Text

theses

Characterizing RNA structure experimentally is a challenging task. Computational methods complement experimental methods. In this thesis, we study, using software tools such as DSSR, Matlab, and Excel, the three-dimensional structures of a group of non-redundant RNA structures. These structures are those identifiers as Leontis and Zirbel at January 2017 [1], and the relevant coordinates for these structures downloaded from the Protein Data Bank (PDB) [2]. Specifically, we find the angles between all pairs of chemically linked double helical stems in each of the RNA structures, the distances between the mid points between all these stems, and the distributions for the calculated angles and distances. Additionally, we separate the above calculations to consider stems within the same helix. A helix is composed of at least two stacked base pairs and these base pairs are not necessarily chemically linked. The third part contains these calculations separated for stems in different helices. Based on these calculations, the stems in the same helix can be classified into two groups. The first group has small angles and mid distance among its stems. The stems all lie in the same direction. In the second group, the angle is large, while the distance is small, which means that the stem directions are opposite to each other. There are different probability density functions that fit closely to the data histograms. While the details are given in Chapter 3, the fitted probability density functions confirm that the proposed classification methods are correct. Finally, we plot the distribution of stems lengths to find that the lengths interacting stems tend to be of equal lengths and that interacting stems are more likely to be shorter.

ETD_8430

M.S.

Includes bibliographical references

by Zainab Fadhil

doi:10.7282/T3DF6VBD

ETD graduate

The author owns the copyright to this work.