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Journal articles on the topic 'DNA-protein complexes'

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Author: Grafiati

Published: 7 September 2022

Last updated: 18 September 2022

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1

Gololobov, G. V., S. V. Mikhalap, A. V. Starov, A. F. Kolesnikov, and A. G. Gabibov. "DNA-protein complexes." Applied Biochemistry and Biotechnology 47, no. 2-3 (May 1994): 305–15. http://dx.doi.org/10.1007/bf02787942.

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2

Běgusová, Marie, Nathalie Gillard, Denise Sy, Bertrand Castaing, Michel Charlier, and Melanie Spotheim-Maurizot. "Radiolysis of DNA–protein complexes." Radiation Physics and Chemistry 72, no. 2-3 (February 2005): 265–70. http://dx.doi.org/10.1016/j.radphyschem.2004.01.009.

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3

Sen, Taner Z., Andrzej Kloczkowski, and Robert L. Jernigan. "A DNA-Centric Look at Protein-DNA Complexes." Structure 14, no. 9 (September 2006): 1341–42. http://dx.doi.org/10.1016/j.str.2006.08.003.

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4

Spotheim-Maurizot, M., and M. Davídková. "Radiation damage to DNA in DNA–protein complexes." Mutation Research/Fundamental and Molecular Mechanisms of Mutagenesis 711, no. 1-2 (June 2011): 41–48. http://dx.doi.org/10.1016/j.mrfmmm.2011.02.003.

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5

Boryskina, O. P., M. Yu Tkachenko, and A. V. Shestopalova. "Protein-DNA complexes: specificity and DNA readout mechanisms." Biopolymers and Cell 27, no. 1 (January 20, 2011): 3–16. http://dx.doi.org/10.7124/bc.00007c.

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6

Travers, Andrew A. "DNA conformation and configuration in protein-DNA complexes." Current Opinion in Structural Biology 2, no. 1 (February 1992): 71–77. http://dx.doi.org/10.1016/0959-440x(92)90180-f.

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7

Sternberg, Michael JE, Henry A. Gabb, and Richard M. Jackson. "Predictive docking of protein—protein and protein—DNA complexes." Current Opinion in Structural Biology 8, no. 2 (April 1998): 250–56. http://dx.doi.org/10.1016/s0959-440x(98)80047-x.

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8

Sarai, A., Ponraj Prabakaran, Joerg Siebers, Shandar Ahmad, Michael Gromiha, and H. Kono. "QSAR analysis of protein-DNA complexes." Seibutsu Butsuri 43, supplement (2003): S30. http://dx.doi.org/10.2142/biophys.43.s30_4.

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9

Anashkina, A. A., N. G. Esipova, E. N. Kuznetsov, and V. G. Tumanyan. "Contact specificity in protein-DNA complexes." Computer Research and Modeling 1, no. 3 (September 2009): 281–86. http://dx.doi.org/10.20537/2076-7633-2009-1-3-281-286.

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10

Volodin, Alexander A., Helen A. Smirnova, and Tatjana N. Bocharova. "Periodicity in recA protein-DNA complexes." FEBS Letters 407, no. 3 (May 5, 1997): 325–28. http://dx.doi.org/10.1016/s0014-5793(97)00367-0.

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11

Crothers, D. M. "Gel electrophoresis of protein–DNA complexes." Nature 325, no. 6103 (January 1987): 464–65. http://dx.doi.org/10.1038/325464a0.

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12

Spotheim-Maurizot, M., and M. Davídková. "Radiation damage to DNA-protein complexes." Journal of Physics: Conference Series 261 (January 1, 2011): 012010. http://dx.doi.org/10.1088/1742-6596/261/1/012010.

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13

Verdine, Gregory L., and Derek P. G. Norman. "Covalent Trapping of Protein-DNA Complexes." Annual Review of Biochemistry 72, no. 1 (June 2003): 337–66. http://dx.doi.org/10.1146/annurev.biochem.72.121801.161447.

