Journal articles: 'DNA binding'

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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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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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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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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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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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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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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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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11

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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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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13

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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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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15

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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16

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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17

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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18

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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19

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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20

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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21

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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22

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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23

S., Iyyam Pillai* C. Joel K. VIjayaraghavan and S. Subramanian. "MONONUCLEAR COPPER, NICKEL AND ZINC COMPLEXES POSSESSING BIO-POTENTIAL LIGAND PINOCEMBRIN: SYNTHESIS, CHARACTERIZATION AND DNA BINDING CLEAVAGE STUDIES." INDO AMERICAN JOURNAL OF PHARMACEUTICAL SCIENCES 05, no. 10 (October 24, 2018): 10800–10815. https://doi.org/10.5281/zenodo.1470661.

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Flavonoids are widely occurring polyphenol compounds of plant origin with multiple biological and chemical activities. DNA binding studies of flavonoids are needed to understand the reaction mechanism and improve drugs that target DNA. Due to the presence of carbonyl and hydroxyl groups they can coordinate metal ions and form complexes. Pinocembrin is a natural flavonoid compound which is capable of antioxidant, antibacterial, anti-inflammatory, and antineoplastic activities. Present research work reports the new metal [Cu(II), Ni(II) and Zn(II)] complexes of Pinocembrin. Their structural features and other properties has been characterized by FT-IR and Mass spectral analysis. Interactions of the synthesized complexes towards calf thymus-DNA were determined by emission, absorption, circular dichroism, and viscosity techniques. Detailed investigation reveals that these complexes bind with DNA via intercalation binding. The present effort shows the potential of spectroscopic analysis to characterize the nature of drug–metal complex and the effects of such interaction on the structure of biomolecule. Key words: Flavonoid, Pinocembrin, DNA binding, Intercalation, DNA–drug interaction

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24

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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25

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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26

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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27

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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28

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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29

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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30

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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31

Shaista Sabir and Naghmmana Rashid, Shaista Sabir and Naghmmana Rashid. "Organocatalyzed Synthesis, DNA Binding and Microbial Studies of Warfarin Analogues." Journal of the chemical society of pakistan 46, no. 1 (2024): 107. http://dx.doi.org/10.52568/001426/jcsp/46.01.2024.

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A noval chiral sec-amine/amidine-base hybrid catalyst, N [S-carbonylprolyl] cyclohexyl Amine is described, which is able to catalyze conjugate addition of 6-Methyl-4-hydroxypyran and 2-Hydroxy-naphthaquinone with various benzylideneacetones through Michael reactions that directly gives anticoagulant Warfarin analogues. These analogues were prepared in good yields (54–82%) and in good enantiomeric excess (50–75%). Identification of synthesized compounds was done by physio-chemical properties and spectral analysis (1H-NMR andamp; 13C-NMR).These compounds were further investigated for their antimicrobial (antibacterial andamp; antifungal) activities and DNA-binding studies. Antimicrobial studies were carried out by Disc Diffusion while DNA-binding studies were carried out by Cyclic Voltammetry and UV-Visible spectroscopy. These studies showed that the compounds showed significant interaction with DNA. Some analogues also imparted prominent antimicrobial activities.

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32

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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33

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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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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34

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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35

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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36

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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37

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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38

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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39

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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40

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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41

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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42

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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43

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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44

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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45

Noble, Christian G., Faye M. Barnard, and Anthony Maxwell. "Quinolone-DNA Interaction: Sequence-Dependent Binding to Single-Stranded DNA Reflects the Interaction within the Gyrase-DNA Complex." Antimicrobial Agents and Chemotherapy 47, no. 3 (March 2003): 854–62. http://dx.doi.org/10.1128/aac.47.3.854-862.2003.

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ABSTRACT We have investigated the interaction of quinolones with DNA by a number of methods to establish whether a particular binding mode correlates with quinolone potency. The specificities of the quinolone-mediated DNA cleavage reaction of DNA gyrase were compared for a number of quinolones. Two patterns that depended on the potency of the quinolone were identified. Binding to plasmid DNA was examined by measuring the unwinding of pBR322 by quinolones; no correlation with quinolone potency was observed. Quinolone binding to short DNA oligonucleotides was measured by surface plasmon resonance. The quinolones bound to both single- and double-stranded oligonucleotides in an Mg2+-dependent manner. Quinolones bound to single-stranded DNA with a higher affinity, and the binding exhibited sequence dependence; binding to double-stranded DNA was sequence independent. The variations in binding in the presence of metal ions showed that Mg2+ promoted tighter, more specific binding to single-stranded DNA than softer metal ions (Mn2+ and Cd2+). Single-stranded DNA binding by quinolones correlated with the in vitro quinolone potency, indicating that this mode of interaction may reflect the interaction of the quinolone with DNA in the context of the gyrase-DNA complex.

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46

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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47

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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48

Chinnathambi, Shanmugavel, Subramani Karthikeyan, Devadasan Velmurugan, Nobutaka Hanagata, Prakasarao Aruna, and Singaravelu Ganesan. "Investigations on the Interactions of 5-Fluorouracil with Herring Sperm DNA: Steady State/Time Resolved and Molecular Modeling Studies." Biophysical Reviews and Letters 10, no. 02 (June 2015): 115–33. http://dx.doi.org/10.1142/s1793048015500034.

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In the present study, the interaction of 5-Fluorouracil with herring sperm DNA is reported using spectroscopic and molecular modeling techniques. This binding study of 5-FU with hs-DNA is of paramount importance in understanding chemico–biological interactions for drug design, pharmacy and biochemistry without altering the original structure. The challenge of the study was to find the exact binding mode of the drug 5-Fluorouracil with hs-DNA. From the absorption studies, a hyperchromic effect was observed for the herring sperm DNA in the presence of 5-Fluorouracil and a binding constant of 6.153 × 103 M-1 for 5-Fluorouracil reveals the existence of weak interaction between the 5-Fluorouracil and herring sperm DNA. Ethidium bromide loaded herring sperm DNA showed a quenching in the fluorescence intensity after the addition of 5-Fluorouracil. The binding constants for 5-Fluorouracil stranded DNA and competitive bindings of 5-FU interacting with DNA–EB systems were examined by fluorescence spectra. The Stern–Volmer plots and fluorescence lifetime results confirm the static quenching nature of the drug-DNA complex. The binding constant Kb was 2.5 × 104 L mol-1 and the number of binding sites are 1.17. The 5-FU on DNA system was calculated using double logarithmic plot. From the Forster nonradiative energy transfer study it has been found that the distance of 5-FU from DNA was 4.24 nm. In addition to the spectroscopic results, the molecular modeling studies also revealed the major groove binding as well as the partial intercalation mode of binding between the 5-Fluorouracil and herring sperm DNA. The binding energy and major groove binding as -6.04 kcal mol-1 and -6.31 kcal mol-1 were calculated from the modeling studies. All the testimonies manifested that binding modes between 5-Fluorouracil and DNA were evidenced to be groove binding and in partial intercalative mode.

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49

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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50

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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Journal articles on the topic 'DNA binding'

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