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14. Beskrive hvilke interaktioner der danner de sekundære og tertiære struktur
af stabile RNA'er (tRNA og rRNA), herunder tRNAs hårnålestruktur,
kløverbladsstruktur og L-form
Devlin, s.79-82;
fig.
2.56; 2.58; 2.59; 2.60
Stryer, s.815-817;
fig. 29.4;
29.6
RNA’s secondary structure
RNA molecules are single stranded, and their secondary structure results from relatively short regions of intramolecular base pairing, that is, base pairs formed from complementary sequences in the same molecule. The base pairing is created of double or triple hydrogen bonds between the complementary bases.
Even non-paired sequences of single stranded RNAs contain considerable helical structure, due to strong base stacking. The base stacking phenomenon is due to Van der Walls and hydrophobic bonds between the heterocyclic rings of the bases.
There
are 11 bp. per turn; RNA resembles the A-DNA form.
Hairpins - representing RNA secondary structure, are double helical stem-loop regions in RNA-molecules. They can vary in connection with the length of the base paired regions and the size and number of loops.
RNA’s tertiary structure – results from base-stacking and hydrogen bonds between different parts lying far away from eachother in the molecule.
tRNAs are excellent examples for both base-stacking, hydrogen bonding in a single RNA strand, creating a secondary and tertiary structure of the molecule.
tRNA Hairpins
– double helical stem-loop regions in the tRNA. There are all in all four
hairpins in tRNA, which I will describe in the cloverleaf structure.
Cloverleaf structure of tRNA
tRNA is a single chain containing between 73 and 93 ribonucleotides. About 60% of bases are paired in four double-helical stems. Five regions are not paired:
the 3’-CCA terminal region
TψC loop
The extra arm, which contains variable number of residues
DHU loop
the anticodon loop, made up of seven nucleotides. This loop is present near the center of the entire tRNA sequence. The partial helix caused by base stacking in this loop, binds, by base-pairing to a complementary codon in the mRNA so translation can occur.
These
unpaired regions have the capability of forming base-pairs with bases in the
same or other looped regions, contributing in this way to the tertiary structure
of the tRNA.
tRNA L-form – a tertiary structure of tRNA. It is a very compact folded structure, stabilized by:
hydrogen bonds (Watson-Crick base pairing) between bases laying in distant parts of the tRNA
base interaction involving more then two nucleotides. The bases can donate hydrogen atoms to the phosphate backbone. The 2’-OH of ribose can be an important acceptor or donor of hydrogen. (fig.2.60)
All these interaction contribute to the folding of the tRNA.
In the L-form of the tRNA, the CCA terminus extends from one end of the L, while the anticodon site is located on the other end of the L. (fig. 2.59)
Interactions found in tRNA are also seen in rRNA.
rRNAs are folded into definite structures with many short duplex regions and a lot of loops.
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