Thermodynamic stability and conformational dynamics of model H-type RNA pseudoknots /
Hairpin (H)-type RNA pseudoknots have been shown to be involved in the regulation of protein synthesis at all phases of protein translation. The thermodynamic contributions of individual structural features to the stability of H-type RNA pseudoknots, other than nearest-neighbor base pair stacking i...
| Main Author: | |
|---|---|
| Format: | Thesis Book |
| Language: | English |
| Published: |
[Place of publication not identified] :
[publisher not identified] ;
2000.
|
| Subjects: | |
| Online Access: | http://proxy.library.tamu.edu/login?url=http://proquest.umi.com/pqdweb?did=727726441&sid=1&Fmt=2&clientId=2945&RQT=309&VName=PQD |
| Summary: | Hairpin (H)-type RNA pseudoknots have been shown to be involved in the regulation of protein synthesis at all phases of protein translation. The thermodynamic contributions of individual structural features to the stability of H-type RNA pseudoknots, other than nearest-neighbor base pair stacking interactions and loop length entropic penalties, are not known and may have a significant impact on the stability, structure, and equilibrium population distribution of the pseudoknot and folding intermediates. The equilibrium unfolding pathways and thermodynamic contributions of individual structural features for three mRNA pseudoknots have been investigated: the autoregulatory gene 32 mRNA pseudoknot from bacteriophage T4, the gag-pro frameshifting pseudoknot from mouse intracisternal A-type particles (mIAP) and the gag-pro frameshifting pseudoknot mouse mammary tumor virus (MMTV). Investigation of the stability contributions of various structural elements in the T4 pseudoknot revealed that substitution of the loop 1 sequence, or deletion of the 3' single-stranded capping interaction, both of which are physically proximal to stem 2, gave rise to a long-range non-nearest neighbor destabilization of stem 1. This destabilization is likely transmitted through an altered helical junction, which itself was found not to be maximally stable in this pseudoknot. In the mlAP and MMTV pseudoknots, mutations in the loop 2 sequence or perturbations of the helix-helix junction gave rise to similar effects which resulted in the destabilization of the weakest part of the molecule, which was, in this case, stem 2. An intercalated adenosine at the helical junction was found to be stabilizing with a []G⁰ (37⁰C) of [] 1 kcal mol⁻¹. Time-resolved fluorescence resonance energy transfer experiments on MMTV pseudoknots with or without this intercalated adenosine suggest that there are conformation dynamics associated with these molecules and that these dynamic properties may be altered in the presence of Mg²⁺. Overall, these H-type RNA pseudoknots display coupling of the two pseudoknot stems through the helical junction which can not be explained based on nearest-neighbor interactions and are characterized by a helical junction which is not maximally stable. The stability of the junction will directly influence the flexibility of the pseudoknot, which is reported on in the fluorescence experiments. |
|---|---|
| Item Description: | Vita. "Major Subject: Biochemistry". |
| Physical Description: | xv, 249 leaves : illustrations ; 28 cm. Issued also on microfiche from University Microfilm Inc. |
| Bibliography: | Includes bibliographical references (leaves 231-246). |