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Journal articles on the topic 'Non-specific binding'

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Published: 4 June 2021
Last updated: 28 January 2023

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1

Flintoft, Louisa. "Surveying non-specific binding." Nature Reviews Genetics 14, no. 10 (September 18, 2013): 676. http://dx.doi.org/10.1038/nrg3586.

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2

Chen, Shi-Jie. "Site-Specific Binding of Non-Site-Specific Ions." Biophysical Journal 116, no. 12 (June 2019): 2237–39. http://dx.doi.org/10.1016/j.bpj.2019.04.038.

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3

Zenei, Taira, and Terada Hiroshi. "Specific and non-specific ligand binding to serum albumin." Biochemical Pharmacology 34, no. 11 (June 1985): 1999–2005. http://dx.doi.org/10.1016/0006-2952(85)90322-3.

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4

Shimizu, Seishi, Steven Abbott, Katarzyna Adamska, and Adam Voelkel. "Quantifying non-specific interactionsvialiquid chromatography." Analyst 144, no. 5 (2019): 1632–41. http://dx.doi.org/10.1039/c8an02244e.

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5

Mendel, C. M., and D. B. Mendel. "‘Non-specific’ binding. The problem, and a solution." Biochemical Journal 228, no. 1 (May 15, 1985): 269–72. http://dx.doi.org/10.1042/bj2280269.

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The concept of ‘non-specific’ binding, as it relates to studies of the binding of hormones to their receptors, is reviewed. It is concluded that the most widely used operational definition, namely binding that is not displaceable by an excess of unlabelled ligand, is often inaccurate, resulting either in overestimation of the number of high-affinity receptors and underestimation of the affinity of a given hormone for its receptor, or in a curvilinear Scatchard plot suggesting (artifactually) the presence of negative co-operativity or multiple classes of binding sites. The general use of an alternative approach to non-specific binding, in which the non-specific component is assessed from an analysis of total binding, is advocated. The superiority of this approach is illustrated with data on the binding of high-density lipoproteins to their receptors.
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6

Oda, Masayuki, Koji Furukawa, Kazuhiro Ogata, Akinori Sarai, and Haruki Nakamura. "Thermodynamics of specific and non-specific DNA binding by the c-myb DNA-binding domain." Journal of Molecular Biology 276, no. 3 (February 1998): 571–90. http://dx.doi.org/10.1006/jmbi.1997.1564.

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7

de Bruijn, Peter, Inge M. Ghobadi Moghaddam-Helmantel, Walter J. Loos, Ron H. J. Mathijssen, and Erik A. C. Wiemer. "The issue of non-specific binding of cabazitaxel." Journal of Chromatography B 932 (August 2013): 74–75. http://dx.doi.org/10.1016/j.jchromb.2013.06.016.

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8

Taylor, Thomas J., Gerald W. Parker, Abram B. Fajer, and Kay A. Mereish. "Non-specific binding of palytoxin to plastic surfaces." Toxicology Letters 57, no. 3 (August 1991): 291–96. http://dx.doi.org/10.1016/0378-4274(91)90203-i.

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9

Smith, Phil M., Indorica Sutradhar, Maxwell Telmer, Rishikesh Magar, Amir Barati Farimani, and B. Reeja-Jayan. "Isolating Specific vs. Non-Specific Binding Responses in Conducting Polymer Biosensors for Bio-Fingerprinting." Sensors 21, no. 19 (September 22, 2021): 6335. http://dx.doi.org/10.3390/s21196335.

