RNA Challenges for Computational Chemists

Abstract

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...

RNA design rules from a massive open laboratory

“…Mechanistic work will be required to give atomic-level explanations for the rules' predictive power. In this sense, the EteRNA rules are analogous to energetic models, such as the nearest neighbor rules (25), which are also empirically derived but not yet derivable from first principles (26,27) or other design heuristics (28). From a mechanistic perspective, one interesting feature shared across many of the EteRNA design rules collected so far is the use of negative design rules.…”

NMR Structures of (rGCUGAGGCU)2 and (rGCGGAUGCU)2: Probing the Structural Features That Shape the Thermodynamic Stability of GA Pairs,

“…The sequence dependence of internal loop stability and structure has been extensively studied experimentally and some computational approaches have also been tested (39)(40)(41). Despite this effort, there are many unknowns regarding the nature of the physicochemical forces shaping internal loop stability, structure, and dynamics (19,42,43). In order to gain further insight into the nature of these forces, this paper presents the solution three dimensional structures of tandem GA pairs closed by GU pairs.…”

Stacking Effects on Local Structure in RNA: Changes in the Structure of Tandem GA Pairs when Flanking GC Pairs Are Replaced by isoG−isoC Pairs

“…The stability [1][2][3][4][5][6][7] and three-dimensional structure [7][8][9][10][11][12][13][14][15] of RNA tandem GA pairs are dependent on sequence context. Tandem sheared GA (trans Hoogsteen/ Sugar edge A-G) pairs ( Figure 1) form with cross-strand base stacking in the symmetric contexts (CGAG) 2 with loop free energy of −0.7 kcal/mol 1,3,8 and (UGAA) 2 with loop free energy of 0.7 kcal/mol.…”

“…1,4,9 These results suggest that base stacking interactions (e.g., Coulombic and overlap) determine the hydrogen bonding patterns of RNA tandem GA pairs in these internal loops. 7,9,16 Different shapes of GA pairs in turn provide different molecular features, e.g., van der Waals and electrostatic surface, and hydrogen bonding donors and acceptors, for higher order RNA folding and molecular recognition. [13][14][15][17][18][19] The Watson-Crick like iGiC pair, with the amino and carbonyl groups transposed relative to the Watson-Crick GC pair, provides an expanded alphabet [20][21][22][23][24][25][26] for further understanding interactions that shape nucleic acid structure (Figure 1).…”

“…[13][14][15][17][18][19] The Watson-Crick like iGiC pair, with the amino and carbonyl groups transposed relative to the Watson-Crick GC pair, provides an expanded alphabet [20][21][22][23][24][25][26] for further understanding interactions that shape nucleic acid structure (Figure 1). 7,[25][26][27][28][29][30][31][32] Here, thermodynamic studies of tandem GA pairs flanked by iGiC pairs are reported along with NMR structures of the RNA duplexes (GCiGGAiCGCA) 2 and (GGiCGAiGCCA) 2 . NMR restrained molecular dynamics and energy minimization of (GCiGGAiCGCA) 2 reveal a conformation of tandem sheared GA pairs closed by Watson-Crick like iGiC pairs.…”