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Journal articles on the topic 'DNA looping'

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Published: 10 December 2022
Last updated: 28 January 2023

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1

Schleif, Robert. "DNA Looping." Annual Review of Biochemistry 61, no. 1 (June 1992): 199–223. http://dx.doi.org/10.1146/annurev.bi.61.070192.001215.

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2

Schleif, R. "DNA looping." Science 240, no. 4849 (April 8, 1988): 127–28. http://dx.doi.org/10.1126/science.3353710.

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3

Matthews, K. S. "DNA looping." Microbiological Reviews 56, no. 1 (1992): 123–36. http://dx.doi.org/10.1128/mmbr.56.1.123-136.1992.

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4

Matthews, K. S. "DNA looping." Microbiological Reviews 56, no. 1 (1992): 123–36. http://dx.doi.org/10.1128/mr.56.1.123-136.1992.

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5

Travers, Andrew. "DNA Topology: Dynamic DNA Looping." Current Biology 16, no. 19 (October 2006): R838—R840. http://dx.doi.org/10.1016/j.cub.2006.08.070.

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6

Perez, Pamela, Nicolas Clauvelin, Michael Grosner, Andrew Colasanti, and Wilma Olson. "What Controls DNA Looping?" International Journal of Molecular Sciences 15, no. 9 (August 27, 2014): 15090–108. http://dx.doi.org/10.3390/ijms150915090.

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7

Halford, Stephen E., Abigail J. Welsh, and Mark D. Szczelkun. "Enzyme-Mediated DNA Looping." Annual Review of Biophysics and Biomolecular Structure 33, no. 1 (June 9, 2004): 1–24. http://dx.doi.org/10.1146/annurev.biophys.33.110502.132711.

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8

Crellin, Paul, Sven Sewitz, and Ronald Chalmers. "DNA Looping and Catalysis." Molecular Cell 13, no. 4 (February 2004): 537–47. http://dx.doi.org/10.1016/s1097-2765(04)00052-8.

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9

Carter, Ashley R., Obinna A. Ukogu, Adam D. Smith, Luka M. Devenica, Ryan McMillan, Yuxing Ma, and Hilary Bediako. "Protamin-Induced DNA Looping." Biophysical Journal 114, no. 3 (February 2018): 443a—444a. http://dx.doi.org/10.1016/j.bpj.2017.11.2452.

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10

Hao, Nan, Adrienne E. Sullivan, Keith E. Shearwin, and Ian B. Dodd. "The loopometer: a quantitative in vivo assay for DNA-looping proteins." Nucleic Acids Research 49, no. 7 (January 28, 2021): e39-e39. http://dx.doi.org/10.1093/nar/gkaa1284.

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Abstract Proteins that can bring together separate DNA sites, either on the same or on different DNA molecules, are critical for a variety of DNA-based processes. However, there are no general and technically simple assays to detect proteins capable of DNA looping in vivo nor to quantitate their in vivo looping efficiency. Here, we develop a quantitative in vivo assay for DNA-looping proteins in Escherichia coli that requires only basic DNA cloning techniques and a LacZ assay. The assay is based on loop assistance, where two binding sites for the candidate looping protein are inserted internally to a pair of operators for the E. coli LacI repressor. DNA looping between the sites shortens the effective distance between the lac operators, increasing LacI looping and strengthening its repression of a lacZ reporter gene. Analysis based on a general model for loop assistance enables quantitation of the strength of looping conferred by the protein and its binding sites. We use this ‘loopometer’ assay to measure DNA looping for a variety of bacterial and phage proteins.
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11

Hao, Nan, Kim Sneppen, Keith E. Shearwin, and Ian B. Dodd. "Efficient chromosomal-scale DNA looping in Escherichia coli using multiple DNA-looping elements." Nucleic Acids Research 45, no. 9 (February 4, 2017): 5074–85. http://dx.doi.org/10.1093/nar/gkx069.

