Atomistic insight into sequencedirected DNA bending and minicircle formation propensity in the absence and presence of phased Atracts Bending of doublestranded (ds) DNA plays a crucial role in many important biological processes and is relevant for nanotechnological applications. Among all the elements that have been studied in relation to dsDNA bending, Atracts stand out as one of the most controversial. The xe2x80x9cApA wedgexe2x80x9d theory was disproved when a series of linear polynucleotides containing phased 5xe2x80xb2A4T43xe2x80xb2 or 5xe2x80xb2T4A43xe2x80xb2 runs were shown to be bent or straight, respectively, and crystallographic evidence revealed that Atracts are unbent. Furthermore, some of the smallest dsDNA minicircles described to date ( 100 bp in size) lack Atracts and are subjected to varying levels of torsional stress. Representative DNA sequences from this experimental background were modeled in atomic detail and their dynamic behavior was simulated over hundreds of nanoseconds using the AMBER force field ParmBSC1. Subsequent analysis of the resulting trajectories allowed us to (i) unambiguously establish the location of the bends in all cases; (ii) identify the structural elements that are directly responsible for the macroscopically detected curvature; and (iii) reveal the importance not only of coherently summing the effects of the bending elements when they are in synchrony with the natural repeat of the helix (i.e. separated by an integral number of helical turns) but also when alternated with a halfintegral separation of opposite effects. We conclude that the major determinant of the macroscopically observed bending is the proper grouping and phasing of the positive roll imposed by pyrimidinepurine (YR) steps and the negative or null roll characteristic of RY steps and Atracts, respectively. This conclusion is in very good agreement with the structural parameters experimentally derived for much smaller DNA molecules either alone or as found in DNAxe2x80x93protein complexes. We expect that this work will pave the way for future studies on druginduced DNA bending, DNA shape readout by transcription factors, structure of circular extrachromosomal DNA, and custom design of curved DNA origami scaffolds.

Computational Generation of Polymer Chains For the development of polymeric amorphous materials with desired properties new algorithms are needed to help in the process of rationalizing the relationship between the atomic structure and the macroscopic observables. Even though numerical simulations, such as Molecular Dynamics, have become an efficient tool for giving a detailed description of the structural changes in atomic arrangements under different temperature and pressure, the computation time that can be simulated are below the time span of relevant physical and chemical phenomena. In this work an algorithm to replicate the equilibrium structure in linear homopolymers is developed. The algorithm focuses on performing local movements of dihedral angles to minimize the total potential energy. The procedure generates chains of arbitrary length in a simulation volume with the constrain of a fixed endtoend radius. Preliminary results show that the algorithm succeed in decreasing the potential energy substantially while approximating the target averaged endtoend radius asymptotically.