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14

Watton, Stephen P., Hua Cao, and Thomas V. O'Halloran. "Bimetallic complexes as DNA-protein crosslinkers." Journal of Inorganic Biochemistry 43, no. 2-3 (August 1991): 431. http://dx.doi.org/10.1016/0162-0134(91)84413-4.

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15

Lyubchenko, Yuri L. "Nanoscale Dynamics of Protein-DNA Complexes." Biophysical Journal 104, no. 2 (January 2013): 386a. http://dx.doi.org/10.1016/j.bpj.2012.11.2154.

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16

Darcy, Isabel K. "Modeling protein–DNA complexes with tangles." Computers & Mathematics with Applications 55, no. 5 (March 2008): 924–37. http://dx.doi.org/10.1016/j.camwa.2006.12.099.

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17

Griffith, Jack D. "Visualization of DNA and DNA-protein complexes by TEM." Proceedings, annual meeting, Electron Microscopy Society of America 48, no. 3 (August 12, 1990): 970. http://dx.doi.org/10.1017/s0424820100162442.

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A large class of DNA and DNA-protein complexes of great interest to modern molecular biologists lie in a realm of size and complexity that it is too large for structural approaches using X ray diffraction or NMR techniques. Such complexes are usually highly irregular so that EM methods employing the formation of 2 dimensional crystals or dense-packing followed by image averaging are not usable. Examples of such complexes include topoisomerase II heterodimers bound to supercoiled DNA, plasmid DNAs being replicated by the battery of nearly 20 different proteins that initiate and carry out replication in E. coli, complexes of reverse transcriptase enzyme degrading the RNA strand of an RNA/DNA hybrid duplex, and many of the recombinational intermediates of DNA strand exchanges. In the latter complexes large protein scaffolds built of hundreds of RecA protein monomers form filaments with in which the events of DNA strand exchange occur.To visualize such large and complex structures the demands of the biochemical reactions must be given first prior ity: is ATP, glycerol, or salt required for the on going reactions? Do the reactions occur at room temperature or only at 37 degrees? Efforts in this laboratory have been focused on determining which of the various routes for visualizing macromolecules provides the best general approach to obtaining useful structural information that can be directly related to the biochemical processes.

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18

Bazett-Jones, D. P., and M. L. Brown. "Electron Spectroscopic Imaging of DNA and Protein-DNA Complexes." Proceedings, annual meeting, Electron Microscopy Society of America 46 (1988): 172–73. http://dx.doi.org/10.1017/s0424820100102948.

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Elemental distributions in cells and molecular spreads can now be produced at the spatial resolution attainable in the electron microscope by the collection of X-rays or by the collection of and imaging with inellastically scattered electrons. With the latter method, known as Electron Spectroscopic Imaging (ESI), an image is produced with electrons that have lost characteristic amounts of energy from ionizing or exciting specific elements in the specimen. ESI can generate an elemental map of a specimen at a resolution of about 0.5 nm. It can be carried out in a fixed beam microscope equipped with a parallel energy filter inserted into the column of the microscope below the specimen (1,2). An instrument equipped with a prism-mirror-prism electron spectrometer was used in this study to image purified DNA molecules and a complex of the transcription factor TFIIIA with DNA.Transcription of most genes is activated by the binding of transcription factors to promoter elements.

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19

Gao, Mu, and Jeffrey Skolnick. "From Nonspecific DNA–Protein Encounter Complexes to the Prediction of DNA–Protein Interactions." PLoS Computational Biology 5, no. 3 (April 3, 2009): e1000341. http://dx.doi.org/10.1371/journal.pcbi.1000341.

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20

Wang, Hong-Wei. "Cryo-EM of DNA Repair Protein Complexes." Biophysical Journal 108, no. 2 (January 2015): 498a. http://dx.doi.org/10.1016/j.bpj.2014.11.2726.

