Effects of magnesium ions on the stabilization of RNA oligomers of defined structures

Serra, Martin J.; Baird, John D.; Dale, Taraka; Fey, Bridget L; Retatagos, Kimberly; Westhof, Éric

doi:10.1017/s1355838202024226

Cited by 120 publications

(134 citation statements)

References 56 publications

Supporting

Mentioning

115

Contrasting

Unclassified

Order By: Relevance

“…MgCl 2 is presumably due to the complexation of Mg 2+ with a phosphodiesterase group and it may also stabilize the secondary structure of RNA (29,32). This is consistent with the importance of Mg 2+ in ribozymes, and such metal selectivity in enzyme mimics could be of considerable interest with respect to imitating biological selectivities (33).…”

Section: Resultssupporting

confidence: 63%

Deoxypolypeptides bind and cleave RNA

Cheng

Mahendran

Gonzalez

et al. 2014

Proc. Natl. Acad. Sci. U.S.A.

View full text Add to dashboard Cite

We have prepared L-and D-deoxypolypeptides (DOPPs) by selective reduction of appropriately protected polyhistidines with borane, reducing the carbonyl groups to methylenes. The result is a chiral polyamine, not amide, with a mainly protonated backbone and chirally mounted imidazolylmethylene side chains that are mostly unprotonated at neutrality because of the nearby polycationic backbone. We found that, in contrast with the D-octahistidine DOPP, the L-octahistidine DOPP is able to cooperatively bind to a D-polyuridylic acid RNA; this is consistent with results of previous studies showing that, relative to D-histidine, L-histidine is able to more strongly bind to RNA. The L-DOPP was also a better catalyst for cleaving the RNA than the D-DOPP, consistent with evidence that the L-DOPP uses its imidazole groups for catalysis, in addition to the backbone cations, but the D-DOPP does not use the imidazoles. The L-DOPP bifunctional process probably forms a phosphorane intermediate. This is a mechanism we have proposed for models of ribonuclease cleavage and for the ribonuclease A enzyme itself, based on our studies of the cleavage and isomerization of UpU catalyzed by imidazole buffers as well as other relevant studies. This mechanism contrasts with earlier, generally accepted ribonuclease cleavage mechanisms where the proton donor coordinates with the oxygen of the leaving group as the 2-hydroxyl of ribose attacks the unprotonated phosphate. T he enzyme ribonuclease A (RNase A) hydrolyzes RNA with bifunctional catalysis, using His-12 as a base and protonated His-119 as an acid to form the first products, a 2,3-cyclic phosphate of one ribose and the free next ribose with a new terminal 5′-hydroxyl group (1, 2). Lys-41 is also involved in stabilizing intermediate anions (3). In a second step the cyclic phosphate is hydrolyzed using the now-protonated His-12 and now-deprotonated His-119 in essentially a reverse of the cyclization step, with water replacing the second ribose unit (4). In the classical mechanism of this process it had been generally accepted, including in textbooks, that the protonated His-119 donates its proton to the leaving group whereas the 2′-hydroxyl group attacks the phosphate (1, 2) [isotope studies show that two protons are "in flight" during the hydrolysis step, essentially the reverse of the cyclization, both moving at the same time (5)]. We also showed the two-proton-in-flight process in a model system (6).However, our extensive studies on the cleavage of RNA with imidazole-imidazolium catalysts and on catalysis by RNase A itself indicated that a different mechanism is used ( Fig. 1) (7, 8). The proton donor BH + hydrogen binds to a phosphate oxyanion and donates the proton to the phosphate as the ribose 2′-hydroxyl adds while losing a proton to base :B. This process results in an intermediate phosphorane species. This then expels the 5′-hydroxyl group of the second nucleotide to cleave the P-O bond in a second step. We proposed this two-step phosphorane process to be the preferred path for th...

show abstract

Section: Resultssupporting

confidence: 63%

Deoxypolypeptides bind and cleave RNA

Cheng

Mahendran

Gonzalez

et al. 2014

Proc. Natl. Acad. Sci. U.S.A.

View full text Add to dashboard Cite

show abstract

“…The greater sensitivity of tertiary interactions to divalent metal ions compared with secondary structure has been observed in many RNAs (e.g., see refs. [47][48][49]. What is unusual in this system is that the assembly of core helices (I C ) is separated by its Mg 2ϩ requirement from the formation of stable tertiary interactions (N).…”

Section: D Model Of the Azoarcus Ribozymementioning

confidence: 99%

Assembly of core helices and rapid tertiary folding of a small bacterial group I ribozyme

Rangan

Masquida

Westhof

et al. 2003

Proc. Natl. Acad. Sci. U.S.A.