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12

Shin, Jaeoh, and Anatoly B. Kolomeisky. "Facilitation of DNA loop formation by protein–DNA non-specific interactions." Soft Matter 15, no. 26 (2019): 5255–63. http://dx.doi.org/10.1039/c9sm00671k.

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13

Brennan, Lucy D., Robert A. Forties, Smita S. Patel, and Michelle D. Wang. "DNA Looping Mediates Nucleosome Transfer." Biophysical Journal 112, no. 3 (February 2017): 513a. http://dx.doi.org/10.1016/j.bpj.2016.11.2774.

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14

Baumann, Kim. "Looping smoothens repetitive DNA replication." Nature Reviews Molecular Cell Biology 17, no. 6 (May 5, 2016): 332. http://dx.doi.org/10.1038/nrm.2016.61.

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15

Roscoe, Donna M., Ashwin Balaji, Luka Matej Devenica, and Ashley Carter. "DNA Looping by Multivalent Cations." Biophysical Journal 118, no. 3 (February 2020): 476a. http://dx.doi.org/10.1016/j.bpj.2019.11.2640.

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16

Wu, Hai-Young, and Leroy F. Liu. "DNA looping alters local DNA conformation during transcription." Journal of Molecular Biology 219, no. 4 (June 1991): 615–22. http://dx.doi.org/10.1016/0022-2836(91)90658-s.

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17

Lin, Xingcheng, Rachel Leicher, Shixin Liu, and Bin Zhang. "Cooperative DNA looping by PRC2 complexes." Nucleic Acids Research 49, no. 11 (May 31, 2021): 6238–48. http://dx.doi.org/10.1093/nar/gkab441.

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Abstract Polycomb repressive complex 2 (PRC2) is an essential protein complex that silences gene expression via post-translational modifications of chromatin. This paper combined homology modeling, atomistic and coarse-grained molecular dynamics simulations, and single-molecule force spectroscopy experiments to characterize both its full-length structure and PRC2-DNA interactions. Using free energy calculations with a newly parameterized protein-DNA force field, we studied a total of three potential PRC2 conformations and their impact on DNA binding and bending. Consistent with cryo-EM studies, we found that EZH2, a core subunit of PRC2, provides the primary interface for DNA binding, and its curved surface can induce DNA bending. Our simulations also predicted the C2 domain of the SUZ12 subunit to contact DNA. Multiple PRC2 complexes bind with DNA cooperatively via allosteric communication through the DNA, leading to a hairpin-like looped configuration. Single-molecule experiments support PRC2-mediated DNA looping and the role of AEBP2 in regulating such loop formation. The impact of AEBP2 can be partly understood from its association with the C2 domain, blocking C2 from DNA binding. Our study suggests that accessory proteins may regulate the genomic location of PRC2 by interfering with its DNA interactions.
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18

Zhang, Yongli, Abbye E. McEwen, Donald M. Crothers, and Stephen D. Levene. "Statistical-Mechanical Theory of DNA Looping." Biophysical Journal 90, no. 6 (March 2006): 1903–12. http://dx.doi.org/10.1529/biophysj.105.070490.

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19

Becker, Nicole A., Tanya L. Schwab, Karl J. Clark, and L. James Maher. "Engineering DNA Looping in E. Coli." Biophysical Journal 112, no. 3 (February 2017): 68a. http://dx.doi.org/10.1016/j.bpj.2016.11.411.

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20

Amitai, Assaf, Ivan Kupka, and David Holcman. "The Mean Looping Time of DNA." Biophysical Journal 100, no. 3 (February 2011): 76a. http://dx.doi.org/10.1016/j.bpj.2010.12.623.

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21

Le, Tung, and Harold Kim. "Measuring Sequence-Dependent DNA Looping Kinetics." Biophysical Journal 102, no. 3 (January 2012): 276a. http://dx.doi.org/10.1016/j.bpj.2011.11.1522.

