A calorimetric investigation of melting of tRNAAsp from brewer's yeast

Probing the conformation of human tRNA(3)(Lys) in solution by NMR

Human tRNA(3)(Lys) acts as a primer for the reverse transcription of human immunodeficiency virus genomic RNA. To form an initiation complex with genomic RNA, tRNA(3)(Lys) must reorganize its secondary structure. To provide a starting point for mechanistic studies of the formation of the initiation complex, we here present solution NMR investigations of human tRNA(3)(Lys). We use a straightforward set of NMR experiments to show that tRNA(3)(Lys) adopts a standard transfer ribonucleic acid tertiary structure in solution, and that Mg(2+) is required for this folding. The results underscore the power of NMR to reveal rapidly the conformation of RNAs.

Post-transcriptional nucleotide modification and alternative folding of RNA

Alternative foldings are an inherent property of RNA and a ubiquitous problem in scientific investigations. To a living organism, alternative foldings can be a blessing or a problem, and so nature has found both, ways to harness this property and ways to avoid the drawbacks. A simple and effective method employed by nature to avoid unwanted folding is the modulation of conformation space through post-transcriptional base modification. Modified nucleotides occur in almost all classes of natural RNAs in great chemical diversity. There are about 100 different base modifications known, which may perform a plethora of functions. The presumably most ancient and simple nucleotide modifications, such as methylations and uridine isomerization, are able to perform structural tasks on the most basic level, namely by blocking or reinforcing single base-pairs or even single hydrogen bonds in RNA. In this paper, functional, genomic and structural evidence on cases of folding space alteration by post-transcriptional modifications in native RNA are reviewed.

The interaction between resistance modifiers such as pyrido[3,2-g]quinoline, aza-oxafluorene and pregnane derivatives with DNA, plasmid DNA and tRNA

Various resistance mechanisms such as complex formation with DNA, tRNA and MDR1 p-glycoprotein were modified in bacteria and cancer cells in presence of pregnane, pyridoquinoline, and aza-oxafluorene derivatives. Interaction between the compounds, plasmid DNA and tRNA was shown and compared to the interaction with calf thymus DNA. Complex formation with MDR1 p-glycoprotein and drug accumulation increased in cancer cells. Both plasmid DNA and p-gp complex formation were related to the chemical structures of the resistance modifiers.

Folding rate dependence on the chain length of RNA-like heteropolymers

BACKGROUND

Computer experiments and analytical estimates have shown that protein and RNA chains can reach their most stable folds without an exhaustive search over all their possible conformations. Protein-like chain folding proceeds via a specific nucleus and under conditions optimal for the fastest folding of these chains the dependence of the folding time (t) on the chain length (L) is in accord with the power law t integral of Lb (b is a constant).

RESULTS

Using Monte-Carlo folding simulations for a simple model of RNA secondary structure formation, we estimated the RNA chain length dependence of the time necessary to reach the lowest energy fold. Our results are compatible with a relatively weak power dependence of the folding time on the chain length, t integral of Lb. Such dependencies have been observed for different folding conditions, both for random sequences (here, b > 5) and for sequences edited to stabilize their lowest energy folds (for extremely edited sequences b < 2). Although folding transitions in RNA chains are not an all-or-none type in terms of thermodynamics, they proceed via a folding nucleus in terms of kinetics. The peculiarity (compared with protein folding) is that the RNA critical nucleus is big and non-specific.

CONCLUSIONS

We have obtained a general scaling for the dependence of the RNA secondary structure on the chain length. The obtained power dependence is very weak compared with an exponential dependence for an exhaustive sorting.

Cooperative thermal denaturation of the assembly origin region of TMV RNA

The assembly origin (AO) region of the tobacco mosaic virus RNA melts in an usually narrow (2.5 degrees C) temperature range. In an 0.01 M phosphate buffer the melting temperature of AO was found to be 41.5 degrees C. This value corresponds to the regions with the most stable secondary/tertiary structure of the whole TMV RNA molecule. It is assumed that the AO region has a specific tertiary structure, which is maintained by the long-range interactions as well as by interactions of the pseudoknot type.