Free energy calculation of modified base-pair formation in explicit solvent: A predictive model

Abstract

The maturation of RNAs includes site-specific post-transcriptional modifications that contribute significantly to hydrogen bond formation within RNA and between different RNAs, especially in formation of mismatch base pairs. Thus, an understanding of the geometry and strength of the base-pairing of modified ribonucleoside 59-monophosphates, previously not defined, is applicable to investigations of RNA structure and function and of the design of novel RNAs. The geometry and free energies of base-pairings were calculated in aqueous solution under neutral conditions with AMBER force fields and molecular dynamics simulations (MDSs). For example, unmodified uridines were observed to bind to uridine and cytidine with significant stability, but the ribose C19-C19 distances were far short (;8.9 Å ) of distances observed for canonical A-form RNA helices. In contrast, 5-oxyacetic acid uridine, known to bind adenosine, wobble to guanosine, and form mismatch base pairs with uridine and cytidine, bound adenosine and guanosine with geometries and energies comparable to an unmodified uridine. However, the 5-oxyacetic acid uridine base paired to uridine and cytidine with a C19-C19 distance comparable to that of an A-form helix, ;11 Å , when a H 2 O molecule migrated between and stably hydrogen bonded to both bases. Even in formation of canonical base pairs, intermediate structures with a second energy minimum consisted of transient H 2 O molecules forming hydrogen bonded bridges between the two bases. Thus, MDS is predictive of the effects of modifications, H 2 O molecule intervention in the formation of base-pair geometry, and energies that are important for native RNA structure and function.

Nucleotide modifications and tRNA anticodon–mRNA codon interactions on the ribosome

“…The inclusion of Mg 2+ ions does not seem to affect the effect of the modifications on the binding energies, but the energies are generally higher with Mg 2+ present. Other observations are that the base pair between guanine and the enol form of U34 would be very stable if the unusual enol form was attainable (this issue is not addressed in our calculations), even more so than the cognate adenine and that, in accordance with previous observations (Weixlbaumer et al 2007;Vendeix et al 2009), uracil binds better than cytosine to U34.…”

Structural determinants for ligand capture by a class II preQ 1 riboswitch

“…We found that A35G substitution has a smaller (compared with A50G) but nevertheless significant effect on K D , increasing it to 950 ± 300 nM, consistent with its importance in closing off the minor groove side of the binding pocket. The ΔΔG compared with WT was 1.9 kcal/mol, in the range of the expected cost of losing one hydrogen bond (59). Despite its apparent importance for preQ 1 binding affinity, the reported nucleotide identity for A35 is only 75% conserved (27); however, we noticed that the sequence adjacent to P4 is A 33 CA 35 C, whereas the shorter J2-4 loop in Lra preQ 1 -II has only a single AC sequence next to P4 (39).…”

Lack of tRNA-i6A modification causes mitochondrial-like metabolic deficiency in S. pombe by limiting activity of cytosolic tRNATyr, not mito-tRNA

“…In addition to relatively low tRNA Tyr GUA supply/demand, it may be relevant that one of the two Tyr codons, UAU, constitutes the only codon-anticodon interaction among the S. pombe i6A37-tRNAs that is devoid of a G:C base pair. This suggests that the interaction of tRNA Tyr with its codons is further diminished relative to the other i6A37-tRNAs in S. pombe (Lagerkvist 1978;Vendeix et al 2009;Stadler and Fire 2011;Ran and Higgs 2012) and therefore may benefit more from i6A37 modification than the other tRNAs (Discussion).…”