Invariant adenosine residues stabilize tRNA D stems

Helix Capping in RNA Structure

“…More surprisingly, the tertiary contacts made by the IVS associated with D-caps occur almost exclusively through the 5′-IVS ( Figure 4B ). Furthermore, when two unpaired nucleotides are simultaneously available immediately 3′ and 5′ to a helix end, C′-capping is favored 7-fold with the one 3′ to the helix end over the one 5′ to the helix end (27 vs. 4) ( Table 1 and Figure 4C ), consistent with previous melting studies demonstrating that a 3′-dangling nucleotide stabilize a canonical helix far more than a 5′-dangling nucleotide does [12], [13], [14], [15], [16], [19]. Altogether, these suggest that, while stabilizing helix ends against fraying, the 5′-nt of helix capping basepair motifs and its associated IVS be rather intrinsically entropic, making many long-range tertiary contacts largely responsible for hierarchically driving RNA folding.…”

“…The ends of short canonical helices in structured RNAs, however, are frequently flanked by tetraloops [23], lonepair triloops [24], G:A and A:A basepairs [25], or other canonical helices [26]. Consistently, previous melting studies have shown that canonical RNA helices are greatly stabilized in the presence of tetraloops or various mismatches at their ends [13], [17], [27], [28], [29], [30], [31], [32]. In particular, UUCG and GAAA tetraloops are known to nucleate the formation of unusually stable hairpin structures and serve as a reverse transcription termination signal of bacteriophage T4 mRNA or as a rho-independent transcription terminator of prokaryotic mRNAs [27], [33].…”

“…Additional analysis demonstrated that nearly all helix ends in other classes of structured RNAs are involved in end-stacking ( Table S1 ). Provided that helix ends fray [20], [21], [22], such preponderance of end-stacking in structured RNAs reflects its significance not merely in protecting short canonical RNA helices against fraying as indicated by earlier studies [12], [13], [14], [15], [16], [17], [18], [19], [27], [28], [29], [30], [31], [32].…”

“…Together with basepairing interactions, base-stacking contributes significantly to the stability of DNA and RNA helices [11], [12], [13], [14], [15], [16], [17], [18], [19]. While internal basepairs are stacked on both sides, the ends of RNA secondary structure helices are stacked on their internal side and exposed to the loop side, potentially susceptible to fraying in that their imino protons exchange with solvent [20], [21], [22].…”

Characterization of GU‐Base Pairing in Double Helical Polynucleotides by IR‐Difference Spectroscopy

“…Alternating poly (G-U) forms an ordered structure at low temperatures [IT], but thc structure of this complex has remained uncertain and with respect to naturally occuring nucleic acids it is more imporlant to study the properties of GU-base pairing in the neighbourhood of normal Watson-Crick base pairs. Stability parameters of the GU-base pair could bc estimated roughly from a number of experiments with oligonucleotides [18 -211 and the temperature dependence of the chemical shift of nonexchangeable protons of such complexes was examined by NMR-spectroscopy [18,19]. It was suggested that CU-base pairs are more stable in the neighbourhood of GC-than of AUbasepairs.…”