Investigation of the role of metal ions and non-canonical base pairs on the structure and stability of RNA pseudoknots /
The energetics governing the formation of RNA pseudoknots are poorly understood, especially the contributions derived from the presence of non-canonical base pairs between pseudoknot loops and helical stems. Investigation of the thermodynamics of the unfolding of model pseudoknot systems provides a...
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| Format: | Thesis Book |
| Language: | English |
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[Place of publication not identified] :
[publisher not identified] ;
2002.
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| Online Access: | http://proxy.library.tamu.edu/login?url=http://proquest.umi.com/pqdweb?did=726460341&sid=1&Fmt=2&clientId=2945&RQT=309&VName=PQD |
| Summary: | The energetics governing the formation of RNA pseudoknots are poorly understood, especially the contributions derived from the presence of non-canonical base pairs between pseudoknot loops and helical stems. Investigation of the thermodynamics of the unfolding of model pseudoknot systems provides a means to probe the forces which direct the formation of pseudoknots, and, by extension, RNA tertiaty structures. The T2 gene 32 autoregulatory pseudoknot and the P1-P2 frameshifting pseudoknots from plant Luteoviridae serve as model H-type pseudoknots used to probe the energetics of pseudoknot formation focusing on the role of loop sequence and metal ions. Studies on the T2 pseudoknot revealed that helical stems in a pseudoknot structure can display altered stability and cooperativity which is coupled to an increased requirement for counterions to achieve the predicted stability of the pseudoknot stems. Investigation of the non-canonical pairings in the P1-P2 frameshift pseudoknots from BWYV reveals that over 30 kcal mol⁻¹ of stabilizing enthalpy is contributed to the pseudoknot structure in a pH dependent manner by coupling to an A([n]₋₁)·C⁺·G-C[n] base quadruple. The similarity between the thermodynamics of the BWYV pseudoknot and the P1-P2 frameshifting pseudoknots from PLRV and PEMV suggest that the presence of loop-stem non-canonical base pairings is required for frameshifting and is a conserved feature of the P1-P2 frameshifting pseudoknots from plant Luteoviridae. The structure of the PEMV-1 pseudoknot reveals an inverted A([n]₋₁)·C⁺·G-C[n] and a novel A·U loop-loop Hoogsteen base pair producing a new type of bent, over-rotated frameshifting pseudoknot. The function of these two structural features in stimulating frameshifting is unknown, but the stability of the PEMV-1 pseudoknot suggests that it would not form without the stabilizing non-canonical pairings. Overall, the pseudoknot loops seem to play an intricate role in the energetics of pseudoknot formation in low concentrations of counterions, and the sequence of the loops can alter the global stability of the pseudoknot as well as the local stability and cooperativity of helical stems. |
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| Item Description: | Vita. "Major Subject: Biochemistry". |
| Physical Description: | xv, 276 leaves : illustrations ; 28 cm. Issued also on microfiche from University Microfilm Inc. |
| Bibliography: | Includes bibliographical references (leaves 244-261). |