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21

Draper, D. E. "Protein-DNA complexes: the cost of recognition." Proceedings of the National Academy of Sciences 90, no. 16 (August 15, 1993): 7429–30. http://dx.doi.org/10.1073/pnas.90.16.7429.

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22

Musheev, Michael U., Yuri Filiptsev, Victor Okhonin, and Sergey N. Krylov. "Electric Field Destabilizes Noncovalent Protein−DNA Complexes." Journal of the American Chemical Society 132, no. 39 (October 6, 2010): 13639–41. http://dx.doi.org/10.1021/ja105754h.

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23

Heller, Iddo, Tjalle P. Hoekstra, Graeme A. King, Erwin J. G. Peterman, and Gijs J. L. Wuite. "Optical Tweezers Analysis of DNA–Protein Complexes." Chemical Reviews 114, no. 6 (January 21, 2014): 3087–119. http://dx.doi.org/10.1021/cr4003006.

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24

Contreras-Moreira, Bruno, Pierre-Alain Branger, and Julio Collado-Vides. "TFmodeller: comparative modelling of protein–DNA complexes." Bioinformatics 23, no. 13 (April 25, 2007): 1694–96. http://dx.doi.org/10.1093/bioinformatics/btm148.

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25

Tereshkin, E. V., K. B. Tereshkina, V. V. Kovalenko, N. G. Loiko, and Yu F. Krupyanskii. "Structure of DPS Protein Complexes with DNA." Russian Journal of Physical Chemistry B 13, no. 5 (September 2019): 769–77. http://dx.doi.org/10.1134/s199079311905021x.

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26

Villa, Elizabeth, Alexander Balaeff, L. Mahadevan, and Klaus Schulten. "Multiscale Method for Simulating Protein-DNA Complexes." Multiscale Modeling & Simulation 2, no. 4 (January 2004): 527–53. http://dx.doi.org/10.1137/040604789.

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27

Avramova, Zoya, and Roumen Tsanev. "Stable DNA-protein complexes in eukaryotic chromatin." Journal of Molecular Biology 196, no. 2 (July 1987): 437–40. http://dx.doi.org/10.1016/0022-2836(87)90704-2.

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28

Musacchio, Alexis, Diogenes Quintana, Antonieta M. Herrera, Belkis Sandez, Jullio Cesar Alvarez, Viviana Falcón, Marı́a Cristina la Rosa, Félix Alvarez, and Dagmara Pichardo. "Plasmid DNA–recombinant Opc protein complexes for nasal DNA immunization." Vaccine 19, no. 27 (June 2001): 3692–99. http://dx.doi.org/10.1016/s0264-410x(01)00076-7.

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29

Olson, W. K., A. A. Gorin, X. J. Lu, L. M. Hock, and V. B. Zhurkin. "DNA sequence-dependent deformability deduced from protein-DNA crystal complexes." Proceedings of the National Academy of Sciences 95, no. 19 (September 15, 1998): 11163–68. http://dx.doi.org/10.1073/pnas.95.19.11163.

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30

Simicevic, Jovan, and Bart Deplancke. "DNA-centered approaches to characterize regulatory protein–DNA interaction complexes." Mol. BioSyst. 6, no. 3 (2010): 462–68. http://dx.doi.org/10.1039/b916137f.

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31

Siggers, Trevor, and Raluca Gordân. "Protein–DNA binding: complexities and multi-protein codes." Nucleic Acids Research 42, no. 4 (November 16, 2013): 2099–111. http://dx.doi.org/10.1093/nar/gkt1112.

