ABSTRACT
Without rigorous theoretical underpinnings, intuitive arguments and phenomenology are often used in modeling complex biological processes. Here, also the level of description depends on length scales. In nucleic acids, at short length scales (l < ∼5 Å), detailed chemical environment determines the basic forces (hydrogen bonds and dispersion forces) between two nucleotides. On the scale l ∼ 1−3 nm interactions between two bases, base stacks and grooves of the nucleic acids become relevant. Understanding how RNA folds (l ∼ 1−3 nm) requires energy functions that provide at least a CG description of nucleotides and interactions between them in the native state and excitations around the folded structure. On the persistence-length scale lp ≈ 150 bp ≈ 50 nm [3] and beyond, it suces to treat double-stranded DNA (dsDNA) as a sti elastic lament without explicitly capturing the base pairs. If l ∼ O(1) μm, dsDNA behaves like a self-avoiding polymer [4]. On the scale of chromosomes (l ∼ mm), a much coarser description suces. us, models for nucleic acids vary because the scale of structural organization changes from nearly mm in chromosome to several nm in the folded states of RNA.
