[SY-H8] Modeling and Simulation of DNA Foldback Intercoil Structure
Invited
The stem-loop foldback intercoil (FBI) DNA is one of unique four-stranded DNA structures. Its intercoil stem region is constructed by interwinding DNA duplexes in their major groove. Although the FBI DNA is closely related with DNA homologous recombination, inversion, and deletion process, its structural and dynamic characteristics have not been yet revealed. In this study, we create a 3D FBI computer model based on homologous and palindromic DNA base sequences and its structural validity is confirmed by a variety of topological comparison with B-DNA including its diameter and helicity such as 22 angstrom and 10.5 base pairs per turn, respectively. Then, its dynamic features are investigated by normal mode analysis (NMA). NMA results show that the stem part has more rigidity compared to the other parts during the major bending and twisting motions. It is also cross-validated by the AFM experiment in which the height different of stem part is apparently measured. In addition, the DNA homologous recombination phenomenon is observed by using molecular dynamics simulation (MD) in atomic details. MD results imply that homologous recombination of the DNA FBI structure is triggered by base flipping of the stem region resulting in B-Z DNA junctions at the interface between stem and loop. Consequently, this computational modelling and simulation study enables us to better understand both structural and biological features of the FBI DNA.