3D molecular assembling of B-DNA sequences using nucleotides as building blocks q Adriano N. Raposo, Abel J.P. Gomes ⇑ Instituto de Telecomunicações, Universidade da Beira Interior, Portugal article info Article history: Received 4 March 2012 Received in revised form 3 May 2012 Accepted 4 May 2012 Available online 15 May 2012 Keywords: DNA geometry DNA assembling DNA shape composition DNA base stacking DNA conformations Molecular surface Gaussian surface Molecular modeling Biomolecular visualization abstract 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 atomis- tic 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 applica- tions. Moreover, it allows us to grasp the DNA shape at different levels of shape composi- tion: atom, nucleotide, and DNA macromolecule as a whole. Ó 2012 Elsevier Inc. All rights reserved. 1. Introduction Molecular shape determines how most biological molecules recognize and interact to one another. Also, molecular shape can be understood at different levels of abstraction and composition of shape. More specifically, our goal is to speed up the assembling and visualization of DNA molecules using molecular composition of nucleo- tides. Thus, unlike the traditional atomistic model for molecules, the primary building blocks of our DNA model are nucleotides, instead of atoms. In this paper, we deal with only the predominant form of DNA found in cells, the B-form DNA, but there are other forms of DNA [5]. Basically, our model is structured into three levels: atomic level, molecular level, and macromolecular level. In other words, a macromolecule is a set of smaller mole- cules, and in turn a molecule is a set of atoms. Thus, we can say that DNA is a macromolecule composed by a num- ber of nucleotides (i.e., molecules), each one of which holds a collection of overlapping atoms. It is true that molecular composition and visualization based on the assembly mechanism of atoms is useful for small molecules, or even for mid range molecules as pro- teins, but not for macromolecules as DNA that are made up of hundreds of thousands or even millions of atoms. For example, one of the smallest DNA is that one of pUC19 that has about 180,000 atoms (for 2686 base pairs, one base per nucleotide), while the human DNA has about 204 billion atoms (or, equivalently, 3 billion base pairs). Thus, in the case of DNA, we have a clear change of scale because we may have to deal with molecules having hun- dreds of thousands to billions of atoms. In fact, we need coarse grain shape composition tools for DNA in order to enable: 1524-0703/$ - see front matter Ó 2012 Elsevier Inc. All rights reserved. http://dx.doi.org/10.1016/j.gmod.2012.05.001 q This paper has been recommended for acceptance by Jarek Rossignac. ⇑ Corresponding author. Address: Universidade da Beira Interior, Departamento de Informática, Av. Marquês d’ Ávila e Bolama, 6200-001 Covilhã, Portugal. E-mail address: agomes@di.ubi.pt (A.J.P. Gomes). URL: http://www.di.ubi.pt/~agomes (A.J.P. Gomes). Graphical Models 74 (2012) 244–254 Contents lists available at SciVerse ScienceDirect Graphical Models journal homepage: www.elsevier.com/locate/gmod