Knowing the precise locations of nucleosomes in a genome is key to understanding how genes are regulated. We investigate the correlation of sequence complexity and DNA structure by using a prevailing model of DNA curvature prediction and recent experimental data on sequence curvature affinity. We reproduced the curvature experimental results with state-of-the-art atomistic simulations (MOSAICS) and found correlations across universal measures of complexity ranging from classical information to algorithmic complexity, in agreement with literature on regulation dependence of DNA curvature similar and beyond GC-content prediction. We validated these ideas with experimentally validated data of nucleosome occupancy from a Yeast chromosome thereby potentially contributing to positioning prediction. We introduce methods and tools written in a software library for DNA conformational analysis written in the Wolfram Language as an interface between the atomistic simulation soft ware and mainstream DNA structural analysis software (3DNA and Curves+) for the analysis of local and global properties of nucleic acids.
Code and paper here
Flow chart of experimental setting from linear sequence to re construction of 3D structure (mainly curvature) through simulation, comparison, calibration, validation from two experiments that can be seen as undertaken separately (atomistic simulation and Dinucleotide Wedge modelling) suggest a common validation with nucleosome occupancy leading to the identification of candidate measures for positioning prediction betterthan GC-content alone.
MOSIACS
MOSAICS is a software package THAT offers a rich variety of user defined coordinates (degrees of freedom or DoF) in combination with a variety of conformational sampling algorithms (e.g. Multicanonical Markov Chain Monte Carlo) guiding the exploration of the conformational space. The most unique feature of MOSAICS is Hierarchical Nature Move Monte Carlo (see below) with primary application areas on the atomistic modelling of nucleic acids (DNA and RNA). It is compatible with most of the widely used empirical all-atom energy functions and statistical (knowledge based) potentials. For proteins the recommended use is one of the available coarse-grained models
pymol:
PyMOL is a user-sponsored molecular visualization system on an open-source foundation, maintained and distributed by Schrödinger.
x3dna
x3dna is a Suite of programs to analyze, rebuild, and visualize three-dimensional nucleic-acid structures. The software determines a wide range of conformational parameters, including the identities and rigid-body parameters of interacting bases and base-pair steps, the nucleotides comprising helical fragments, the area of overlap of stacked bases, etc.
Curves+
Curves+, a revised version of the Curves software for analyzing the conformation of nucleic acid structures, allows the user to upload a nucleic acid structure file, choose the nucleotides to be analyzed and after optionally setting a number of input variables, view the numerical and graphic results online or download files containing a set of helical, backbone and groove parameters that fully describe the structure.