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Single-Molecule Visualization of BLM-DNA2-Mediated DNA End Resection Using DNA Curtains.

Methods Mol Biol

December 2024

Department of Biochemistry & Molecular Biophysics, Columbia University, New York, NY, USA.

Homologous recombination (HR) is the principal pathway undertaken by a cell for the error-free repair of DNA double-strand breaks that are frequently encountered by the cell. HR can be initiated at the sites of DNA double-strand breaks by generating long stretches of single-stranded 3' DNA overhang through a process called DNA end resection. In one DNA end resection pathway, this is achieved via the concerted effort of specialized machinery involving the RecQ family helicase BLM, the helicase/endonuclease DNA2, and a single-strand DNA binding protein complex RPA.

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Single-molecule techniques allow researchers to investigate individual molecules and obtain unprecedented details of the heterogeneous nature of biological entities. They play instrumental roles in studying DNA-protein interactions due to the ability to visualize DNA or proteins and to manipulate individual DNA molecules by applying force or torque. Here, we describe single-molecule DNA-flow stretching assays as hybrid tools that combine forces with fluorescence.

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Biofouling sponges as natural eDNA samplers for marine vertebrate biodiversity monitoring.

Sci Total Environ

October 2024

School of Biological & Environmental Sciences, Liverpool John Moores University, Liverpool L3 3AF, UK. Electronic address:

Environmental DNA (eDNA) analysis has now become a core approach in marine biodiversity research, which typically involves the collection of water or sediment samples. Yet, recently, filter-feeding organisms have received much attention for their potential role as natural eDNA samplers. While the indiscriminate use of living organisms as 'sampling tools' might in some cases raise conservation concerns, there are instances in which highly abundant sessile organisms may become a nuisance as biofouling on artificial marine structures.

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Chromatin is an epigenetic platform for implementation of DNA-dependent processes. Nucleosome, as a basic level of chromatin compaction, largely determines its properties and structure. In the study of nucleosomes structure and functions physicochemical tools are actively used, such as magnetic and optical "tweezers", "DNA curtains", nuclear magnetic resonance, X-ray crystallography, and cryogenic electron microscopy, as well as optical methods based on Förster resonance energy transfer.

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DNA curtains for studying phase separation mechanisms of DNA-organizing proteins.

Methods Cell Biol

February 2024

Gene Center Munich, Ludwig Maximilian University, Munich, Germany. Electronic address:

Phase separation is one key mechanism to organize chromatin into compartments and to regulate the activity of the genome. The formation of liquid-like droplets within the nucleus is driven by protein association to the DNA via multivalent binding and the recruitment of other proteins building a concentrated reaction environment. Common methods to study phase separation and its liquid-like nature are based on microscopy of the formed droplets but lack the resolution to obtain information on the molecular level.

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