow spinning and nanoparticle nucleation. High nanoparticle loading was achieved by introducing silver nanoparticles into the fiber spinning solution. The presence of the silver nanoparticles facilitates improved uptake of silver nanoparticle precursor in subsequent processing steps. The precursor is used to generate a second nanoparticle population, leading to high loading and conductivity. Establishing high nanoparticle loading in a microfibrous block copolymer network generated deformable composites that can sustain electrical conductivities reaching 9000 S/cm under 100% tensile strain. These conductive elastic fabrics can retain at least 70% of their initial electrical conductivity after being stretched to 100% strain and released for 500 cycles. This composite material system has the potential to be implemented in wearable electronics and robotic systems.

Entropic stabilization of folded RNA in crowded solutions measured by SAXS

Non-coding RNAs must fold into specific structures that are stabilized by metal ions and other co-solutes in the cell's interior. Large crowder molecules such as PEG stabilize a bacterial group I ribozyme so that the RNA folds in low Mg²⁺ concentrations typical of the cell's interior. To understand the thermodynamic origins of stabilization by crowder molecules, small angle X-ray scattering was used to measure the folding and helix assembly of a bacterial group I ribozyme at different temperatures and in different MgCl₂ and polyethylene glycol (PEG) concentrations. The resulting phase diagrams show that perturbations to folding by each variable do not overlap. A favorable enthalpy change drives the formation of compact, native-like structures, but requires Mg²⁺ ions at all temperatures studied (5–55°C). PEG reduces the entropic cost of helix assembly and increases correlations between RNA segments at all temperatures. The phase diagrams also revealed a semi-compact intermediate between the unfolded and folded ensemble that is locally more flexible than the unfolded state, as judged by SHAPE modification. These results suggest that environmental variables such as temperature and solute density will favor different types of RNA structures.

Charge screening in RNA: an integral route for dynamical enhancements

Electrostatic interactions of RNA are at the center of determining the dynamical flexibility and structural stability. By analysing neutron scattering spectroscopy, we show that fast dynamics of hydrated tRNA on ps to ns timescales increases with stronger charge screening, while its structural stability either increases or remains largely unchanged. An unprecedented electrostatic threshold for the onset of additional flexibility is induced from the correlation between the charge-screening density of counterions and the promoted dynamical properties. The results demonstrate that the enhanced dynamical flexibility of tRNA originates from local conformational relaxation coupled with stabilized charge screening rather than governed by fluctuation of hydrated counterions. The present study casts light on the specificity of electrostatic interactions in the thermodynamic balance between the dynamical flexibility and structural stability of RNA.

Molecular crowding overcomes the destabilizing effects of mutations in a bacterial ribozyme

The native structure of the Azoarcus group I ribozyme is stabilized by the cooperative formation of tertiary interactions between double helical domains. Thus, even single mutations that break this network of tertiary interactions reduce ribozyme activity in physiological Mg(2+) concentrations. Here, we report that molecular crowding comparable to that in the cell compensates for destabilizing mutations in the Azoarcus ribozyme. Small angle X-ray scattering, native polyacrylamide gel electrophoresis and activity assays were used to compare folding free energies in dilute and crowded solutions containing 18% PEG1000. Crowder molecules allowed the wild-type and mutant ribozymes to fold at similarly low Mg(2+) concentrations and stabilized the active structure of the mutant ribozymes under physiological conditions. This compensation helps explains why ribozyme mutations are often less deleterious in the cell than in the test tube. Nevertheless, crowding did not rescue the high fraction of folded but less active structures formed by double and triple mutants. We conclude that crowding broadens the fitness landscape by stabilizing compact RNA structures without improving the specificity of self-assembly.

NMR Water Self-Diffusion and Relaxation Studies on Sodium Polyacrylate Solutions and Gels in Physiologic Ionic Solutions

Water self-diffusion coefficients and longitudinal relaxation rates in sodium polyacrylate solutions and gels were measured by NMR, as a function of polymer content and structure in a physiological concentration range of monovalent and divalent cations, Ca²⁺ and Na⁺. Several physical models describing the self-diffusion of the solvent were applied and compared. A free-volume model was found to be in good agreement with the experimental results over a wide range of polymer concentrations. The longitudinal relaxation rate exhibited linear dependence on polymer concentration below a critical concentration and showed non-linear behavior at higher concentrations. Both the water self-diffusion and relaxation were less influenced by the polymer in the gel state than in the uncrosslinked polymer solutions. The effect of Na⁺ on the mobility of water molecules was practically undetectable. By contrast, addition of Ca²⁺ strongly increased the longitudinal relaxation rate while its effect on the self-diffusion coefficient was much less pronounced.

