An Investigation of the Thermodynamics of  Two Group I Single Nucleotide Bulges: The Effects of 2 versus 3 Base Pairs Outside the Bulges

Crowther, Claire

An Investigation of the Thermodynamics of Two Group I Single Nucleotide Bulges: The Effects of 2 versus 3 Base Pairs Outside the Bulges

Persistent URL

http://hdl.handle.net/10456/34299

Author(s)

Crowther, Claire

Date Issued

April 12, 2013

Abstract

Eleven RNA sequences with two Group I bulges were optically melted in 1 M NaCl to determine their thermodynamic parameters (ΔH°, ΔS°, ΔG°37, and Tm). The number of nucleotides outside the bulges was varied from two to three and the number of nucleotides between the two bulges was varied. The revised Blose model was used to analyze the data, stating that as the decreased stability of the least stable stem, the effect that a bulge has on the duplex is decreased. The data that was collected was combined with previous research by Jones and Mastrogiacomo and then compared to the revised Blose Model (Jones 2007, unpublished; Mastrogiacomo 2011, unpublished; Blose et al., 2007; McCann et al., 2011). The effect of the each of the two single nucleotide bulges on the thermodynamics were determined to be different for each the bulges. The revised Blose model does not account for the two bulges to have different effects on the duplex, because it does not account for the effect the bulges can have on each other and the least stable stem. The predicted value for the effect of the bulge on the free energy of the duplex and the measured value differ by 2-3 kcal/mol, where the predicted gives a less positive free energy. The revised Blose model agrees with the data that as the stability of the least stable stem decreases the effect of the bulge on the free energy of the duplex decreases. None of the trends were statistically significant, which may be the result of a small data set. With further experimentation a significant trend may be determined.

Honors

Chemistry, 2013

First Reader(s)

Serra, Martin