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Journal articles on the topic 'DNA binding'

Author: Grafiati

Published: 4 June 2021

Last updated: 7 September 2023

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1

PRENDERGAST, GEORGE, and EDWARD B. ZIFF. "DNA-binding motif." Nature 341, no. 6241 (October 1989): 392. http://dx.doi.org/10.1038/341392a0.

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2

Zilliacus, J., K. Dahlman-Wright, A. Wright, J. A. Gustafsson, and J. Carlstedt-Duke. "DNA binding specificity of mutant glucocorticoid receptor DNA-binding domains." Journal of Biological Chemistry 266, no. 5 (February 1991): 3101–6. http://dx.doi.org/10.1016/s0021-9258(18)49959-0.

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3

ZILLIACUS, JOHANNA, ANTHONY P. H. WRIGHT, ULF NORINDER, and JAN-ÅKE GUSTAFSSON. "DNA-Binding Specificity of Mutant Glucocorticoid Receptor DNA-Binding Domains." Annals of the New York Academy of Sciences 684, no. 1 Zinc-Finger P (June 1993): 253–56. http://dx.doi.org/10.1111/j.1749-6632.1993.tb32301.x.

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4

Dashwood, R. H., R. D. Combes, and J. Ashby. "DNA-binding studies with 6BT and 5I: implications for DNA-binding/carcinogenicity and DNA-binding/mutagenicity correlations." Mutation Research/Fundamental and Molecular Mechanisms of Mutagenesis 198, no. 1 (March 1988): 61–68. http://dx.doi.org/10.1016/0027-5107(88)90040-1.

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5

Nafisi, Shohreh, Maryam Adelzadeh, Zeinab Norouzi, and Mohammad Nabi Sarbolouki. "Curcumin Binding to DNA and RNA." DNA and Cell Biology 28, no. 4 (April 2009): 201–8. http://dx.doi.org/10.1089/dna.2008.0840.

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6

Nafisi, Shohreh, Mahyar Bonsaii, Valerie Alexis, and James Glick. "Binding of 2-Acetylaminofluorene to DNA." DNA and Cell Biology 30, no. 11 (November 2011): 955–62. http://dx.doi.org/10.1089/dna.2011.1229.

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7

Kashanian, Soheila, Sanaz Javanmardi, Arash Chitsazan, Kobra Omidfar, and Maliheh Paknejad. "DNA-Binding Studies of Fluoxetine Antidepressant." DNA and Cell Biology 31, no. 7 (July 2012): 1349–55. http://dx.doi.org/10.1089/dna.2012.1657.

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8

HOLTH, LAUREL T., JIAN-MIN SUN, AMANDA S. COUTTS, LEIGH C. MURPHY, and JAMES R. DAVIE. "Estrogen Receptor Diminishes DNA-Binding Activities of Chicken GATA-1 and CACCC-Binding Proteins." DNA and Cell Biology 16, no. 12 (December 1997): 1477–82. http://dx.doi.org/10.1089/dna.1997.16.1477.

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9

Rasimas, Joseph J., Anthony E. Pegg, and Michael G. Fried. "DNA-binding Mechanism ofO6-Alkylguanine-DNA Alkyltransferase." Journal of Biological Chemistry 278, no. 10 (December 20, 2002): 7973–80. http://dx.doi.org/10.1074/jbc.m211854200.

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10

RICH, ALEXANDER. "Z-DNA and Z-DNA-binding proteins." Biochemical Society Transactions 14, no. 2 (April 1, 1986): 202. http://dx.doi.org/10.1042/bst0140202.

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11

sun, yujie, Sangjin Kim, Erik Broströmer, Dong Xing, Jianshi Jin, Shasha Chong, Hao Ge, Siyuan Wang, Xiao-dong Su, and X. Sunney Xie. "Cooperative DNA-Binding Effect through DNA Allostery." Biophysical Journal 104, no. 2 (January 2013): 198a—199a. http://dx.doi.org/10.1016/j.bpj.2012.11.1121.

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12

de Souza, Natalie. "The DNA-binding landscape." Nature Methods 7, no. 4 (April 2010): 254–55. http://dx.doi.org/10.1038/nmeth0410-254a.

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13

Adnan, Najia, Damian P. Buck, Benny J. Evison, Suzanne M. Cutts, Don R. Phillips, and J. Grant Collins. "DNA binding by pixantrone." Organic & Biomolecular Chemistry 8, no. 23 (2010): 5359. http://dx.doi.org/10.1039/c0ob00295j.