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A longstanding challenge for accurate sensing of biomolecules such as proteins concerns specifically detecting a target analyte in a complex sample (e.g., food) without suffering from nonspecific binding or interactions from the target itself or other analytes present in the sample. Every sensor suffers from this fundamental drawback, which limits its sensitivity, specificity, and longevity. Existing efforts to improve signal-to-noise ratio involve introducing additional steps to reduce nonspecific binding, which increases the cost of the sensor. Conducting polymer-based chemiresistive biosensors can be mechanically flexible, are inexpensive, label-free, and capable of detecting specific biomolecules in complex samples without purification steps, making them very versatile. In this paper, a poly (3,4-ethylenedioxyphene) (PEDOT) and poly (3-thiopheneethanol) (3TE) interpenetrating network on polypropylene–cellulose fabric is used as a platform for a chemiresistive biosensor, and the specific and nonspecific binding events are studied using the Biotin/Avidin and Gliadin/G12-specific complementary binding pairs. We observed that specific binding between these pairs results in a negative ΔR with the addition of the analyte and this response increases with increasing analyte concentration. Nonspecific binding was found to have the opposite response, a positive ΔR upon the addition of analyte was seen in nonspecific binding cases. We further demonstrate the ability of the sensor to detect a targeted protein in a dual-protein analyte solution. The machine-learning classifier, random forest, predicted the presence of Biotin with 75% accuracy in dual-analyte solutions. This capability of distinguishing between specific and nonspecific binding can be a step towards solving the problem of false positives or false negatives to which all biosensors are susceptible.
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10

Fowers, K. D., and J. Kopeček. "Development of a fibrinolytic surface: specific and non-specific binding of plasminogen." Colloids and Surfaces B: Biointerfaces 9, no. 6 (September 1997): 315–30. http://dx.doi.org/10.1016/s0927-7765(97)00034-9.

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11

King, David J., Jiri G. Safar, Giuseppe Legname, and Stanley B. Prusiner. "Thioaptamer Interactions with Prion Proteins: Sequence-specific and Non-specific Binding Sites." Journal of Molecular Biology 369, no. 4 (June 2007): 1001–14. http://dx.doi.org/10.1016/j.jmb.2007.02.004.

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12

Shaw, S. M., and M. J. C. Crabbe. "Non-specific binding of advanced-glycosylation end-products to macrophages outweighs specific receptor-mediated interactions." Biochemical Journal 304, no. 1 (November 15, 1994): 121–29. http://dx.doi.org/10.1042/bj3040121.

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On binding to murine peritoneal macrophages, maleylated BSA exhibited saturable-binding kinetics, with about 24000 sites/cell. Prolonged incubation of BSA with > 20 mM glucose or 2 months incubation with > or = 0.5 M glucose induced the modified protein to readily bind non-specifically to both cell and tube surfaces. Kinetic studies on the binding of advanced glycated end-products (AGEs) and other modified proteins to macrophages and hepatocytes showed no evidence for specific receptor binding, as neither binding saturation nor cross-competition (homologous or heterologous) was detected. Although there was evidence for uptake of BSA which had been incubated with 0.5 M glucose for 2 months, there was no uptake or degradation of AGEs which had been produced at physiological concentrations of glucose. This has implications for the role of macrophages in the recognition of AGEs, and suggests that the non-specific binding may be important in adhesion of AGEs, particularly in poorly controlled diabetics, and might act as a ‘damage limitation’ mechanism in the potential development of diabetic complications, while low macrophage levels in the blood could seriously potentiate the long-term effects of non-enzymic post-translational protein modifications.
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13

Nirogi, Ramakrishna, Vishwottam Kandikere, Gopinadh Bhyrapuneni, Vijay Benade, Ramanatha Saralaya, Shantaveer Irappanavar, Nageswararao Muddana, and Devender Reddy Ajjala. "Approach to reduce the non-specific binding in microdialysis." Journal of Neuroscience Methods 209, no. 2 (August 2012): 379–87. http://dx.doi.org/10.1016/j.jneumeth.2012.06.010.

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14

Setiadi, H., and A. C. Herington. "Specific non-saturable binding of insulin by human platelets." Molecular and Cellular Endocrinology 43, no. 1 (November 1985): 23–30. http://dx.doi.org/10.1016/0303-7207(85)90038-3.