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22

Riehn, Robert, and Maedeh Heidarpour-Roushan. "DNA Looping Induced by Tubular Confinement." Biophysical Journal 104, no. 2 (January 2013): 253a—254a. http://dx.doi.org/10.1016/j.bpj.2012.11.1425.

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23

Vemulapalli, Sridhar, Mohtadin Hashemi, Anatoly B. Kolomeisky, and Yuri L. Lyubchenko. "DNA Looping Mediated by Site-Specific SfiI–DNA Interactions." Journal of Physical Chemistry B 125, no. 18 (April 29, 2021): 4645–53. http://dx.doi.org/10.1021/acs.jpcb.1c00763.

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24

AIBA, Hiroji. "DNA bending and DNA looping induced by regulatory proteins." Seibutsu Butsuri 29, no. 1 (1989): 18–24. http://dx.doi.org/10.2142/biophys.29.18.

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25

Yan, Yan, Wenxuan Xu, Sandip Kumar, Alexander Zhang, Fenfei Leng, David Dunlap, and Laura Finzi. "Negative DNA supercoiling makes protein-mediated looping deterministic and ergodic within the bacterial doubling time." Nucleic Acids Research 49, no. 20 (November 1, 2021): 11550–59. http://dx.doi.org/10.1093/nar/gkab946.

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Abstract Protein-mediated DNA looping is fundamental to gene regulation and such loops occur stochastically in purified systems. Additional proteins increase the probability of looping, but these probabilities maintain a broad distribution. For example, the probability of lac repressor-mediated looping in individual molecules ranged 0–100%, and individual molecules exhibited representative behavior only in observations lasting an hour or more. Titrating with HU protein progressively compacted the DNA without narrowing the 0–100% distribution. Increased negative supercoiling produced an ensemble of molecules in which all individual molecules more closely resembled the average. Furthermore, in only 12 min of observation, well within the doubling time of the bacterium, most molecules exhibited the looping probability of the ensemble. DNA supercoiling, an inherent feature of all genomes, appears to impose time-constrained, emergent behavior on otherwise random molecular activity.
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26

Anderson, Marybeth, Julian Haase, Elaine Yeh, and Kerry Bloom. "Function and Assembly of DNA Looping, Clustering, and Microtubule Attachment Complexes within a Eukaryotic Kinetochore." Molecular Biology of the Cell 20, no. 19 (October 2009): 4131–39. http://dx.doi.org/10.1091/mbc.e09-05-0359.

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The kinetochore is a complex protein–DNA assembly that provides the mechanical linkage between microtubules and the centromere DNA of each chromosome. Centromere DNA in all eukaryotes is wrapped around a unique nucleosome that contains the histone H3 variant CENP-A (Cse4p in Saccharomyces cerevisiae). Here, we report that the inner kinetochore complex (CBF3) is required for pericentric DNA looping at the Cse4p-containing nucleosome. DNA within the pericentric loop occupies a spatially confined area that is radially displaced from the interpolar central spindle. Microtubule-binding kinetochore complexes are not involved in pericentric DNA looping but are required for the geometric organization of DNA loops around the spindle microtubules in metaphase. Thus, the mitotic segregation apparatus is a composite structure composed of kinetochore and interpolar microtubules, the kinetochore, and organized pericentric DNA loops. The linkage of microtubule-binding to centromere DNA-looping complexes positions the pericentric chromatin loops and stabilizes the dynamic properties of individual kinetochore complexes in mitosis.
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27

Lobell, R., and R. Schleif. "DNA looping and unlooping by AraC protein." Science 250, no. 4980 (October 26, 1990): 528–32. http://dx.doi.org/10.1126/science.2237403.

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28

Rutkauskas, D., H. Zhan, K. S. Matthews, F. S. Pavone, and F. Vanzi. "Tetramer opening in LacI-mediated DNA looping." Proceedings of the National Academy of Sciences 106, no. 39 (September 21, 2009): 16627–32. http://dx.doi.org/10.1073/pnas.0904617106.

