3D molecular assembling of B-DNA sequences using nucleotides as building blocks

Unlike the current atomistic DNA models, this paper proposes a new 3D space-filling model for sequences of DNA base pairs using nucleotides, instead of atoms, as building blocks of DNA molecules. This nucleotide-based model is more scalable than the traditional atomistic model, and has the advantage that easily adapts to any topological conformation of DNA. Interestingly, this model also allows the building of the molecular surface of the DNA, either partly or entirely, as needed for energy computations in molecular applications. Moreover, it allows us to grasp the DNA shape at different levels of shape composition: atom, nucleotide, and DNA macromolecule as a whole.

Graphical abstractFigure optionsDownload full-size imageDownload as PowerPoint slideHighlights► We propose a geometric assembling method for B-DNA in 3D space that uses nucleotides instead of atoms as building blocks. ► We propose a generic B-DNA assembling method that adapts to arbitrary topological conformations of DNA. ► We propose a geometric framework capable of combining distinct geometric representations in DNA modeling and visualization.