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15

Steiniger, M., C. D. Adams, J. F. Marko, and W. S. Reznikoff. "Defining characteristics of Tn5 Transposase non-specific DNA binding." Nucleic Acids Research 34, no. 9 (May 22, 2006): 2820–32. http://dx.doi.org/10.1093/nar/gkl179.

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16

Waterboer, Tim, Peter Sehr, and Michael Pawlita. "Suppression of non-specific binding in serological Luminex assays." Journal of Immunological Methods 309, no. 1-2 (February 2006): 200–204. http://dx.doi.org/10.1016/j.jim.2005.11.008.

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17

Hanukoglu, Israel. "Elimination of non-specific binding in Western blots from non-reducing gels." Journal of Biochemical and Biophysical Methods 21, no. 1 (June 1990): 65–68. http://dx.doi.org/10.1016/0165-022x(90)90046-f.

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18

Sadana, Ajit, and Zhanchi Chen. "Influence of non-specific binding on antigen-antibody binding kinetics for biosensor applications." Biosensors and Bioelectronics 11, no. 1-2 (January 1996): 17–33. http://dx.doi.org/10.1016/0956-5663(96)83710-9.

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19

DeMet, Edward, Kate Bell, Robert Gerner, Christopher Reist, and Aleksandra Chicz-DeMet. "Chronic imipramine increases platelet non-cyanoimipramine (CNIMI) binding but decreases cnimi specific binding." Biological Psychiatry 25, no. 7 (April 1989): A44. http://dx.doi.org/10.1016/0006-3223(89)91575-8.

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20

Storms, Fred E. M. G., Jos A. Lutterman, Alec H. Ross, Rob Hermsen, and Gerard van Lingen. "Non-specific binding of insulin in an equilibrium binding assay of insulin antibodies." Clinica Chimica Acta 161, no. 2 (December 1986): 147–55. http://dx.doi.org/10.1016/0009-8981(86)90208-1.

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21

Lesuisse, Dominique, Pierre Deprez, Eva Albert, Tran Thien Duc, Benoit Sortais, Dominique Gofflo, Véronique Jean-Baptiste, et al. "Discovery of Thioazepinone Ligands for Src SH2: From Non-specific to Specific Binding." Bioorganic & Medicinal Chemistry Letters 11, no. 16 (August 2001): 2127–31. http://dx.doi.org/10.1016/s0960-894x(01)00386-9.

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22

Hakami, Abdulrahim R., Jonathan K. Ball, and Alexander W. Tarr. "Non-ionic detergents facilitate non-specific binding of M13 bacteriophage to polystyrene surfaces." Journal of Virological Methods 221 (September 2015): 1–8. http://dx.doi.org/10.1016/j.jviromet.2015.04.023.

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23

Stracy, Mathew, Jakob Schweizer, David J. Sherratt, Achillefs N. Kapanidis, Stephan Uphoff, and Christian Lesterlin. "Transient non-specific DNA binding dominates the target search of bacterial DNA-binding proteins." Molecular Cell 81, no. 7 (April 2021): 1499–514. http://dx.doi.org/10.1016/j.molcel.2021.01.039.

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24

Pullen, Mark A., Mark R. Harpel, Theodore M. Danoff, and David P. Brooks. "Comparison of non-digitalis binding properties of digoxin-specific Fabs using direct binding methods." Journal of Immunological Methods 336, no. 2 (July 2008): 235–41. http://dx.doi.org/10.1016/j.jim.2008.05.005.

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25

Sarkar-Banerjee, Suparna, Sachin Goyal, Ning Gao, John Mack, Benito Thompson, David Dunlap, Krishnananda Chattopadhyay, and Laura Finzi. "Specifically bound lambda repressor dimers promote adjacent non-specific binding." PLOS ONE 13, no. 4 (April 2, 2018): e0194930. http://dx.doi.org/10.1371/journal.pone.0194930.

