- Tetramer-Dependent Elastic Energy Model for DNA Conformation
- Project Year:
2021
- REU Student (s):
Zoe Wefers | McGill University
- Student 1 Institution:
McGill Univers
- Project Mentor:
Wilma Olson
- Project Mentor Area:
Chemistry and Chemical Biology
- Project Abstract:
DNA folding plays an important role in gene regulation and genome packaging. The ability for a piece of DNA to bend is largely impacted by the elastic energy stored between base pairs in a segment of DNA. There are well-established techniques to mathematically model the elastic energy of a collection of DNA base pairs. It has long been known that the intrinsic elasticity parameters of DNA are sequence-dependent, but past work only models DNA folding using elasticity parameters that are specific to dimers, a sequence of two base pairs. Recent studies have suggested the intrinsic elasticity parameters of DNA are actually unique to tetramers, a sequence of four base pairs. We present software that can simulate DNA folding by optimizing elastic energy using tetrameric steps. With this new software, we optimized the configuration of DNA minicircles and confirmed that increasing the scope of sequence dependence from dimers to tetramers has an effect on DNA conformation.
