Predicting and stabilising the 3D structure of aptamers using computational methods

Abstract

The purpose of this dissertation was to predict and stabilise the three-dimensional (3D) structure of aptamers. The focus was in the area of bioinformatics. A guideline was provided on how to obtain 3D images of aptamers, predict the binding site and stabilise the aptamer’s structures. Such a study is of importance to facilitate in vivo experiments by using computational methods to determine if stabilising agents and shortened aptamer sequences interfere with the predicted binding site. Research methods included a literature search and creating a protocol on which software and webserver to use, combined with the collection and analysis of figures. The 2D (two dimensional) structures were obtained through Mfold alongside RNAComposer to obtain the PDB file containing the predicted 3D structure. The aptamer’s 3D structures were visualised with YASARA, PyMOL and Chimera. The findings provided evidence that shortening the aptamer’s sequence stabilised the structures. The predicted binding sites show that the ligand binds in the stem-loop region. The main conclusions drawn from this project were that computational methods can be used to analyse and gain insight into 3D aptamer structures. Some common challenges and technological difficulties, such as modifying an aptamer, were discussed. This project recommended Mfold to be used to obtain the secondary structure of aptamers, whereas for the tertiary structure PyMOL and YASARA were the easiest to navigate in providing a clear and detailed structure.