Seminarium z fizyki biologicznej i bioinformatyki

CryoEM imaging of 336bp DNA minicircles by Irobalieva et al (2015) showed a diversity of attained shapes, leading to twist-dependent hydrodynamic properties. Variability of drag coefficients of the samples curtails the use of analytic techniques (gel electrophoresis, analytic ultracentrifugation, FCS) to investigate biochemical interactions of DNA loops with enzymes. For the interpretation of experimental values, we propose a model able of capturing both elastic and hydrodynamic effects. Our two-stage approach starts with finding shapes of minimum elastic energy followed by using an overlapping bead representation to compute hydrodynamic properties. By separating the hydrodynamic and elastic consideration, we simplify the calculations considerably without compromising the accuracy.