Crowders perturb the entropy of RNA energy landscapes to favor folding

Biological macromolecules have evolved to fold and operate in the crowded environment of the cell. We have shown previously that molecular crowding stabilizes folded RNA structures. Here we report SAXS measurements on a 64 kDa bacterial group I ribozyme in the presence of mono- and divalent ions and PEG crowders of different molecular weight. These experiments show that crowders always stabilize the folded RNA, but this stabilization is weaker in NaCl solutions than MgCl2 solutions. Additionally, we find that RNAs with the same global structure, parametrized by Rg, have different scattering functions depending upon the ratio of electrostatic and entropic stabilization by ions and crowders, respectively. We quantify this difference using the scattering length per scattering volume and find that this ratio is larger for RNAs that fold in lower ionic strength solutions due to the higher crowder content. We conclude that lower RNA flexibility, or reduced configurational entropy, widens the free energy gap between the unfolded and folded RNA in crowded MgCl2 solutions.

Hexagonally ordered nanoparticles templated using a block copolymer film through Coulombic interactions

We present a novel and simple method for forming hexagonal gold nanoparticle arrays that uses Coulombic interactions between negatively charged gold nanoparticles on positively charged vertically oriented poly(4-vinylpyridine) cylinders formed in a spin cast polystyrene-b-poly(4-vinylpyridine) block copolymer film. Exposure of the block copolymer film to dibromobutane vapor quaternizes and crosslinks the poly(4-vinylpyridine) domains which allows for the templated deposition of gold nanoparticles into a self-assembled hexagonal array through electrostatic interactions. These systems can form the basis for sensors or next generation nanoparticle based electronics.

Cooperative tertiary interaction network guides RNA folding

Noncoding RNAs form unique 3D structures, which perform many regulatory functions. To understand how RNAs fold uniquely despite a small number of tertiary interaction motifs, we mutated the major tertiary interactions in a group I ribozyme by single-base substitutions. The resulting perturbations to the folding energy landscape were measured using SAXS, ribozyme activity, hydroxyl radical footprinting, and native PAGE. Double- and triple-mutant cycles show that most tertiary interactions have a small effect on the stability of the native state. Instead, the formation of core and peripheral structural motifs is cooperatively linked in near-native folding intermediates, and this cooperativity depends on the native helix orientation. The emergence of a cooperative interaction network at an early stage of folding suppresses nonnative structures and guides the search for the native state. We suggest that cooperativity in noncoding RNAs arose from natural selection of architectures conducive to forming a unique, stable fold.

Dynamics of biological macromolecules: not a simple slaving by hydration water

We studied the dynamics of hydrated tRNA using neutron and dielectric spectroscopy techniques. A comparison of our results with earlier data reveals that the dynamics of hydrated tRNA is slower and varies more strongly with temperature than the dynamics of hydrated proteins. At the same time, tRNA appears to have faster dynamics than DNA. We demonstrate that a similar difference appears in the dynamics of hydration water for these biomolecules. The results and analysis contradict the traditional view of slaved dynamics, which assumes that the dynamics of biological macromolecules just follows the dynamics of hydration water. Our results demonstrate that the dynamics of biological macromolecules and their hydration water depends strongly on the chemical and three-dimensional structures of the biomolecules. We conclude that the whole concept of slaving dynamics should be reconsidered, and that the mutual influence of biomolecules and their hydration water must be taken into account.

Molecular crowding stabilizes folded RNA structure by the excluded volume effect

Crowder molecules in solution alter the equilibrium between folded and unfolded states of biological macromolecules. It is therefore critical to account for the influence of these other molecules when describing the folding of RNA inside the cell. Small angle X-ray scattering experiments are reported on a 64 kDa bacterial group I ribozyme in the presence of polyethylene-glycol 1000 (PEG-1000), a molecular crowder with an average molecular weight of 1000 Da. In agreement with expected excluded volume effects, PEG favors more compact RNA structures. First, the transition from the unfolded to the folded (more compact) state occurs at lower MgCl(2) concentrations in PEG. Second, the radius of gyration of the unfolded RNA decreases from 76 to 64 A as the PEG concentration increases from 0 to 20% wt/vol. Changes to water and ion activities were measured experimentally, and theoretical models were used to evaluate the excluded volume. We conclude that the dominant influence of the PEG crowder on the folding process is the excluded volume effect.

