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Chromatin is a supramolecular DNA-protein complex that compacts eukaryotic genomes and regulates their accessibility and functions. Dynamically disordered histone H3 N-terminal tails are among key chromatin regulatory components. Here, we used high-resolution-magic-angle-spinning NMR measurements of backbone amide N spin relaxation rates to investigate, with residue-specific detail, the dynamics and interactions of H3 tails in recombinant C,N-enriched nucleosome arrays containing 15, 30, or 60 bp linker DNA between the nucleosome repeats. These measurements were compared to analogous data available for mononucleosomes devoid of linker DNA or containing two 20 bp DNA overhangs. The H3 tail dynamics in nucleosome arrays were found to be considerably attenuated compared with nucleosomes with or without linker DNA due to transient electrostatic interactions with the linker DNA segments and the structured chromatin environment. Remarkably, however, the H3 tail dynamics were not modulated by the specific linker DNA length within the 15-60 bp range investigated here.
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http://dx.doi.org/10.1021/acs.jpclett.1c01187 | DOI Listing |
Anal Chem
September 2025
Laboratory of Organic Chemistry, Department of Chemistry and Applied Biosciences, ETH Zurich, 8093 Zurich, Switzerland.
DNA-encoded libraries have become widely used in drug discovery, and several different setups to link chemical compounds to DNA have been employed in the field, including single-stranded and double-stranded DNA tags as well as a variety of linker chemistries. In our previous study, we observed distinct differences in binding affinities between ligands coupled either to single-stranded or double-stranded DNA; however, the molecular basis for these differences remained unclear. Here, we present a native ion mobility mass spectrometry approach that incorporates gas- and solution-phase activation techniques to systematically investigate these differences, specifically the impact of DNA tags on binding performance in protein-ligand interactions.
View Article and Find Full Text PDFAnal Biochem
September 2025
Department of Chemistry and Biotechnology, Graduate School of Engineering, Tottori University, 4-101 Koyama-Cho Minami, Tottori, 680-8552, Japan.
The duplex-forming behavior of an inchworm-type PNA-PEG conjugate (i-PPc), engineered for the selective recognition of point mutations in DNA, was assessed through thermodynamic analysis employing UV melting curves and circular dichroism spectroscopy. The i-PPc demonstrated the ability to form stable duplexes exclusively with fully complementary DNA sequences, while no hybridization with single-base mismatched sequences. This binary on/off hybridization behavior was maintained even under physiologically relevant conditions (37 °C), thereby illustrating the exceptional point mutation discrimination capability of i-PPc.
View Article and Find Full Text PDFBiophys J
September 2025
Department of Chemistry, 100 Washington Square East, Silver Building, New York University, New York, NY 10003 U.S.A; Courant Institute of Mathematical Sciences, New York University, 251 Mercer St., New York, NY 10012 U.S.A; New York University-East China Normal University Center for Computational Ch
The structural organization of chromatin is intricately influenced by the length of linker DNA connecting nucleosomes. Some studies have suggested that preferred linker lengths include 10n and 10n+5 base pairs values (n = integer). Because these lengths dictate the rotational orientation of successive nucleosomes in the fiber axis, they can markedly affect chromatin fiber compaction and topology.
View Article and Find Full Text PDFProtein Expr Purif
August 2025
Key Laboratory for Food Science & Engineering, Harbin University of Commerce, Harbin, 150028, China. Electronic address:
The DNA polymerase from Thermococcus kodakarensis KOD1 (KOD) is widely utilized in polymerase chain reaction (PCR) due to its high processivity and fidelity. However, like many other B-family DNA polymerases, it faces limitations in extension efficiency, amplicon length, and resistance to PCR inhibitors. In order to further enhance its capability, novel mutants were engineered by fusing a 7 kDa nonspecific double-stranded DNA (dsDNA)-binding protein from Sulfolobus tokodaii (Sto7d) to the C-terminus of KOD via distinct peptide linkers, resulting in a set of KOD-Sto7d polymerase variants.
View Article and Find Full Text PDFOrg Lett
August 2025
Department of Chemistry, Chemistry Research Laboratory, University of Oxford, Oxford OX1 3TA, United Kingdom.
We report the methodology to synthesize nucleic acid dendrons on a solid support via Cu(I)-catalyzed alkyne-azide cycloaddition (CuAAC). Current methods require excess coupling reagents and result in low yields. Our alternative strategy is based on standard solid-phase synthesis followed by 5'-end coupling of a multifunction linker to efficiently afford dendrons.
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