## 2 Influence of tRNA Core Modification on tRNA Structure and Stability
### Modifications in the tRNA Core and Their Impact on tRNA Structure and Dynamics  
First, it is important to note that tRNA modifications can have little to no effect on some tRNAs while dramatically affecting others. For instance, in the yeast elongator tRNAPhe, the introduction of m1A58 has no detectable impact on the structure of the tRNA as observed with NMR [68; 69]. On the contrary, the introduction of m1A58 on in vitro transcribed unmodified yeast tRNAMet has a major effect on the tertiary folding of this tRNA and more particularly on the proper assembly of its elbow region [70]. NMR studies showed that unmodified tRNAMet adopts different heterogeneously folded conformations while m1A58-tRNAMet adopts one major homogenously folded conformation. This important structural role of m1A58 in tRNAMet, which has a structural impact reminiscent of that of m1A9 and m2G26, is likely related to the unique tRNA substructure in the elbow region of eukaryotic initiator tRNAs [71]. It should be emphasized that the tRNA-dependent nature of the impact of modifications is perfectly in line with the idea that certain modifications do not necessarily have the same beneficial effect and are not equally useful for all tRNAs (reviewed in [72]). Although dihydrouridines are considered to bring flexibility to tRNAs, their effects can be ambivalent. Dihydrouridines indeed allow greater conformational flexibility and dynamic motion in the tRNA D-loop [73] but also simultaneously constrain the D-stem to adopt a stable conformation, as seen in _S. pombe_ tRNAMet[74]. The stabilization effect of dihydrouridines is also observed in _E. coli_ tRNASer where the absence of D20 decreases the melting temperature of this tRNA [53]. Lastly, it has been suggested that the interplay between the flexibility of D20 and the rigidity of \(\Psi\)55 is needed to stabilize the elbow region of _E. coli_ tRNAMet[75]. Another example affecting the melting temperature of tRNAs concerns the acp\({}^{3}\)U47 core modification, which increases the thermal stability of _E. coli_ tRNAMet by 3 \({}^{\circ}\)C [76]. The exact mechanism of how acp\({}^{3}\)U47 stabilizes the tertiary structure of tRNAs is not well understood. However, it has been suggested that it could be due to its inability to form Watson-Crick base pairing, thus ensuring the correct folding of tRNAs [76]. Although chemical modifications of nucleotides often increase the overall thermal stability of tRNAs, this may be achieved by an increase or a decrease in the local conformational dynamics in solution [45]. For instance, modified _E. coli_ tRNAMet has a higher overall structural and thermal stability, compared to its unmodified version, but presents an increase in local conformational fluctuations [75]. This behavior is attributed to entropic effects in which increased local conformational dynamics lead to a stabilization of the tertiary structure of the tRNA [75], in line with previous molecular dynamics simulations [77; 78]. Interestingly, the authors observed that tRNA core modifications generate a remote effect of stabilization throughout the entire tRNA [75], which correlates well with an earlier report stating that modifications alter the intrinsic correlated motions within the tRNAs [52]. Effects of tRNA core modifications on the conformational dynamics of tRNAs are likely tRNA-dependent, and fully modified human mt-tRNALeu, for instance, displays lesser folding dynamics than the unmodified transcript and exhibits a more constrained native structure that does not allow intermediate conformations [79]. Influence of tRNA Core Modification Enzymes on tRNA Structure: More than Just Their Catalytic Activity  
Modification enzymes have been reported to act as chaperones stabilizing and refolding their substrates independently of their enzymatic activity, thereby giving misfolded tRNAs a second chance to refold into native conformations (reviewed in [80]). Two tRNA modification enzymes acting as chaperones have been identified and characterized in _E.