Self Cite

135

166

View full text Add to dashboard Cite

Compact but non-native intermediates have been implicated in the hierarchical folding of several large RNAs, but there is little information on their structure. In this article, ribonuclease and hydroxyl radical cleavage protection assays showed that base pairing of core helices stabilize a compact state of a small group I ribozyme from Azoarcus pre-tRNA ile . Base pairing of the ribozyme core requires 10-fold less Mg 2؉ than stable tertiary interactions, indicating that assembly of helices in the catalytic core represents a distinct phase that precedes the formation of native tertiary structure. Tertiary folding occurs in <100 ms at 37°C. Such rapid folding is unprecedented among group I ribozymes and illustrates the association between structural complexity and folding time. A 3D model of the Azoarcus ribozyme was constructed by identifying homologous sequence motifs in rRNA. The model reveals distinct structural features, such as a large interface between the P4 -P6 and P3-P9 domains, that may explain the unusual stability of the Azoarcus ribozyme and the cooperativity of folding.RNA modeling ͉ RNA structure ͉ metal ions ͉ hydroxyl radical footprinting T he assembly of RNA into functional structures underlies many steps in gene expression and regulation. Recent work has outlined the Mg 2ϩ -dependent folding pathways of large ribozymes (1, 2). Experimental and theoretical results suggest that the initial association of divalent cations induces collapse of the extended RNA chain into more compact structures that favor formation of tertiary interactions (3-8). The structure of the compact intermediates and the extent to which these interactions lead to the native conformation are not yet characterized.On the one hand, individual domains of the Tetrahymena group I ribozyme and the catalytic domain of RNase P fold on a time scale (10-100 ms) similar to the initial collapse transitions of the ribozyme (6, 9, 10). On the other hand, nonspecific collapse results in an ensemble of native and non-native conformations. Many larger RNAs, such as the Tetrahymena group I and Bacillus subtilis RNase P ribozymes, fold slowly in vitro because a large fraction of the RNA population becomes trapped in misfolded intermediates (11,12). An important question is whether RNAs with a simpler 3D architecture are more likely to fold directly to the native structure, as expected from theoretical models (4). Furthermore, we want to know whether the likelihood of misfolding can be predicted from the specificity of counterion-induced collapse.We investigated the Mg 2ϩ -dependent equilibrium folding pathway and constructed a 3D model of the Azoarcus group I intron. The 205-nt group IC3 intron in the pre-tRNA ile of the Azoarcus bacterium is the smallest known self-splicing group I intron (13). It retains the conserved catalytic core common to all group I introns, but lacks the peripheral domains that stabilize folding intermediates of the larger Tetrahymena intron (14).We observed two macroscopic folding transitions in the Azoarcus ribozyme...

show abstract

“…Some ions, such as Mg 2+ and K + , stabilize tertiary structures better than other ions (45,47,70,71). Such stabilization is not well-understood.…”

Section: Theorymentioning

confidence: 99%

RNA Challenges for Computational Chemists

Yildirim

Turner

2005

Biochemistry

View full text Add to dashboard Cite

Some experimental results for the thermodynamics of RNA folding cannot be explained by simple pairwise hydrogen-bonding models. Such effects include the stabilities of isoguanosineisocytidine (iG-iC) base pairs and of various 2 × 2 nucleotide internal loops. Presumably, these results can be explained by base stacking effects, which can be partitioned into Coulombic and overlap effects. We review experimental measurements that provide benchmarks for testing the approximations and theories used for modeling nucleic acids. Quantitative agreement between experiment and theory will indicate understanding of the interactions determining RNA stability and structure.An understanding of the physical-chemical interactions underlying RNA folding would allow predictions of structure and perhaps function from sequence. The large number of atoms in an RNA molecule necessitates the use of approximate methods, rather than the rigorous equations of quantum mechanics. Many approaches are possible, including coarsegrained potentials (1), which use residue-centered force fields; molecular mechanics, which uses atom-centered force fields such as AMBER (2), CHARMM (3, 4), and GROMOS (5, 6); approximate quantum mechanics, which considers interactions of electrons and nuclei (7,8); and QM/MM, which combines quantum mechanics with molecular mechanics (9-16). Depending on the property to be predicted, the size of the RNA, and the domain of interest, different approaches will provide acceptable approximations.The secondary structure of RNA can sometimes be deduced by sequence comparison, which relies on the Watson-Crick rules for base pairing and the assumption that secondary structures are more conserved than sequences for function (17). Often, however, there are not enough sequences to determine a definitive secondary structure. For these cases, freeenergy minimization with a nearest neighbor model is the most popular method for predicting secondary structures (18-38). In this method, possible secondary structure motifs are assigned free-energy parameters, and these values are added to predict the total free energy of forming a secondary structure. The structure with the lowest free energy is assumed to dominate in solution. Rigorously, however, the concentrations of the various possible structures are predicted to be weighted by a Boltzmann factor, exp(−ΔG°/RT), where ΔG° is the free energy change for folding, R is the gas constant, 1.987 cal K −1 mol −1 , and T is the temperature in kelvins. Understanding intermolecular interactions such as hydrogen bonding, stacking, and so forth would allow accurate prediction of ΔG° and therefore secondary structure for an RNA. † This work was supported by NIH Grant GM22939 (D.H.T. Watson-Crick base pairs are the most common and most extensively studied motif in RNA structures. Configurations with the same base compositions but different permutations of base pairs generally have different free energies. For example, the duplexes (5′CGCG3′) 2 and (5′GGCC3′) 2 both have four GC base pairs, bu...

show abstract

Effects of magnesium ions on the stabilization of RNA oligomers of defined structures

Cited by 120 publications

References 56 publications

Deoxypolypeptides bind and cleave RNA

Deoxypolypeptides bind and cleave RNA

Assembly of core helices and rapid tertiary folding of a small bacterial group I ribozyme

RNA Challenges for Computational Chemists

Contact Info

Product

Resources

About