Multistage collapse of a bacterial ribozyme observed by time-resolved small-angle X-ray scattering

Ribozymes must fold into compact, native structures to function properly in the cell. The first step in forming the RNA tertiary structure is the neutralization of the phosphate charge by cations, followed by collapse of the unfolded molecules into more compact structures. The specificity of the collapse transition determines the structures of the folding intermediates and the folding time to the native state. However, the forces that enable specific collapse in RNA are not understood. Using time-resolved SAXS, we report that upon addition of 5 mM Mg(2+) to the Azoarcus group I ribozyme up to 80% of chains form compact structures in less than 1 ms. In 1 mM Mg(2+), the collapse transition produces extended structures that slowly approach the folded state, while > or = 1.5 mM Mg(2+) leads to an ensemble of random coils that fold with multistage kinetics. Increased flexibility of molecules in the intermediate ensemble correlates with a Mg(2+)-dependent increase in the fast folding population and a previously unobserved crossover in the collapse kinetics. Partial denaturation of the unfolded RNA with urea also increases the fraction of chains following the fast-folding pathway. These results demonstrate that the preferred collapse mechanism depends on the extent of Mg(2+)-dependent charge neutralization and that non-native interactions within the unfolded ensemble contribute to the heterogeneity of the ribozyme folding pathways at the very earliest stages of tertiary structure formation.

Dynamics of tRNA at different levels of hydration

The influence of hydration on the nanosecond timescale dynamics of tRNA is investigated using neutron scattering spectroscopy. Unlike protein dynamics, the dynamics of tRNA is not affected by methyl group rotation. This allows for a simpler analysis of the influence of hydration on the conformational motions in RNA. We find that hydration affects the dynamics of tRNA significantly more than that of lysozyme. Both the characteristic length scale and the timescale of the conformational motions in tRNA depend strongly on hydration. Even the characteristic temperature of the so-called "dynamical transition" appears to be hydration-dependent in tRNA. The amplitude of the conformational motions in fully hydrated tRNA is almost twice as large as in hydrated lysozyme. We ascribe these differences to a more open and flexible structure of hydrated RNA, and to a larger fraction and different nature of hydrophilic sites. The latter leads to a higher density of water that makes the biomolecule more flexible. All-atom molecular-dynamics simulations are used to show that the extent of hydration is greater in tRNA than in lysozyme. We propose that water acts as a "lubricant" in facilitating enhanced motion in solvated RNA molecules.

Persistence length changes dramatically as RNA folds

We determine the persistence length l(p) 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 P(WLC)(r) for a wormlike chain. The l(p) values change dramatically over a narrow range of Mg(2+) concentration from approximately 21 Angstroms in the unfolded state (U) to approximately 10 Angstroms in the compact (I(C)) and native states. Variations in l(p) with increasing Na(+) concentration are more gradual. In accord with the predictions of polyelectrolyte theory we find l(p) alpha 1/kappa(2) where kappa is the inverse Debye-screening length.

Dynamic Transition in tRNA is Solvent Induced

Dynamics of tRNA was studied using neutron scattering spectroscopy. Despite vast differences in the architecture and backbone structure of proteins and RNA, hydrated tRNA undergoes the dynamic transition at the same temperature as hydrated lysozyme. The similarity of the dynamic transition in RNA and proteins supports the idea that it is solvent induced. Because tRNA essentially has no methyl groups, the results also suggest that methyl groups are not the main contributor of the dynamic transition in biological macromolecules. However, they may explain strong differences in the dynamics of tRNA and lysozyme observed at low temperatures.

RNA tertiary interactions mediate native collapse of a bacterial group I ribozyme

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 Mg2+ concentrations too low to support stable tertiary structure and catalytic activity. Here, using small-angle X-ray scattering, we show that Mg2+-induced collapse is a cooperative folding transition that can be fit by a two-state model. The Mg2+ dependence of collapse is similar to the Mg2+ dependence of helix assembly measured by partial ribonuclease T1 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.

Compaction of a bacterial group I ribozyme coincides with the assembly of core helices

Counterions are critical to the self-assembly of RNA tertiary structure because they neutralize the large electrostatic forces which oppose the folding process. Changes in the size and shape of the Azoarcus group I ribozyme as a function of Mg(2+) and Na(+) concentration were followed by small angle neutron scattering. In low salt buffer, the RNA was expanded, with an average radius of gyration (R(g)) of 53 +/- 1 A. A highly cooperative transition to a compact form (R(g) = 31.5 +/- 0.5 A) was observed between 1.6 and 1.7 mM MgCl(2). The collapse transition, which is unusually sharp in Mg(2+), has the characteristics of a first-order phase transition. Partial digestion with ribonuclease T1 under identical conditions showed that this transition correlated with the assembly of double helices in the ribozyme core. Fivefold higher Mg(2+) concentrations were required for self-splicing, indicating that compaction occurs before native tertiary interactions are fully stabilized. No further decrease in R(g) was observed between 1.7 and 20 mM MgCl(2), indicating that the intermediates have the same dimensions as the native ribozyme, within the uncertainty of the data (+/-1 A). A more gradual transition to a final R(g) of approximately 33.5 A was observed between 0.45 and 2 M NaCl. This confirms the expectation that monovalent ions not only are less efficient in charge neutralization but also contract the RNA less efficiently than multivalent ions.