Carbohydrates play an essential role in a large number of chemical and biochemical processes. High structural diversity and conformational heterogeneity make it problematic to link their measurable properties to molecular features. Molecular dynamics simulations carried out at the level of classical force fields are routinely applied to study the complex processes occurring in carbohydrate-containing systems, while the usefulness of such simulations relies on the accuracy of the underlying theoretical model. In this article, we present the coarse-grained force field dedicated to glucopyranose-based carbohydrates and compatible with the recent version of the Martini force field (v. 3.0). The parameterization was based on optimizing bonded and nonbonded parameters with a reference to the all-atom simulation results and the experimental data. Application of the newly developed coarse-grained carbohydrate model to oligosaccharides curdlan and cellulose displays spontaneous formation of aggregates of experimentally identified features. In contact with other biomolecules, the model is capable of recovering the protective effect of glucose monosaccharides on a lipid bilayer and correctly identifying the binding pockets in carbohydrate-binding proteins. The features of the newly proposed model make it an excellent candidate for further extensions, aimed at modeling more complex, functionalized, and biologically relevant carbohydrates.

This work deals with an analysis of the covalent functionalization of a carbon nanotube using polyethylene glycol chains terminated by folic acid fragments. The analysis is focused on theoretical predictions, using molecular dynamics simulations, of the properties of such constructs as pH controlled carriers of the anticancer drug doxorubicin. The analyzed systems are expected to hold the doxorubicin in the inner cavity of the carbon nanotube at neutral pH and unload the drug at slightly acidic pH. This property comes from incorporation into the nanotube of some dye molecules (p-phenylenediamine or neutral red) which undergo protonation at slightly acidic pH. We found that both dyes lead to the formation of a stable, co-absorbed phase of a doxorubicin–dye mixture inside the nanotube at physiological pH. At acidic pH we observed a spontaneous release of dyes from the nanotube, leading finally to the state with only doxorubicin encapsulated in the nanotube interior. Thus, the analyzed constructs can be considered as carriers of doxorubicin that are selective to tumor microenvironments (which exhibit reduced pH due to hypoxia and overexpression of folate receptors). However, we also found that the release of doxorubicin from the nanotube at acidic pH is kinetically blocked, at least in the case of the system sizes studied here. Thus, we also discussed some possible ways of reducing the activation barriers against doxorubicin release at acidic pH.

Molecular dynamics simulations prove that Congo red adsorption on carbon nanotubes is very strong and by varying pH filling/unfilling of inner cavities of the nanotubes can be accomplished.

This article provides a comprehensive examination of non-canonical DNA structures, particularly focusing on G-quadruplexes (G4s) and i-motifs. G-quadruplexes, four-stranded structures formed by guanine-rich sequences, are stabilized by Hoogsteen hydrogen bonds and monovalent cations like potassium. These structures exhibit diverse topologies and are implicated in critical genomic regions such as telomeres and promoter regions of oncogenes, playing significant roles in gene expression regulation, genome stability, and cellular aging. I-motifs, formed by cytosine-rich sequences under acidic conditions and stabilized by hemiprotonated cytosine–cytosine (C:C+) base pairs, also contribute to gene regulation despite being less prevalent than G4s. This review highlights the factors influencing the stability and dynamics of these structures, including sequence composition, ionic conditions, and environmental pH. Molecular dynamics simulations and high-resolution structural techniques have been pivotal in advancing our understanding of their folding and unfolding mechanisms. Additionally, the article discusses the therapeutic potential of small molecules designed to selectively bind and stabilize G4s and i-motifs, with promising implications for cancer treatment. Furthermore, the structural properties of these DNA forms are explored for applications in nanotechnology and molecular devices. Despite significant progress, challenges remain in observing these structures in vivo and fully elucidating their biological functions. The review underscores the importance of continued research to uncover new insights into the genomic roles of G4s and i-motifs and their potential applications in medicine and technology. This ongoing research promises exciting developments in both basic science and applied fields, emphasizing the relevance and future prospects of these intriguing DNA structures.