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Abstract Binding of proteins to particular DNA sites across the genome is a primary determinant of specificity in genome maintenance and gene regulation. DNA-binding specificity is encoded at multiple levels, from the detailed biophysical interactions between proteins and DNA, to the assembly of multi-protein complexes. At each level, variation in the mechanisms used to achieve specificity has led to difficulties in constructing and applying simple models of DNA binding. We review the complexities in protein–DNA binding found at multiple levels and discuss how they confound the idea of simple recognition codes. We discuss the impact of new high-throughput technologies for the characterization of protein–DNA binding, and how these technologies are uncovering new complexities in protein–DNA recognition. Finally, we review the concept of multi-protein recognition codes in which new DNA-binding specificities are achieved by the assembly of multi-protein complexes.

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32

Senear, Donald F., J. B. Alexander Ross, and Thomas M. Laue. "Analysis of Protein and DNA-Mediated Contributions to Cooperative Assembly of Protein–DNA Complexes." Methods 16, no. 1 (September 1998): 3–20. http://dx.doi.org/10.1006/meth.1998.0641.

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33

Lin, Yu-Ling, Li-Yi Chen, Chia-Hung Chen, Yen-Ku Liu, Wei-Tung Hsu, Li-Ping Ho, and Kuang-Wen Liao. "A Soybean Oil-Based Liposome-Polymer Transfection Complex as a Codelivery System for DNA and Subunit Vaccines." Journal of Nanomaterials 2012 (2012): 1–12. http://dx.doi.org/10.1155/2012/427306.

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Inexpensive liposome-polymer transfection complexes (LPTCs) were developed and used as for DNA or protein delivery. The particle sizes of the LPTCs were in the range of 212.2 to 312.1 nm, and the zetapotential was +38.7 mV. LPTCs condensed DNA and protected DNA from DNase I digestion and efficiently delivered LPTC/DNA complexes in Balb/3T3 cells. LPTCs also enhanced the cellular uptake of antigen in mouse macrophage cells and stimulated TNF-αrelease in naïve mice splenocytes, both indicating the potential of LPTCs as adjuvants for vaccines.In vivostudies were performed usingH. pylorirelative heat shock protein 60 as an antigen model. The vaccination of BALB/c mice with LPTC-complexed DNA and protein enhanced the humoral immune response. Therefore, we developed a DNA and protein delivery system using LPTCs that is inexpensive, and we successfully applied it to the development of a DNA and subunit vaccine.

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34

Lyubchenko, Yuri L., and Luda S. Shlyakhtenko. "Imaging of DNA and Protein-DNA Complexes with Atomic Force Microscopy." Critical Reviews in Eukaryotic Gene Expression 26, no. 1 (2016): 63–96. http://dx.doi.org/10.1615/critreveukaryotgeneexpr.v26.i1.70.

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35

Suckow, M., M. Lopata, A. Seydel, B. Kisters-Woike, B. von Wilcken-Bergmann, and B. Müller-Hill. "Mutant bZip-DNA complexes with four quasi-identical protein-DNA interfaces." EMBO Journal 15, no. 3 (February 1996): 598–606. http://dx.doi.org/10.1002/j.1460-2075.1996.tb00392.x.

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36

Arís, Anna, and Antonio Villaverde. "Molecular Organization of Protein–DNA Complexes for Cell-Targeted DNA Delivery." Biochemical and Biophysical Research Communications 278, no. 2 (November 2000): 455–61. http://dx.doi.org/10.1006/bbrc.2000.3824.

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37

Kuo, C. F., A. H. Zou, M. Jayaram, E. Getzoff, and R. Harshey. "DNA-protein complexes during attachment-site synapsis in Mu DNA transposition." EMBO Journal 10, no. 6 (June 1991): 1585–91. http://dx.doi.org/10.1002/j.1460-2075.1991.tb07679.x.

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38

MÜLLER-REICHERT, T., H. J. BUTT, and H. GROSS. "STM of metal embedded and coated DNA and DNA-protein complexes." Journal of Microscopy 182, no. 3 (June 1996): 169–76. http://dx.doi.org/10.1046/j.1365-2818.1996.62426.x.

