A dynamic view of DNA structure within the nucleosome: Biological implications

Exploring the influence of metal cations on individual hydrogen bonds in Watson-Crick guanine-cytosine DNA base pair: An interacting quantum atoms analysis

This study delves into the nature of individual hydrogen bonds and the relationship between metal cations and hydrogen bonding in the Watson-Crick guanine-cytosine (GC) base pair and its alkali and alkaline earth cation-containing complexes (Mn+-GC). The findings reveal how metal cations affect the nature and strength of individual hydrogen bonds. The study employs interacting quantum atoms (IQA) analysis to comprehensively understand three individual hydrogen bonds within the GC base pair and its cationic derivatives. These analyses unveil the nature and strength of hydrogen bonds and serve as a valuable reference for exploring the impact of cations (and other factors) on each hydrogen bond. All the H⋯ $$ \cdots $$ D interactions (H is hydrogen and D is oxygen or nitrogen) in the GC base pair are primarily electrostatic in nature, with the charge transfer component playing a substantial role. Introducing a metal cation perturbs all H⋯ $$ \cdots $$ D interatomic interactions in the system, weakening the nearest hydrogen bond to the cation (indicated by a) and reinforcing the other (b and c) interactions. Notably, the interaction a, the strongest H⋯ $$ \cdots $$ D interaction in the GC base pair, becomes the weakest in the Mn+-GC complexes. A broader perspective on the stability of GC and Mn+-GC complexes is provided through interacting quantum fragments (IQF) analysis. This approach considers all pairwise interactions between fragments and intra-fragment components, offering a complete view of the factors that stabilize and destabilize GC and Mn+-GC complexes. The IQF analysis underscores the importance of electron sharing, with the dominant contribution arising from the inter-fragment exchange-correlation term, in shaping and sustaining GC and Mn+-GC complexes. From this point of view, alkaline and alkaline earth cations have distinct effects, with alkaline cations generally weakening inter-fragment interactions and alkaline earth cations strengthening them. In addition, IQA and IQF calculations demonstrate that the hydration of cations led to small changes in the hydrogen bonding network. Finally, the IQA interatomic energies associated with the hydrogen bonds and also inter-fragment interaction energies provide robust indicators for characterizing hydrogen bonds and complex stability, showing a strong correlation with total interaction energies.

General Designs Reveal a Purine-Pyrimidine Structural Code in Human DNA

The human genome carries a vast amount of information within its DNA sequences. The chemical bases A, T, C, and G are the basic units of information content, that are arranged into patterns and codes. Expansive areas of the genome contain codes that are not yet well understood. To decipher these, mathematical and computational tools are applied here to study genomic signatures or general designs of sequences. A novel binary components analysis is devised and utilized. This seeks to isolate the physical and chemical properties of DNA bases, which reveals sequence design and function. Here, information theory tools break down the information content within DNA bases, in order to study them in isolation for their genomic signatures and non-random properties. In this way, the RY (purine/pyrimidine), WS (weak/strong), and KM (keto/amino) general designs are observed in the sequences. The results show that RY, KM, and WS components have a similar and stable overall profile across all human chromosomes. It reveals that the RY property of a sequence is most distant from randomness in the human genome with respect to the genomic signatures. This is true across all human chromosomes. It is concluded that there exists a widespread potential RY code, and furthermore, that this is likely a structural code. Ascertaining this feature of general design, and potential RY structural code has far-reaching implications. This is because it aids in the understanding of cell biology, growth, and development, as well as downstream in the study of human disease and potential drug design.

Nucleosome assembly and disassembly pathways in vitro

Structural fluctuations of nucleosomes modulate the access to internal DNA in eukaryotic cells; clearly characterisation of this fundamental process is crucial to understanding gene regulation. Here we apply PhAST (Photochemical Analysis of Structural Transitions) to monitor at a base pair level, structural alterations induced all along the DNA upon histone binding or release. By offering the first reliable, detailed comparison of nucleosome assembly and disassembly in vitro, we reveal similarities and differences between the two processes. We identify multiple, sequential intermediate states characterised by specific PhAST signals whose localisation and amplitude reflect asymmetries of DNA/histone interactions with respect to the nucleosome pseudo dyad. These asymmetries involve not only the DNA extremities but also regions close to the pseudo dyad. Localisations of asymmetries develop in a consistent manner during both assembly and disassembly processes; they primarily reflect the DNA sequence effect on the efficiency of DNA-histone binding. More unexpectedly, the amplitude component of PhAST signals not only evolves as a function of intermediate states but does so differently between assembly and disassembly pathways. Our observation of differences between assembly and disassembly opens up new avenues to define the role of the DNA sequence in processes underlying the regulation of gene expression. Overall, we provide new insights into how the intrinsic properties of DNA are integrated into a holistic mechanism that controls chromatin structure.