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29

Perros, M., T. A. Steitz;, M. G. Fried, J. M. Hudson;, and M. Lewis. "DNA Looping and Lac Repressor-CAP Interaction." Science 274, no. 5294 (December 13, 1996): 1929–32. http://dx.doi.org/10.1126/science.274.5294.1929.

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30

Fried, M. G., and J. M. Hudson. "DNA Looping and Lac Repressor--CAP Interaction." Science 274, no. 5294 (December 13, 1996): 1930–31. http://dx.doi.org/10.1126/science.274.5294.1930.

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31

Jeong, Jiyoun, Tung T. Le, and Harold D. Kim. "Single-molecule fluorescence studies on DNA looping." Methods 105 (August 2016): 34–43. http://dx.doi.org/10.1016/j.ymeth.2016.04.005.

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32

Saiz, Leonor, and Jose MG Vilar. "DNA looping: the consequences and its control." Current Opinion in Structural Biology 16, no. 3 (June 2006): 344–50. http://dx.doi.org/10.1016/j.sbi.2006.05.008.

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33

Chen, Yih-Fan, J. N. Milstein, and Jens-Christian Meiners. "Fluctuating Forces Facilitate Protein-Mediated DNA Looping." Biophysical Journal 98, no. 3 (January 2010): 73a. http://dx.doi.org/10.1016/j.bpj.2009.12.413.

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34

Canals-Hamann, A. Z., J. E. Reittie, V. J. Buckle, and F. J. Iborra. "DNA looping in the α-globin locus." Blood Cells, Molecules, and Diseases 38, no. 2 (March 2007): 129. http://dx.doi.org/10.1016/j.bcmd.2006.10.025.

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35

Hanke, Andreas, and Ralf Metzler. "Entropy Loss in Long-Distance DNA Looping." Biophysical Journal 85, no. 1 (July 2003): 167–73. http://dx.doi.org/10.1016/s0006-3495(03)74463-4.

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36

Le, Tung T., and Harold D. Kim. "Measuring Shape-Dependent Looping Probability of DNA." Biophysical Journal 104, no. 9 (May 2013): 2068–76. http://dx.doi.org/10.1016/j.bpj.2013.03.029.

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37

Lia, Giuseppe, Marco Indrieri, Tom Owen-Hughes, Laura Finzi, Alessandro Podesta, Paolo Milani, and David Dunlap. "ATP-dependent looping of DNA by ISWI." Journal of Biophotonics 1, no. 4 (September 2008): 280–86. http://dx.doi.org/10.1002/jbio.200810027.

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38

Wentzell, Lois M., and Stephen E. Halford. "DNA looping by the SfiI restriction endonuclease." Journal of Molecular Biology 281, no. 3 (August 1998): 433–44. http://dx.doi.org/10.1006/jmbi.1998.1967.

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39

Gowetski, Daniel B., Erin J. Kodis, and Jason D. Kahn. "Rationally designed coiled-coil DNA looping peptides control DNA topology." Nucleic Acids Research 41, no. 17 (July 3, 2013): 8253–65. http://dx.doi.org/10.1093/nar/gkt553.

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40

Cary, R. B., S. R. Peterson, J. Wang, D. G. Bear, E. M. Bradbury, and D. J. Chen. "DNA looping by Ku and the DNA-dependent protein kinase." Proceedings of the National Academy of Sciences 94, no. 9 (April 29, 1997): 4267–72. http://dx.doi.org/10.1073/pnas.94.9.4267.

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41

Amouyal, M. "The remote control of transcription, DNA looping and DNA compaction." Biochimie 73, no. 10 (October 1991): 1261–68. http://dx.doi.org/10.1016/0300-9084(91)90086-g.

