Surprising Twists in Nucleosomal DNA with Implication for Higher-order Folding

The Free Energy of Nucleosomal DNA Based on the Landau Model and Topology

The free energy of nucleosomal DNA plays a key role in the formation of nucleosomes in eukaryotes. Some work on the free energy of nucleosomal DNA have been carried out in experiments. However, the relationships between the free energy of nucleosomal DNA and its conformation, especially its topology, remain unclear in theory. By combining the Landau theory, the Hopfion model and experimental data, we find that the free energy of nucleosomal DNA is at the lower level. With the help of the energy minimum principle, we conclude that nucleosomal DNA stays in a stable state. Moreover, we discover that small perturbations on nucleosomal DNA have little effect on its free energy. This implies that nucleosomal DNA has a certain redundancy in order to stay stable. This explains why nucleosomal DNA will not change significantly due to small perturbations.

The effects of RNA.DNA-DNA triple helices on nucleosome structures and dynamics

Noncoding RNAs (ncRNAs) are an emerging epigenetic factor and have been recognized as playing a key role in many gene expression pathways. Structurally, binding of ncRNAs to isolated DNA is strongly dependent on sequence complementary and results in the formation of an RNA.DNA-DNA (RDD) triple helix. However, in vivo DNA is not isolated but is rather packed in chromatin fibers, the fundamental unit of which is the nucleosome. Biochemical experiments have shown that ncRNA binding to nucleosomal DNA is elevated at DNA entry and exit sites and is dependent on the presence of the H3 N-terminal tails. However, the structural and dynamical bases for these mechanisms remain unknown. Here, we have examined the mechanisms and effects of RDD formation in the context of the nucleosome using a series of all-atom molecular dynamics simulations. Results highlight the importance of DNA sequence on complex stability, elucidate the effects of the H3 tails on RDD structures, show how RDD formation impacts the structure and dynamics of the H3 tails, and show how RNA alters the local and global DNA double-helical structure. Together, our results suggest ncRNAs can modify nucleosome, and potentially higher-order chromatin, structures and dynamics as a means of exerting epigenetic control.

Twisting DNA by salt

The structure and properties of DNA depend on the environment, in particular the ion atmosphere. Here, we investigate how DNA twist -one of the central properties of DNA- changes with concentration and identity of the surrounding ions. To resolve how cations influence the twist, we combine single-molecule magnetic tweezer experiments and extensive all-atom molecular dynamics simulations. Two interconnected trends are observed for monovalent alkali and divalent alkaline earth cations. First, DNA twist increases monotonously with increasing concentration for all ions investigated. Second, for a given salt concentration, DNA twist strongly depends on cation identity. At 100 mM concentration, DNA twist increases as Na⁺ < K⁺ < Rb⁺ < Ba²⁺ < Li⁺ ≈ Cs⁺ < Sr²⁺ < Mg²⁺ < Ca²⁺. Our molecular dynamics simulations reveal that preferential binding of the cations to the DNA backbone or the nucleobases has opposing effects on DNA twist and provides the microscopic explanation of the observed ion specificity. However, the simulations also reveal shortcomings of existing force field parameters for Cs⁺ and Sr²⁺. The comprehensive view gained from our combined approach provides a foundation for understanding and predicting cation-induced structural changes both in nature and in DNA nanotechnology.

emDNA - A Tool for Modeling Protein-decorated DNA Loops and Minicircles at the Base-pair Step Level

Computational modeling of nucleic acids plays an important role in molecular biology, enhancing our general understanding of the relationship between structure and function. Biophysical studies have provided a wealth of information on how double-helical DNA responds to proteins and other molecules in its local environment but far less understanding of the larger scale structural responses found in protein-decorated loops and minicircles. Current computational models of DNA range from detailed all-atom molecular dynamics studies, which produce rich time and spatially dependent depictions of small DNA fragments, to coarse-grained simulations, which sacrifice detailed physical and chemical information to treat larger scale systems. The treatment of DNA used here, at the base-pair step level with rigid-body parameters, allows one to develop quality models hundreds of base pairs long from local, sequence-specific features found from experiment. The emDNA software takes advantage of this framework, producing elastically optimized models of DNA at thermal equilibrium with built-in or user-generated elastic models. This versatile program, in combination with case studies included in this article, allows users of any skill level to develop and investigate mesoscale models of their own design. The functionality of emDNA includes a tool to incorporate experiment-specific configurations, e.g. protein-bound and/or melted DNA from known high-resolution structures, within higher-order 3D models by fixing the orientation and position of user-specified base pairs. The software provides a new avenue into multiscale genetic modeling, giving a wide range of users a deeper understanding of DNA mesoscale organization and the opportunity to pose new questions in genetic research. The publicly available emDNA software, including build instructions and usage information, is available on GitHub (https://nicocvn.github.io/emDNA/).