The functional exchangeability of pk- and k-turns in RNA structure
| Autor: | Benoît Masquida, David M.J. Lilley, Peter Daldrop |
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| Rok vydání: | 2013 |
| Předmět: |
Models
Molecular RNA Folding RNase P RNA Stability Biology Ribonuclease P 03 medical and health sciences Bacterial Proteins Fluorescence Resonance Energy Transfer Thermotoga maritima Nucleotide Motifs Nucleic acid structure Binding site RNA structure SAM-I riboswitch Molecular Biology kink turn 030304 developmental biology 0303 health sciences 030302 biochemistry & molecular biology Ribozyme RNA Hydrogen Bonding Cell Biology RNA Bacterial Biochemistry Riboswitch biology.protein Nucleic acid Biophysics Nucleic Acid Conformation lipids (amino acids peptides and proteins) Rna folding Small nuclear RNA Research Paper |
| Zdroj: | RNA Biology |
| ISSN: | 1555-8584 1547-6286 |
| DOI: | 10.4161/rna.23673 |
| Popis: | Ribonuclease P RNA requires a sharply kinked RNA helix to make a loop-receptor interaction that creates the binding site for the substrate. In some forms of the ribozyme, this is accomplished by a k-turn, while others have a different element called the pk-turn. The structure of the pk-turn in RNase P of Thermotoga maritima is globally very similar to a k-turn, but lacks all the standard features of that structure, including long-range hydrogen bonds between the two helical arms. We show here that in an isolated RNA duplex, the pk-turn fails to adopt a tightly kinked structure, but rather is a flexible element. This suggests that the tertiary contacts of RNase P assist its folding into the required kinked structure. We find that we can replace the k-turn of the SAM-I riboswitch with the pk-turn, such that the resulting RNA retains its ability to bind SAM, although with lower affinity. We also find that we can replace the pk-turn of T. maritima RNase P with a standard k-turn (in either orientation) with retention of ribozyme activity. Thus, although the pk-turn cannot intrinsically fold into the kinked structure, it can be induced to fold correctly in context. And the pk-turn and k-turns can substitute functionally for one another. |
| Databáze: | OpenAIRE |
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