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39

Ticli, Giulio, and Ennio Prosperi. "In Situ Analysis of DNA-Protein Complex Formation upon Radiation-Induced DNA Damage." International Journal of Molecular Sciences 20, no. 22 (November 15, 2019): 5736. http://dx.doi.org/10.3390/ijms20225736.

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The importance of determining at the cellular level the formation of DNA–protein complexes after radiation-induced lesions to DNA is outlined by the evidence that such interactions represent one of the first steps of the cellular response to DNA damage. These complexes are formed through recruitment at the sites of the lesion, of proteins deputed to signal the presence of DNA damage, and of DNA repair factors necessary to remove it. Investigating the formation of such complexes has provided, and will probably continue to, relevant information about molecular mechanisms and spatiotemporal dynamics of the processes that constitute the first barrier of cell defense against genome instability and related diseases. In this review, we will summarize and discuss the use of in situ procedures to detect the formation of DNA-protein complexes after radiation-induced DNA damage. This type of analysis provides important information on the spatial localization and temporal resolution of the formation of such complexes, at the single-cell level, allowing the study of heterogeneous cell populations.

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40

Vemulapalli, Sridhar, Mohtadin Hashemi, and Yuri L. Lyubchenko. "Site-Search Process for Synaptic Protein-DNA Complexes." International Journal of Molecular Sciences 23, no. 1 (December 25, 2021): 212. http://dx.doi.org/10.3390/ijms23010212.

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The assembly of synaptic protein-DNA complexes by specialized proteins is critical for bringing together two distant sites within a DNA molecule or bridging two DNA molecules. The assembly of such synaptosomes is needed in numerous genetic processes requiring the interactions of two or more sites. The molecular mechanisms by which the protein brings the sites together, enabling the assembly of synaptosomes, remain unknown. Such proteins can utilize sliding, jumping, and segmental transfer pathways proposed for the single-site search process, but none of these pathways explains how the synaptosome assembles. Here we used restriction enzyme SfiI, that requires the assembly of synaptosome for DNA cleavage, as our experimental system and applied time-lapse, high-speed AFM to directly visualize the site search process accomplished by the SfiI enzyme. For the single-site SfiI-DNA complexes, we were able to directly visualize such pathways as sliding, jumping, and segmental site transfer. However, within the synaptic looped complexes, we visualized the threading and site-bound segment transfer as the synaptosome-specific search pathways for SfiI. In addition, we visualized sliding and jumping pathways for the loop dissociated complexes. Based on our data, we propose the site-search model for synaptic protein-DNA systems.

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41

Chikhirzhina, E., A. Polyanichko, Z. Leonenko, H. Wieser, and V. Vorob'ev. "C-terminal domain of nonhistone protein HMGB1 as a modulator of HMGB1–DNA structural interactions." Spectroscopy 24, no. 3-4 (2010): 361–66. http://dx.doi.org/10.1155/2010/268452.

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The HMGB1 protein (High Mobility Group protein 1) participates in the formation of functionally significant DNA-protein complexes. HMGB1 protein contains two DNA-binding domains and negatively charged C-terminal region. The latter consists of continuous sequence of dicarboxylic amino acids residues. Structural changes in DNA-protein complexes were studied by circular dichroism spectroscopy (CD) and atomic force microscopy (AFM). Natural HMGB1 and recombinant protein HMGB1(A + B) lacked negatively charged C-terminal region were used. The DNA–HMGB1(A + B) complexes demonstrate an unusually high optical activity in 150 mM NaCl solutions. AFM of the latter complexes shows, that at the low concentration of HMGB1 in the complex the protein is distributed along DNA in a random way. Increase of HMGB1 content leads to cooperative interaction and a redistribution of the bound protein molecules on DNA is observed. Based on the data obtained we conclude that protein–protein interactions play a key role in the formation of highly ordered DNA–HMGB1 complexes. It was shown that C-terminal domain modulate the interactions of DNA with HMGB1 protein. We suggest that the C-terminal domain of HMGB1 also modulates the “packing” of HMGB1 molecules on the DNA.

