The thermodynamics of DNA loop formation, from J to Z

2013 ◽  
Vol 41 (2) ◽  
pp. 513-518 ◽  
Author(s):  
Stephen D. Levene ◽  
Stefan M. Giovan ◽  
Andreas Hanke ◽  
Massa J. Shoura
Keyword(s):  
Dna Looping ◽  
Biological Processes ◽  
Loop Formation ◽  
Base Pairs ◽  
Dna Molecule ◽  
Dna Loop ◽  
Sensitive Function ◽  
Statistical Mechanical ◽  
Single Dna Molecule ◽  
Dna Cyclization

The formation of DNA loops is a ubiquitous theme in biological processes, including DNA replication, recombination and repair, and gene regulation. These loops are mediated by proteins bound at specific sites along the contour of a single DNA molecule, in some cases many thousands of base pairs apart. Loop formation incurs a thermodynamic cost that is a sensitive function of the length of looped DNA as well as the geometry and elastic properties of the DNA-bound protein. The free energy of DNA looping is logarithmically related to a generalization of the Jacobson–Stockmayer factor for DNA cyclization, termed the J factor. In the present article, we review the thermodynamic origins of this quantity, discuss how it is measured experimentally and connect the macroscopic interpretation of the J factor with a statistical-mechanical description of DNA looping and cyclization.

scholarly journals A major role for Eco1 in regulating cohesin-mediated mitotic chromosome folding

2019 ◽  
Author(s):  
Lise Dauban ◽  
Rémi Montagne ◽  
Agnès Thierry ◽  
Luciana Lazar-Stefanita ◽  
Olivier Gadal ◽  
...  
Keyword(s):  
Mitotic Chromosome ◽  
Dna Looping ◽  
Loop Formation ◽  
Dna Loops ◽  
Sister Chromatids ◽  
Topologically Associating Domains ◽  
Dna Loop ◽  
Main Barrier ◽  
Structural Maintenance Of Chromosomes ◽  
Mitotic Chromatin

AbstractUnderstanding how chromatin organizes spatially into chromatid and how sister chromatids are maintained together during mitosis is of fundamental importance in chromosome biology. Cohesin, a member of the Structural Maintenance of Chromosomes (SMC) complex family, holds sister chromatids together 1–3 and promotes long-range intra-chromatid DNA looping 4,5. These cohesin-mediated DNA loops are important for both higher-order mitotic chromatin compaction6,7 and, in some organisms, compartmentalization of chromosomes during interphase into topologically associating domains (TADs) 8,9. Our understanding of the mechanism(s) by which cohesin generates large DNA loops remains incomplete. It involves a combination of molecular partners and active expansion/extrusion of DNA loops. Here we dissect the roles on loop formation of three partners of the cohesin complex: Pds5 10, Wpl1 11 and Eco1 acetylase 12, during yeast mitosis. We identify a new function for Eco1 in negatively regulating cohesin translocase activity, which powers loop extrusion. In the absence of negative regulation, the main barrier to DNA loop expansion appears to be the centromere. Those results provide new insights on the mechanisms regulating cohesin dependent DNA looping.

DNA loop extrusion by human cohesin

Science ◽  
2019 ◽  
Vol 366 (6471) ◽  
pp. 1338-1345 ◽  
Author(s):  
Iain F. Davidson ◽  
Benedikt Bauer ◽  
Daniela Goetz ◽  
Wen Tang ◽  
Gordana Wutz ◽  
...  
Keyword(s):  
Gene Regulation ◽  
Atpase Activity ◽  
Chromatin Structure ◽  
Adenosine Triphosphatase ◽  
Gene Recombination ◽  
Loop Formation ◽  
Base Pairs ◽  
Topologically Associating Domains ◽  
Dna Loop ◽  
Eukaryotic Genomes

Eukaryotic genomes are folded into loops and topologically associating domains, which contribute to chromatin structure, gene regulation, and gene recombination. These structures depend on cohesin, a ring-shaped DNA-entrapping adenosine triphosphatase (ATPase) complex that has been proposed to form loops by extrusion. Such an activity has been observed for condensin, which forms loops in mitosis, but not for cohesin. Using biochemical reconstitution, we found that single human cohesin complexes form DNA loops symmetrically at rates up to 2.1 kilo–base pairs per second. Loop formation and maintenance depend on cohesin’s ATPase activity and on NIPBL-MAU2, but not on topological entrapment of DNA by cohesin. During loop formation, cohesin and NIPBL-MAU2 reside at the base of loops, which indicates that they generate loops by extrusion. Our results show that cohesin and NIPBL-MAU2 form an active holoenzyme that interacts with DNA either pseudo-topologically or non-topologically to extrude genomic interphase DNA into loops.

scholarly journals Facilitation of DNA loop formation by protein–DNA non-specific interactions

Soft Matter ◽  
2019 ◽  
Vol 15 (26) ◽  
pp. 5255-5263 ◽  
Author(s):  
Jaeoh Shin ◽  
Anatoly B. Kolomeisky
Keyword(s):  
Specific Protein ◽  
Dna Looping ◽  
Specific Interactions ◽  
Loop Formation ◽  
Dna Interactions ◽  
Dna Loop ◽  
Protein Dna Interactions

