Sequence Dependent Elasticity of DNA

The DNA contained in every living cell not only stores the genetic information; it functions in a complex molecular network that can condense, transcribe, replicate and repair genes. The essential role played by the sequence dependent structure and deformability of DNA in these basic processes of life, has received increasing attention over the past years. The present work aims at better understanding sequence dependent elasticity of double stranded DNA elasticity, across biologically relevant length scales. A theoretical description is developed that makes is possible to relate structural, biochemical and biophysical experiments and simulation. It is based on the rigid base–pair chain (rbc) model which captures all basic deformation modes on the scale of individual base–pair (bp) steps. Existing microscopic parametrizations of the rbc model rely on indirect methods. A way to relate them to biochemical experiments is provided by the indirect readout mechanism, where DNA elasticity determines protein–DNA complexation affinities. By correlating theoretical affinity predictions with in vitro measurements in a well–studied test case, different parameter sets were evaluated. As a result a new, hybrid parameter set is proposed which greatly reduces prediction errors. Indirect readout occurs mostly at particular binding subsites in a complex. A statistical marker is developed which localizes indirect readout subsites, by detecting elastically optimized sub-sequences. By a systematic coarse–graining of the rbc to the well–characterized worm–like chain (wlc) model, a quantitative connection between microscopic and kbp scale elasticity is established. The general helical rbc geometry is mapped to an effective, linear ‘on-axis’ version, yielding the full set of wlc elastic parameters for any given sequence repeat. In the random sequence case, structural variability adds conformational fluctuations which are correlated by sequence continuity. The sequence disorder correction to entropic elasticity in the rbc model is shown to coincide with the conformational correction. The results show remarkable overall agreement of the coarse–grained with the mesoscale wlc parameters, lending support to the model and to the microscopic parameter sets. A continuum version of the rbc is formulated as Brownian motion on the rigid motion group. Analytic expressions for angular correlation functions and moments of the end–to–end distance distribution are given. In an equivalent Lagrangian approach, conserved quantities along, and the linear response around, a general equilibrium shape are explored.