Table 1.
Modified nucleoside relative entropic contributions to transfer RNAs
| Modified nucleosidea | ΔΔSRbR | References |
|---|---|---|
| D17,18 | −/− − | Sipa et al, 2007 |
| Cm32 | − | Ashraf et al, 2000 |
| f5C34 | − − | H. Lusic, P.F. Agris & A. Deiters, unpublished data |
| Gm34 | +/− | Schmidt et al, 1987; Ashraf et al, 2000 |
| Q34 | + | Morris et al, 1999 |
| cmo5U34 | ++ | Vendeix et al, 2008 |
| s2U8 | ++ | Testa et al, 1999; Sipa et al, 2007 |
| mcm5s2U34 | + | Bajji & Davis, 2000 |
| mcm5U34 | ++ | Bajji & Davis, 2000 |
| mnm5s2U34 | + | Durant et al, 2005; Vendeix et al, 2008c |
| mnm5U34 | ++ | Yarian et al, 2000 |
| i6A37 | + | Cabello-Villegas et al, 2002; Kierzek & Kierzek, 2001 |
| t6A37 | + | Yarian et al, 2000; Vendeix et al, 2008c |
| ms2t6A37 | +/− | Durant et al, 2005; Vendeix et al, 2008c |
| m1G37 | + | Ashraf et al, 2000 |
| yW37 | + | Schmidt et al, 1987 |
| Ψ39 | + | Yarian et al, 1999; Ashraf, 2000; Bajji & Davis, 2000; Tworowska & Nikonowicz, 2006 |
| m5C40 | − | Ashraf et al, 2000 |
| m5U54 (T54) | 0 | Schmidt et al, 1987; Sengupta et al, 2000 |
| Ψ55 | 0 | Sengupta et al, 2000 |
aContributions of modified nucleosides at their most common positions in the anticodon stem and loop domain (ASL), dihydrouridine stem and loop domain (DSL) or ribothymidine stem and loop domain (TSL) of transfer RNA (tRNA), and in short RNA duplexes (12–15 residues) with site-specific modifications. Stability measurements of the modified and unmodified RNAs were assessed by 13C-methyl-relaxation measurements, ultraviolet (UV) absorbance at 260 nm and nuclear magnetic resonance (NMR). UV analysis of D is problematic because of its saturated ring structure. Modifications are defined in the text.
bThe relative change in entropy, ΔΔSR, is taken from empirically recorded thermodynamic parameters, and from comparisons of NMR-derived families of modified and unmodified structures in solution from the Protein Data Bank (PDB). In general, the cited laboratories conducted NMR spectrometry under conditions of low salt (10–20 mM) and pH (5.8–6.8), and at temperatures of 10–25°C. The PDB structures were achieved using either AMBER or CHARMM-based software for molecular-dynamics calculations from NMR-derived torsion angle and distance restraints. Relative values of ΔΔS•T are in ranges of kcal/mol as follows: +, 1−4; ++, 5–10; 0, −1 to +1; −, −4 to −1; and − −, −4 to −10.
cSome thermodynamic data on ms2t6A37 have been published (Durant et al, 2005), but these have been expanded by F.A.P. Vendeix, A. Malkiewicz & P.F. Agris, unpublished data.