Computational 3D Assembling Methods for DNA: A Survey

Abstract

DNA encodes the genetic information of most living beings, except viruses that use RNA. Unlike other types of molecules, DNA is not usually described by its atomic structure being instead usually described by its base-pair sequence, i.e., the textual sequence of its subsidiary molecules known as nucleotides ( adenine (A), cytosine (C), guanine (G), and thymine (T)). The three-dimensional assembling of DNA molecules based on its base-pair sequence has been, for decades, a topic of interest for many research groups all over the world. In this paper, we survey the major methods found in the literature to assemble and visualize DNA molecules from their base-pair sequences. We divided these methods into three categories: predictive methods, adaptive methods, and thermodynamic methods . Predictive methods aim to predict a conformation of the DNA from its base pair sequence, while the goal of adaptive methods is to assemble DNA base-pairs sequences along previously known conformations, as needed in scenarios such as DNA Monte Carlo simulations. Unlike these two geometric methods, thermodynamic methods are energy-based and aim to predict secondary structural motifs of DNA in cases where hydrogen bonds between base pairs might be broken because of temperature changes. We also present the major software tools that implements predictive, adaptive, and thermodynamic methods.

Flexibility of short DNA helices under mechanical stretching

“…In general, the strength of the applied force sets the length scale in the single molecule elastic response with larger forces sampling shorter scales, down to the covalent bond distance between adjacent nucleotides along the strands. 13 Groundbreaking experiments on l-phage DNA [14][15][16] have revealed a force versus extension pattern with distinct regimes. In the limit of weak applied forces, the chain extension is lower than L and DNA behaves as a linear spring whose force constant is inversely proportional both to the persistence length (l p ) and to L. By increasing the force in the intermediate regime, more work is done against the random fluctuations of the thermal bath and the DNA behavior becomes progressively non-linear.…”