Models of chromatin fibers structures with linear regions of linker DNA were analysed. Limitations put by end dimensions of linker DNA and nucleosomes are considered. Good agreement between the structural properties of model and real chromatin fibers was obtained. It has been shown that the models with three and more configurations of closely located nucleosomes have linker DNA of 19-53 base pairs length, which is characteristic of real chromatin of the majority of somatic cells.
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Nucleic Acids Res
January 2025
Guangdong Provincial Key Laboratory of Digestive Cancer Research, Digestive Diseases Center, Scientific Research Center, The Seventh Affiliated Hospital of Sun Yat-sen University, Shenzhen, Guangdong 518107, P.R. China.
CRISPR-Cas12a technology has transformative potential, but as its applications grow, enhancing its inherent functionalities is essential to meet diverse demands. Here, we reveal a regulatory mechanism for LbCas12a through direct repeat (DR) region 3' end modifications and de-modifications, which can regulate LbCas12a's cis- and trans-cleavage activities. We extensively explored the effects of introducing phosphorylation, DNA, photo-cleavable linker, DNA modifications at the DR 3' end on LbCas12a's functionality.
View Article and Find Full Text PDFChemistry
January 2025
Indian Institute of Science Education and Research Thiruvananthapuram, Chemistry, Trivandrum, Trivandrum, Trivandrum, 695551, Trivandrum, INDIA.
Recent years have witnessed the rapid growth of combination therapy for the treatment of cancer. Chemo and antisense DNA therapies are two clinically proven and efficient treatment modalities for cancer. However, direct delivery of both chemo and antisense oligonucleotides into the cancerous cells is challenging and hence there is a high demand for the development of new strategies that permit the direct delivery of chemo and antisense therapeutic agents in a targeted fashion.
View Article and Find Full Text PDFBiopolymers
March 2025
Departmento de Química Inorgánica y Orgánica, Universidad Jaume I, Castellón, Spain.
We report the reversible redox-controlled DNA condensation using a simple dicationic diphenylalanine derivative which contains a disulfide unit as linker. Despite the conventional belief that DNA condensing agents require a charge of +3 or higher, this dicationic molecule functions below its critical aggregation concentration, representing a non-canonical DNA condensing agent. The interaction with DNA of the studied compound combines electrostatic effects with hydrophobic/stacking interactions provided with the diphenylalanine moiety.
View Article and Find Full Text PDFLife Metab
June 2024
Shanghai Key Laboratory of Metabolic Remodeling and Health, Institute of Metabolism and Integrative Biology, Fudan University, Shanghai 200438, China.
Unlabelled: Compartmentalization of the nucleus into heterochromatin and euchromatin is highly conserved across eukaryotes. Constitutive heterochromatin (C-Het) constitutes a liquid-like condensate that packages the repetitive regions of the genome through the enrichment of histone modification H3K9me3 and recruitment of its cognate reader protein Heterochromatin Protein-1 (HP1a). The ability for well-ordered nucleosome arrays and HP1a to independently form biomolecular condensates suggests that the emergent material properties of C-Het compartments may contribute to its functions such as force-buffering, dosage-dependent gene silencing, and selective permeability.
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