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26

Rosso, Lula, A. D. Gee, and I. R. Gould. "Towards in silico descriptors of PET ligands non-specific binding." NeuroImage 41 (January 2008): T99. http://dx.doi.org/10.1016/j.neuroimage.2008.04.068.

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27

Chan, Tom, Andrea Whitcher-Johnstone, Young-Sun Scaringella, and Mitchell Taub. "P6 - Comparison of techniques to assess non-specific microsomal binding." Drug Metabolism and Pharmacokinetics 35, no. 1 (2020): S24. http://dx.doi.org/10.1016/j.dmpk.2020.04.007.

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28

Nicholson, Suellen, David E. Leslie, Theodora Efandis, Christopher K. Fairley, and Ian D. Gust. "Hepatitis C antibody testing: problems associated with non-specific binding." Journal of Virological Methods 33, no. 3 (August 1991): 311–17. http://dx.doi.org/10.1016/0166-0934(91)90031-t.

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29

Farajollahi, Mohammad M., David B. Cook, Sepideh Hamzehlou, and Colin H. Self. "Reduction of non-specific binding in immunoassays requiring long incubations." Scandinavian Journal of Clinical and Laboratory Investigation 72, no. 7 (August 31, 2012): 531–39. http://dx.doi.org/10.3109/00365513.2012.702352.

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30

Mou, Tung-Chung, Michelle Shen, Saada Abdalla, Diego Delamora, Elena Bochkareva, Alexey Bochkarev, and Donald M. Gray. "Effects of ssDNA sequences on non-sequence-specific protein binding." Chirality 18, no. 5 (2006): 370–82. http://dx.doi.org/10.1002/chir.20262.

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31

Dai, H. "Use of hybridization kinetics for differentiating specific from non-specific binding to oligonucleotide microarrays." Nucleic Acids Research 30, no. 16 (August 15, 2002): 86e—86. http://dx.doi.org/10.1093/nar/gnf085.

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32

Segall, A. M., S. D. Goodman, and H. A. Nash. "Architectural elements in nucleoprotein complexes: interchangeability of specific and non-specific DNA binding proteins." EMBO Journal 13, no. 19 (October 1994): 4536–48. http://dx.doi.org/10.1002/j.1460-2075.1994.tb06775.x.

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33

Pray, Todd R., David S. Burz, and Gary K. Ackers. "Cooperative non-specific DNA binding by octamerizing λcI repressors: a site-specific thermodynamic analysis." Journal of Molecular Biology 282, no. 5 (October 1998): 947–58. http://dx.doi.org/10.1006/jmbi.1998.2056.

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34

Marques, Tiago Reis, Mattia Veronese, David R. Owen, Eugenii A. Rabiner, Graham E. Searle, and Oliver D. Howes. "Specific and non-specific binding of a tracer for the translocator-specific protein in schizophrenia: an [11C]-PBR28 blocking study." European Journal of Nuclear Medicine and Molecular Imaging 48, no. 11 (April 6, 2021): 3530–39. http://dx.doi.org/10.1007/s00259-021-05327-x.

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Abstract Objective The mitochondrial 18-kDa translocator protein (TSPO) is expressed by activated microglia and positron emission tomography enables the measurement of TSPO levels in the brain. Findings in schizophrenia have shown to vary depending on the outcome measure used and this discrepancy in TSPO results could be explained by lower non-displaceable binding (VND) in schizophrenia, which could obscure increases in specific binding. In this study, we have used the TSPO ligand XBD173 to block the TSPO radioligand [11C]-PBR28 and used an occupancy plot to quantify VND in patients with schizophrenia. Methods A total of 7 patients with a diagnosis of schizophrenia were recruited for this study. Each patient received two separate PET scans with [11C]PBR28, one at baseline and one after the administration of the TSPO ligand XBD173. All patients were high-affinity binders (HABs) for the TSPO gene. We used an occupancy plot to quantify the non-displaceable component (VND) using 2TCM kinetic estimates with and without vascular correction. Finally we computed the VND at a single subject level using the SIME method. Results All patients showed a global and generalized reduction in [11C]PBR28 uptake after the administration of XBD173. Constraining the VND to be equal for all patients, the population VND was estimated to be 1.99 mL/cm3 (95% CI 1.90 to 2.08). When we used vascular correction, the fractional TSPO occupancy remained similar. Conclusions In schizophrenia patients, a substantial component of the [11C]PBR28 signal represents specific binding to TSPO. Furthermore, the VND in patients with schizophrenia is similar to that previously reported in healthy controls. These results suggest that changes in non-specific binding between schizophrenia patients and healthy controls do not account for discrepant PET findings in this disorder.
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35