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42

Brown, M., and P. A. Sharp. "Human estrogen receptor forms multiple protein-DNA complexes." Journal of Biological Chemistry 265, no. 19 (July 1990): 11238–43. http://dx.doi.org/10.1016/s0021-9258(19)38582-5.

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43

Tullius, T. D. "Physical Studies of Protein-DNA Complexes by Footprinting." Annual Review of Biophysics and Biophysical Chemistry 18, no. 1 (June 1989): 213–37. http://dx.doi.org/10.1146/annurev.bb.18.060189.001241.

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44

Nguyen Le Minh, Phu, Indra Bervoets, Dominique Maes, and Daniel Charlier. "The protein–DNA contacts in RutR·carAB operator complexes." Nucleic Acids Research 38, no. 18 (May 14, 2010): 6286–300. http://dx.doi.org/10.1093/nar/gkq385.

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45

Peña, Carol E. A., J. Michelle Kahlenberg, and Graham F. Hatfull. "Protein-DNA Complexes in Mycobacteriophage L5 Integrative Recombination." Journal of Bacteriology 181, no. 2 (January 15, 1999): 454–61. http://dx.doi.org/10.1128/jb.181.2.454-461.1999.

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ABSTRACT The temperate mycobacteriophage L5 integrates site specifically into the genomes of Mycobacterium smegmatis,Mycobacterium tuberculosis, and Mycobacterium bovis bacillus Calmette-Guérin. This integrative recombination event occurs between the phage L5 attP site and the mycobacterial attB site and requires the phage-encoded integrase and mycobacterial-encoded integration host factor mIHF. Here we show that attP, Int-L5, and mIHF assemble into a recombinationally active complex, the intasome, which is capable of attB capture and formation of products. The arm-type integrase binding sites within attP play specialized roles in the formation of specific protein-DNA architectures; the intasome is constructed by the formation of intramolecular integrase bridges between one pair of sites, P4-P5, and the attP core, while an additional pair of sites, P1-P2, is required for interaction with attB.

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46

Sidorova, Nina Y., Stevephen Hung, and Donald C. Rau. "Stabilizing labile DNA-protein complexes in polyacrylamide gels." ELECTROPHORESIS 31, no. 4 (January 2010): 648–53. http://dx.doi.org/10.1002/elps.200900573.

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47

Darcy, Isabel K., and Mariel Vazquez. "Determining the topology of stable protein–DNA complexes." Biochemical Society Transactions 41, no. 2 (March 21, 2013): 601–5. http://dx.doi.org/10.1042/bst20130004.

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Difference topology is an experimental technique that can be used to unveil the topological structure adopted by two or more DNA segments in a stable protein–DNA complex. Difference topology has also been used to detect intermediates in a reaction pathway and to investigate the role of DNA supercoiling. In the present article, we review difference topology as applied to the Mu transpososome. The tools discussed can be applied to any stable nucleoprotein complex.

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48

Jain, Swapan S., and Thomas D. Tullius. "Footprinting protein–DNA complexes using the hydroxyl radical." Nature Protocols 3, no. 6 (June 2008): 1092–100. http://dx.doi.org/10.1038/nprot.2008.72.

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49

christianson, Anastasia M. Khoury, and Fotis C. Kafatos. "Antibody detection of protein complexes bound to DNA." Nucleic Acids Research 21, no. 18 (1993): 4416–17. http://dx.doi.org/10.1093/nar/21.18.4416.

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50

Sidorova, Nina Y., Stevephen Hung, and Donald C. Rau. "Stabilizing Labile DNA-Protein Complexes in Polyacrylamide Gels." Biophysical Journal 102, no. 3 (January 2012): 484a. http://dx.doi.org/10.1016/j.bpj.2011.11.2655.

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