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42

Gowetski, Daniel B., Erin J. Kodis, and Jason D. Kahn. "Rationally Designed Coiled-Coil DNA Looping Peptides Control DNA Topology." Biophysical Journal 104, no. 2 (January 2013): 420a. http://dx.doi.org/10.1016/j.bpj.2012.11.2338.

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43

Halford, S. E. "Hopping, jumping and looping by restriction enzymes." Biochemical Society Transactions 29, no. 4 (August 1, 2001): 363–73. http://dx.doi.org/10.1042/bst0290363.

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Type II restriction endonucleases recognize specific DNA sequences and cleave both strands of the DNA at fixed locations at or near their recognition sites. Many of these enzymes are dimeric proteins that recognize, in symmetrical fashion, palindromic DNA sequences. They generally catalyse independent reactions at each recognition site on the DNA, although in some cases they act processively; cutting the DNA first at one site, then translocating along the DNA to another site and cutting that before leaving the DNA. The way in which the degree of processivity varies with the length of DNA between the sites can reveal the mechanism of translocation. In contrast with the common view that proteins move along DNA by ‘sliding’, the principal mode of transfer of the EcoRV endonuclease is by ‘hopping’ and ‘jumping’, i.e. the dissociation of the protein from one site followed by its re-association with another site in the same DNA molecule, either close to or distant from the original site. Other type II restriction enzymes require two copies of their recognition sites for their DNA cleavage reactions. Many of these enzymes, such as SfiI, are tetramers with two DNA-binding surfaces. SfiI has no activity when bound to just one recognition site, and instead both DNA-binding surfaces have to be filled before it becomes active. Although the two sites can be on separate DNA molecules, SfiI acts optimally with two sites on the same DNA, where it traps the DNA between the sites in a loop. SfiI thus constitutes a test system for the analysis of DNA looping.
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44

Felipe, Cayke, Jaeoh Shin, and Anatoly B. Kolomeisky. "DNA Looping and DNA Conformational Fluctuations Can Accelerate Protein Target Search." Journal of Physical Chemistry B 125, no. 7 (February 11, 2021): 1727–34. http://dx.doi.org/10.1021/acs.jpcb.0c09599.

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45

Azad, Zubair, Maedeh Roushan, and Robert Riehn. "DNA Brushing Shoulders: Targeted Looping and Scanning of Large DNA Strands." Nano Letters 15, no. 8 (July 13, 2015): 5641–46. http://dx.doi.org/10.1021/acs.nanolett.5b02476.

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46

Goyal, Sachin, Todd Lillian, Seth Blumberg, Jens-Christian Meiners, Edgar Meyhöfer, and N. C. Perkins. "Intrinsic Curvature of DNA Influences LacR-Mediated Looping." Biophysical Journal 93, no. 12 (December 2007): 4342–59. http://dx.doi.org/10.1529/biophysj.107.112268.

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47

Johnson, Stephanie, Martin Lindén, and Rob Phillips. "Sequence dependence of transcription factor-mediated DNA looping." Nucleic Acids Research 40, no. 16 (June 19, 2012): 7728–38. http://dx.doi.org/10.1093/nar/gks473.

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48

Pehrson, John R., and Leonard H. Cohen. "Effects of DNA looping on pyrimidine dimer formation." Nucleic Acids Research 20, no. 6 (1992): 1321–24. http://dx.doi.org/10.1093/nar/20.6.1321.

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49

Cuylen, Sara, and Christian H. Haering. "A New Cohesive Team to Mediate DNA Looping." Cell Stem Cell 7, no. 4 (October 2010): 424–26. http://dx.doi.org/10.1016/j.stem.2010.09.006.

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50

Vilar, José M. G., and Stanislas Leibler. "DNA Looping and Physical Constraints on Transcription Regulation." Journal of Molecular Biology 331, no. 5 (August 2003): 981–89. http://dx.doi.org/10.1016/s0022-2836(03)00764-2.

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