Stenlund, A. "E1 initiator DNA binding specificity is unmasked by selective inhibition of non-specific DNA binding." EMBO Journal 22, no. 4 (February 17, 2003): 954–63. http://dx.doi.org/10.1093/emboj/cdg091.

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36

Nedved, Michael L., and Gregory R. Moe. "Cooperative, non-specific binding of a Zinc finger peptide to DNA." Nucleic Acids Research 22, no. 22 (1994): 4705–11. http://dx.doi.org/10.1093/nar/22.22.4705.

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37

Artigas, Francesc, Emili Martínez, and Albert Adell. "Non-specific inhibition of imipramine binding argues against an endogenous ligand." European Journal of Pharmacology 181, no. 1-2 (May 1990): 9–15. http://dx.doi.org/10.1016/0014-2999(90)90239-3.

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38

Jones, Carolyn J. P., Sally M. Mosley, Iona J. M. Jeffrey, and R. W. Stoddart. "Elimination of the non-specific binding of avidin to tissue sections." Histochemical Journal 19, no. 5 (May 1987): 264–68. http://dx.doi.org/10.1007/bf01675685.

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39

Lesuisse, Dominique, and et al et al. "ChemInform Abstract: Discovery of Thioazepinone Ligands for Src SH2: From Non-specific to Specific Binding." ChemInform 32, no. 45 (May 23, 2010): no. http://dx.doi.org/10.1002/chin.200145206.

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40

Karamyan, Vardan T., Florian Gembardt, Felicia M. Rabey, Thomas Walther, and Robert C. Speth. "Characterization of the brain-specific non-AT1, non-AT2 angiotensin binding site in the mouse." European Journal of Pharmacology 590, no. 1-3 (August 2008): 87–92. http://dx.doi.org/10.1016/j.ejphar.2008.05.035.

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41

van Zoelen, E. J. J. "Receptor-ligand interaction: a new method for determining binding parameters without a priori assumptions on non-specific binding." Biochemical Journal 262, no. 2 (September 1, 1989): 549–56. http://dx.doi.org/10.1042/bj2620549.

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Analysis of receptor-ligand binding characteristics can be greatly hampered by the presence of non-specific binding, defined as low-affinity binding to non-receptor domains which is not saturable within the range of ligand concentrations used. Conventional binding analyses, e.g. according to the methods described by Scatchard or Klotz, relate the amount of specific receptor-ligand binding to the concentration of free ligand, and therefore require assumptions on the amount of non-specific binding. In this paper a method is described for determining the parameters of specific receptor-ligand interaction which does not require any assumption or separate determination of the amount of non-specific binding. If the concentration of labelled free ligand is constant, a plot of Fu/(B0*-B*) versus Fu yields a linear relationship, in the case of a single receptor class, in which Fu is the concentration of unlabelled free ligand, B0* is the total amount of labelled bound ligand in the absence of unlabelled ligand and B* is the total amount of labelled bound ligand in the presence of an unlabelled ligand concentration Fu; all of these data are readily obtained from binding studies. This linear relationship holds irrespective of the amount of non-specific binding, and the values for receptor density, ligand dissociation constant and a constant for non-specific binding can be readily obtained from it. If the concentration of labelled free ligand is not a constant for all data points, data are first converted according to a straightforward normalization procedure to permit the use of this relationship. The presence of multiple receptor classes with dissociation constants in the range of the ligand concentrations used results in a negative deviation from this linearity, and therefore the presence of multiple receptor classes can be discriminated unequivocally from non-specific binding. Both theoretical and practical advantages of the present method are described. The method, which will be referred to as the linear subtraction method, is illustrated using the binding of tumour promoters and polypeptide growth factors to their specific cellular receptors.
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42