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14

Voytas, D. F., and J. K. Joung. "DNA Binding Made Easy." Science 326, no. 5959 (December 10, 2009): 1491–92. http://dx.doi.org/10.1126/science.1183604.

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15

Tullius, Tom. "DNA binding shapes up." Nature 461, no. 7268 (October 2009): 1225–26. http://dx.doi.org/10.1038/4611225a.

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16

Smalheiser, Neil R., and Octavio L. A. Gomes. "Mammalian Argonaute-DNA binding?" Biology Direct 10, no. 1 (2014): 27. http://dx.doi.org/10.1186/preaccept-1466302485137399.

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17

GUMPORT, RICHARD I. "Protein binding to DNA." Nature 328, no. 6125 (July 1987): 21. http://dx.doi.org/10.1038/328021b0.

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18

FRAMPTON, JONATHAN, ACHIM LEUTZ, TOBY J. GIBSON, and THOMAS GRAF. "DNA-binding domain ancestry." Nature 342, no. 6246 (November 1989): 134. http://dx.doi.org/10.1038/342134a0.

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19

Edwards, Aled M., Alexey Bochkarev, and Lori Frappier. "Origin DNA-binding proteins." Current Opinion in Structural Biology 8, no. 1 (February 1998): 49–53. http://dx.doi.org/10.1016/s0959-440x(98)80009-2.

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20

Koonin, Eugene V., and Peer Bork. "FMN- or DNA-binding?" Trends in Biochemical Sciences 19, no. 6 (June 1994): 234–35. http://dx.doi.org/10.1016/0968-0004(94)90145-7.

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21

Schleif, R. "DNA binding by proteins." Science 241, no. 4870 (September 2, 1988): 1182–87. http://dx.doi.org/10.1126/science.2842864.

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22

Jones, S. "Using electrostatic potentials to predict DNA-binding sites on DNA-binding proteins." Nucleic Acids Research 31, no. 24 (December 15, 2003): 7189–98. http://dx.doi.org/10.1093/nar/gkg922.

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23

Wichser, Urszula, and Christine Brack. "Rapid isolation fo specific DNA-binding proteins and their DNA-binding domains." Nucleic Acids Research 20, no. 15 (1992): 4103–4. http://dx.doi.org/10.1093/nar/20.15.4103.

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24

Cornille, F. "DNA binding properties of a chemically synthesized DNA binding domain of hRFX1." Nucleic Acids Research 26, no. 9 (May 1, 1998): 2143–49. http://dx.doi.org/10.1093/nar/26.9.2143.

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25

SUZUKI, M., J. SUCKOW, B. KISTERSWOIKE, H. ARAMAKI, and K. MARINO. "Multi-helical DNA-binding domains: Their structures and modes of DNA-binding." Advances in Biophysics 32 (1996): 31–52. http://dx.doi.org/10.1016/0065-227x(96)84740-x.

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26

Kim, Jeong-Ho. "Immobilized DNA-binding assay, an approach for in vitro DNA-binding assay." Analytical Biochemistry 334, no. 2 (November 2004): 401–2. http://dx.doi.org/10.1016/j.ab.2004.06.045.

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27

Hutchinson, Kevin A., Gordana Matić, Michael J. Czar, and William B. Pratt. "DNA-binding and non-DNA-binding forms of the transformed glucocorticoid receptor." Journal of Steroid Biochemistry and Molecular Biology 41, no. 3-8 (March 1992): 715–18. http://dx.doi.org/10.1016/0960-0760(92)90410-k.

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28

Hoffman, Ross C., Rachel E. Klevit, and Suzanna J. Horvath. "Structures of DNA-binding mutant zinc finger domains: Implications for DNA binding." Protein Science 2, no. 6 (June 1993): 951–65. http://dx.doi.org/10.1002/pro.5560020609.

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29

Kashanian, Soheila, and Sahar Heidary Zeidali. "DNA Binding Studies of Tartrazine Food Additive." DNA and Cell Biology 30, no. 7 (July 2011): 499–505. http://dx.doi.org/10.1089/dna.2010.1181.

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30

Bhadra, Kakali, Motilal Maiti, and Gopinatha Suresh Kumar. "DNA-Binding Cytotoxic Alkaloids: Comparative Study of the Energetics of Binding of Berberine, Palmatine, and Coralyne." DNA and Cell Biology 27, no. 12 (December 2008): 675–85. http://dx.doi.org/10.1089/dna.2008.0779.

