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| Content Provider | PubMed Central |
|---|---|
| Author | Grant, Gian Paola G. Boyd, Nathan Herschlag, Daniel Qin, Peter Z. |
| Abstract | The Tetrahymena group I intron recognizes its oligonucleotide substrate in a two-step process. First, a substrate recognition duplex, called the P1 duplex, is formed. The P1 duplex then docks into the pre-folded ribozyme core by forming tertiary contacts. P1 docking controls both the rate and the fidelity of substrate cleavage, and has been extensively studied as a model for the formation of RNA tertiary structure. However, previous work has been limited to study millisecond or slower motions. Here we investigated nanosecond P1 motions in the context of the ribozyme using site-directed spin labeling (SDSL) and electron paramagnetic resonance (EPR) spectroscopy. A nitroxide spin label (R5a) was covalently attached to a specific site of the substrate oligonucleotide, the labeled substrate was bound to a pre-folded ribozyme to form the P1 duplex, and X-band EPR spectroscopy was used to monitor nitroxide motions in the 0.1 – 50 nanosecond regime. Using substrates that favor the docked or the undocked states, it was established that R5a was capable of reporting P1 duplex motions. Using R5a-labeled substrates it was found that the J1/2 junction connecting P1 to the ribozyme core controls nanosecond P1 mobility in the undocked state. This may account for previous observations that J1/2 mutations weaken substrate binding and give rise to cryptic cleavage. This study establishes the use of SDSL to probe nanosecond dynamic behaviors of individual helices within large RNA and RNA/protein complexes. This approach may help in understanding the relationship between RNA structure, dynamics, and function. |
| Related Links | http://dx.doi.org/10.1021/ja808217s |
| Starting Page | 3136 |
| File Format | |
| ISSN | 15205126 |
| e-ISSN | 15205126 |
| Journal | Journal of the American Chemical Society |
| Issue Number | 9 |
| Volume Number | 131 |
| Language | English |
| Publisher Date | 2009-03-11 |
| Access Restriction | Open |
| Subject Keyword | Research in Higher Education |
| Content Type | Text |
| Resource Type | Article |
| Subject | Chemistry Colloid and Surface Chemistry Biochemistry Catalysis |
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