PubMed · 352728
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S K Mitra. 1978-07-01. Yeast tRNALys1 (anticodon CUU) translates AAA codon.. https://doi.org/10.1016/0014-5793(78)80021-0
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The pattern of codon utilization in the variable and constant regions of immunoglobulin genes are compared. It is shown that, in these regions, codon utilizations are quite distinct from one another: For most degenerate codons, there is a selective bias that prefers C and/or G ending codons to U and/or A ending codons in the constant region compared with the bias in the variable region. This would strongly suggest that, in immunoglobulin genes, the bias in code word usage is determined by other factors than those concerning with the translational mechanism such as tRNA availability and codon-anticodon interaction. A possibility is also suggested that this differance of code word usage between them is due to the existence of secondary structure in the constant region but not in the variable region.
Initiator tRNAs have an anticodon loop conformation distinct from that of elongation tRNAs as detected by susceptibility to S1 nuclease. We now find the anticodon loop conformation of E. coli tRNAfMet to be stable under different salt conditions as detected by using S1 nuclease as a structural probe. In contrast, a conformational change is observed in the T- and D- loop of this tRNA in the absence of added Mg2+. This change can be suppressed by spermine. Even under those conditions effecting a change in T- and D- loop conformation, the anticodon loop does not change. This suggests that the conformational shift is controlled by Mg2+ and restricted to the D- and T- loop region only without affecting the anticodon domain. The use of S1 nuclease as a conformational probe requires the use of kinetic studies to determine the initial cleavage sites. Thus, the use of a strong inhibitor which immediately stops the action of this nuclease is necessary. ATP is shown to be such an inhibitor.
The hydration phenomena of A-RNA double helix and the anticodon loop of transfer RNA have been theoretically investigated using the empirical potential energy functions. The hydration schemes of a model compound of A-RNA and a polynucleotide which has the structure of the anticodon loop of yeast tRNAPhe have been determined, and their stabilization energies produced by the introduction of water in the first hydration shell were calculated by considering the hydrated ones as supermolecules. The results indicate that hydration scheme of A-RNA considerably differs from that of B-DNA and stabilization energy due to hydration of A-RNA is not so great as B-DNA. In the anticodon loop structure, however, stabilizing effect of the bound water molecules upon the structure is significant. From the results, the reason why the structure of RNA remains unchanged with the change of hydration degree while that of DNA is altered was studied.