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31

Lohman, T. M., and M. E. Ferrari. "Escherichia Coli Single-Stranded DNA-Binding Protein: Multiple DNA-Binding Modes and Cooperativities." Annual Review of Biochemistry 63, no. 1 (June 1994): 527–70. http://dx.doi.org/10.1146/annurev.bi.63.070194.002523.

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32

Siggers, Trevor, Michael H. Duyzend, Jessica Reddy, Sidra Khan, and Martha L. Bulyk. "Non‐DNA‐binding cofactors enhance DNA‐binding specificity of a transcriptional regulatory complex." Molecular Systems Biology 7, no. 1 (January 2011): 555. http://dx.doi.org/10.1038/msb.2011.89.

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33

Biswas-Fiss, Esther E., Jirayu Kukiratirat, and Subhasis B. Biswas. "Thermodynamic analysis of DNA binding by a Bacillus single stranded DNA binding protein." BMC Biochemistry 13, no. 1 (2012): 10. http://dx.doi.org/10.1186/1471-2091-13-10.

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34

Inoue, Toshiaki, Wataru Shoji, and Masuo Obinata. "MIDA1 is a sequence specific DNA binding protein with novel DNA binding properties." Genes to Cells 5, no. 9 (September 2000): 699–709. http://dx.doi.org/10.1046/j.1365-2443.2000.00362.x.

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35

Dahlman-Wright, K., H. Siltala-Roos, J. Carlstedt-Duke, and J. A. Gustafsson. "Protein-protein interactions facilitate DNA binding by the glucocorticoid receptor DNA-binding domain." Journal of Biological Chemistry 265, no. 23 (August 1990): 14030–35. http://dx.doi.org/10.1016/s0021-9258(18)77452-8.

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36

Kozlov, Alexander G., Julie M. Eggington, Michael M. Cox, and Timothy M. Lohman. "Binding of the DimericDeinococcus radioduransSingle-Stranded DNA Binding Protein to Single-Stranded DNA." Biochemistry 49, no. 38 (September 28, 2010): 8266–75. http://dx.doi.org/10.1021/bi100920w.

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37

Russo, Cristina, Erin Asbury, Meredith Wall, and Marcia O. Fenley. "Salt-Dependence of DNA-Protein Binding: A Study of Four DNA-Binding Families." Biophysical Journal 98, no. 3 (January 2010): 41a. http://dx.doi.org/10.1016/j.bpj.2009.12.236.

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38

Dubiel, Katarzyna, Angela R. Myers, Alexander G. Kozlov, Olivia Yang, Jichuan Zhang, Taekjip Ha, Timothy M. Lohman, and James L. Keck. "Structural Mechanisms of Cooperative DNA Binding by Bacterial Single-Stranded DNA-Binding Proteins." Journal of Molecular Biology 431, no. 2 (January 2019): 178–95. http://dx.doi.org/10.1016/j.jmb.2018.11.019.

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39

Rupert, Peter B., Gary W. Daughdrill, Bruce Bowerman, and Brian W. Matthews. "A new DNA-binding motif in the Skn-1 binding domain–DNA complex." Nature Structural Biology 5, no. 6 (June 1998): 484–91. http://dx.doi.org/10.1038/nsb0698-484.

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40

Stearns, Nancy A., Jaewoo Lee, Kam W. Leong, Bruce A. Sullenger, and David S. Pisetsky. "The Inhibition of Anti-DNA Binding to DNA by Nucleic Acid Binding Polymers." PLoS ONE 7, no. 7 (July 11, 2012): e40862. http://dx.doi.org/10.1371/journal.pone.0040862.

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41

Inukai, Sachi, Kian Hong Kock, and Martha L. Bulyk. "Transcription factor–DNA binding: beyond binding site motifs." Current Opinion in Genetics & Development 43 (April 2017): 110–19. http://dx.doi.org/10.1016/j.gde.2017.02.007.

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42

Brown, Andrew J., Steven Jupe, and Celia P. Briscoe. "A Family of Fatty Acid Binding Receptors." DNA and Cell Biology 24, no. 1 (January 2005): 54–61. http://dx.doi.org/10.1089/dna.2005.24.54.

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43

Lu, Chung-Kuang, Yi-Chyi Lai, Hau-Ren Chen, and Ming-Ko Chiang. "Rbms3, an RNA-Binding Protein, Mediates the Expression ofPtf1aby Binding to Its 3′UTR During Mouse Pancreas Development." DNA and Cell Biology 31, no. 7 (July 2012): 1245–51. http://dx.doi.org/10.1089/dna.2012.1619.