DNA looping is facilitated by non-specific protein–DNA interactions.

scholarly journals Fork pausing allows centromere DNA loop formation and kinetochore assembly

2018 ◽  
Vol 115 (46) ◽  
pp. 11784-11789 ◽  
Author(s):  
Diana M. Cook ◽  
Maggie Bennett ◽  
Brandon Friedman ◽  
Josh Lawrimore ◽  
Elaine Yeh ◽  
...  
Keyword(s):  
Replication Fork ◽  
De Novo ◽  
Directed Assembly ◽  
Thermal Fluctuations ◽  
Dna Looping ◽  
Loop Formation ◽  
Replication Fork Progression ◽  
Kinetochore Assembly ◽  
Dna Loop ◽  
Fork Stalling

De novo kinetochore assembly, but not template-directed assembly, is dependent on COMA, the kinetochore complex engaged in cohesin recruitment. The slowing of replication fork progression by treatment with phleomycin (PHL), hydroxyurea, or deletion of the replication fork protection protein Csm3 can activate de novo kinetochore assembly in COMA mutants. Centromere DNA looping at the site of de novo kinetochore assembly can be detected shortly after exposure to PHL. Using simulations to explore the thermodynamics of DNA loops, we propose that loop formation is disfavored during bidirectional replication fork migration. One function of replication fork stalling upon encounters with DNA damage or other blockades may be to allow time for thermal fluctuations of the DNA chain to explore numerous configurations. Biasing thermodynamics provides a mechanism to facilitate macromolecular assembly, DNA repair, and other nucleic acid transactions at the replication fork. These loop configurations are essential for sister centromere separation and kinetochore assembly in the absence of the COMA complex.

scholarly journals Kinetics of DNA looping by Anabaena sensory rhodopsin transducer (ASRT) by using DNA cyclization assay

2021 ◽  
Vol 11 (1) ◽  
Author(s):  
Jae Jin Lee ◽  
Sung Hyun Kim ◽  
Keon Ah Lee ◽  
Kimleng Chuon ◽  
Kwang-Hwan Jung ◽  
...  
Keyword(s):  
Gene Regulation ◽  
Single Molecule ◽  
Essential Role ◽  
Molecular Structures ◽  
Dna Looping ◽  
Loop Formation ◽  
Sensory Rhodopsin ◽  
Single Molecule Fret ◽  
Dna Cyclization ◽  
Kinetics Of

AbstractDNA cyclization assay together with single-molecule FRET was employed to monitor protein-mediated bending of a short dsDNA (~ 100 bp). This method provides a simple and easy way to monitor the structural change of DNA in real-time without necessitating prior knowledge of the molecular structures for the optimal dye-labeling. This assay was applied to study how Anabaena sensory rhodopsin transducer (ASRT) facilitates loop formation of DNA as a possible mechanism for gene regulation. The ASRT-induced DNA looping was maximized at 50 mM of Na+, while Mg2+ also played an essential role in the loop formation.

The elastic theory of a single DNA molecule

Pramana ◽  
2003 ◽  
Vol 61 (2) ◽  
pp. 353-360
Author(s):  
Haijun Zhou ◽  
Yang Zhang ◽  
Zhang-Can Ou-Yang
Keyword(s):  
Elastic Theory ◽  
Dna Molecule ◽  
Single Dna Molecule

Label-free plasmonic assisted optical trapping of single DNA molecule

2021 ◽  
Author(s):  
Lei Chen ◽  
Wei Liu ◽  
Dongyi Shen ◽  
Zhihao Zhou ◽  
Yuehan Liu ◽  
...  
Keyword(s):  
Optical Trapping ◽  
Label Free ◽  
Dna Molecule ◽  
Single Dna Molecule

Analysis of an origin of DNA amplification in Sciara coprophila by a novel three-dimensional gel method

1994 ◽  
Vol 14 (2) ◽  
pp. 1520-1529
Author(s):  
C Liang ◽  
S A Gerbi
Keyword(s):  
Three Dimensional ◽  
Dna Amplification ◽  
Gel Method ◽  
Dna Molecule ◽  
Cutting Out ◽  
Origin Region ◽  
2D Gel ◽  
Third Dimension ◽  
Single Dna Molecule ◽  
Replication Intermediates

The replication origin region for DNA amplification in Sciara coprophila DNA puff II/9A was analyzed with a novel three-dimensional (3D) gel method. Our 3D gel method involves running a neutral/neutral 2D gel and then cutting out vertical gel slices from the area containing replication intermediates, rotating these slices 90 degrees to form the third dimension, and running an alkaline gel for each of the slices. Therefore, replication intermediates are separated into forks and bubbles and then are resolved into parental and nascent strands. We used this technique to determine the size of forks and bubbles and to confirm the location of the major initiation region previously mapped by 2D gels to a 1-kb region. Furthermore, our 3D gel analyses suggest that only one initiation event in the origin region occurs on a single DNA molecule and that the fork arc in the composite fork-plus-bubble pattern in neutral/neutral 2D gels does not result from broken bubbles.

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