Biophysical Society Thematic Meeting| Lima 2019

Revisiting the Central Dogma of Molecular Biology at the Single-Molecule Level

Poster Abstracts

28-POS Board 28 THREE-DIMENSIONAL HELICOIDAL MESOSCOPIC MODEL FOR DNA WITHIN THE FRAMEWORK OF THE TRANSFER INTEGRAL TECHNIQUE Mateus R. Leal 1 ; Gerald Weber 1 ; 1 Universidade Federal de Minas Gerais, Departamento de Física, Belo Horizonte, Brazil The Peyrard-Bishop model is a two-dimensional physical statistics method proposed in 1989 for calculating thermodynamic properties of DNA and RNA molecules. This model can be used with several theoretical techniques such as molecular dynamics and path integrals, but its main application still lies within the original method which is the transfer-integral technique. It also used to predict hydrogen bonds and stacking interaction in oligonucleotides from melting temperature experiments, complementing experimental techniques such as NRM and X-ray diffraction. One of the key simplifications of the model is to ignore the helical structure of DNA, nevertheless it has been highly successful in predicting melting temperatures and other important properties of DNA. Here, we add the missing helical torsion to the original 2D Hamiltonian while maintaining the existing framework of numerical techniques for solving the classical partition function. We introduce some approximations to avoid an excessive increase in degrees of freedom which would make the problem intractable. This allows us to use the same transfer integral technique for both the 2D and 3D models. The 3D model shows similar anti-crossings in the eigenvalue spectra as the 2D models leading to very sharp increases in the average strand displacement. The approximations introduced in the 3D model were validated by comparing them with the numerical integration of the exact 3D Hamiltonian. With this new 3D approach we are now able to use mesoscopic models to investigate structural properties of DNA such as the helical rise distance and torsion angle from melting temperatures, in the same way as we obtained hydrogen bonds from the 2D model. Funding: Capes, CNPq and Fapemig.

64