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44

Aktas, Gülsen Betül, Arnau Ribera, Vasso Skouridou, and Lluis Masip. "DNA immobilization and detection using DNA binding proteins." Analytical and Bioanalytical Chemistry 413, no. 7 (January 27, 2021): 1929–39. http://dx.doi.org/10.1007/s00216-021-03162-5.

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45

Reeves, Westley H., Minoru Satoh, Jingsong Wang, Chih-Hao Chou, and Ajay K. Ajmani. "ANTIBODIES TO DNA, DNA-BINDING PROTEINS, AND HISTONES." Rheumatic Disease Clinics of North America 20, no. 1 (February 1994): 1–28. http://dx.doi.org/10.1016/s0889-857x(21)00223-4.

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46

Dubey, Ashok K., and Richard J. Roberts. "Sequence-specific DNA binding by theMspl DNA methyltransferase." Nucleic Acids Research 20, no. 12 (1992): 3167–73. http://dx.doi.org/10.1093/nar/20.12.3167.

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47

Bill, Roslyn M., Neal B. Blatt, and Gary D. Glick. "Anti-DNA autoantibodies: the other DNA-binding proteins." Bioorganic & Medicinal Chemistry 5, no. 3 (March 1997): 467–72. http://dx.doi.org/10.1016/s0968-0896(96)00275-1.

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48

Utsuno, Kuniharu, and Hasan Uludağ. "Thermodynamics of Polyethylenimine-DNA Binding and DNA Condensation." Biophysical Journal 99, no. 1 (July 2010): 201–7. http://dx.doi.org/10.1016/j.bpj.2010.04.016.

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49

Nieves, Daniel, Katharina Gaus, and Matthew Baker. "DNA-Based Super-Resolution Microscopy: DNA-PAINT." Genes 9, no. 12 (December 11, 2018): 621. http://dx.doi.org/10.3390/genes9120621.

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Abstract:

Super-resolution microscopies, such as single molecule localization microscopy (SMLM), allow the visualization of biomolecules at the nanoscale. The requirement to observe molecules multiple times during an acquisition has pushed the field to explore methods that allow the binding of a fluorophore to a target. This binding is then used to build an image via points accumulation for imaging nanoscale topography (PAINT), which relies on the stochastic binding of a fluorescent ligand instead of the stochastic photo-activation of a permanently bound fluorophore. Recently, systems that use DNA to achieve repeated, transient binding for PAINT imaging have become the cutting edge in SMLM. Here, we review the history of PAINT imaging, with a particular focus on the development of DNA-PAINT. We outline the different variations of DNA-PAINT and their applications for imaging of both DNA origamis and cellular proteins via SMLM. Finally, we reflect on the current challenges for DNA-PAINT imaging going forward.

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50

Turgay Tun, Turgay Tun, Nadir Demirel Nadir Demirel, Mahmut Emir Mahmut Emir, Asl han G. nel Asl han G nel, R. fk Kad o. lu R fk Kad o lu, and Nurcan Karacan Nurcan Karacan. "Three New Copper (II) Complexes with CHIRAL SCHIFF BASES: Synthesis, Characterization, DNA Binding and DNA-Cleavage Studies." Journal of the chemical society of pakistan 41, no. 2 (2019): 334. http://dx.doi.org/10.52568/000730/jcsp/41.02.2019.

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Abstract:

New mononuclear copper (II) complexes (1, 2 and 3) were synthesized from Schiff bases (H2L) of chiral amino alcohols. The structures of the copper complexes were proposed by a combination of elemental analyses, FTIR, LCMS, magnetic susceptibility and molar conductance measurement methods. Spectroscopic and analytical data of the complexes suggest four-coordinated structures. Geometry optimization carried out with DFT/6-31G (d,p) were proposed to be distorted square planar geometry for the complexes. The similarity between experimental and theoretical IR spectra confirms the proposed structures. The interaction of copper (II) complexes with calf thymus (CT-DNA) was investigated using absorption titration method. The results suggest that the complex 1 and 2 can bind to DNA by intercalation. Binding constants Kb were found to be 2.46and#215;105 for 1, 5.41and#215;105 for 2 and 7.00and#215;104 for 3. Moreover, agarose gel electrophoresis assay demonstrates that all complexes were found to cleavage of plasmid pentry/d-topo plasmid DNA. Complex 2 shows the best cleavage activity (5 and#181;M).

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