Cox, Dermot, Toshiaki Aoki, Jiro Seki, Yukio Motoyama, and Keizo Yoshida. "Pentamidine Is a Specific, Non-Peptide, GPIIb/llla Antagonist." Thrombosis and Haemostasis 75, no. 03 (1996): 503–9. http://dx.doi.org/10.1055/s-0038-1650305.

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SummaryPentamidine was previously shown to act on glycoprotein (GP) Ilb/IIIa (Cox et al., Thromb Haemost 1992; 68: 731). In this paper we study the effect of pentamidine on other RGD-dependent receptors. In a cell adhesion assay, pentamidine was 500 times more potent than RGDS at inhibiting platelet adhesion to fibrinogen. While RGDS inhibited platelet adhesion to fibronectin, endothelial cell adhesion to vitronectin or fibronectin, 293 cell adhesion to vitronectin, IMR 32 cell adhesion to fibronectin and C32 cell adhesion to vitronectin; pentamidine failed to inhibit these interactions at doses as high as 1 mM. Resting platelets fixed in the presence of 1 mM RGDS had increased binding of fibrinogen, i.e., RGDS activated GPIMIIa, while pentamidine at 100 ΜM had no effect. Similarly, RGDS induced the binding of an anti-LIBS monoclonal antibody, while pentamidine had no effect. Pentamidine partially, but significantly, inhibited lysosome and a-granule release induced by the thrombin agonist peptide, while RGDS had no effect. Neither pentamidine nor RGDS affected ADP-induced Ca2+ influx. Pentamidine had no effect on ADP-induced intracellular pH changes while RGDS prevented the pH from returning to normal. Thus, pentamidine is a non-peptide GPIIb/IIIa antagonist that is non-activating and is specific for GPIIb/IIIa.
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43

Caccianini, Laura, Davide Normanno, Ignacio Izeddin, and Maxime Dahan. "Single molecule study of non-specific binding kinetics of LacI in mammalian cells." Faraday Discussions 184 (2015): 393–400. http://dx.doi.org/10.1039/c5fd00112a.

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Many key cellular processes are controlled by the association of DNA-binding proteins (DBPs) to specific sites. The kinetics of the search process leading to the binding of DBPs to their target locus are largely determined by transient interactions with non-cognate DNA. Using single-molecule microscopy, we studied the dynamics and non-specific binding to DNA of the Lac repressor (LacI) in the environment of mammalian nuclei. We measured the distribution of the LacI–DNA binding times at non-cognate sites and determined the mean residence time to be τ1D = 182 ms. This non-specific interaction time, measured in the context of an exogenous system such as that of human U2OS cells, is remarkably different compared to that reported for the LacI in its native environment in E. coli (<5 ms). Such a striking difference (more than 30 fold) suggests that the genome, its organization, and the nuclear environment of mammalian cells play important roles on the dynamics of DBPs and their non-specific DNA interactions. Furthermore, we found that the distribution of off-target binding times follows a power law, similar to what was reported for TetR in U2OS cells. We argue that a possible molecular origin of such a power law distribution of residence times is the large variability of non-cognate sequences found in the mammalian nucleus by the diffusing DBPs.
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44

Vipond, I. Barry, and Stephen E. Halford. "Structure?function correlation for the EcoRV restriction enzyme: from non-specific binding to specific DNA cleavage." Molecular Microbiology 9, no. 2 (July 1993): 225–31. http://dx.doi.org/10.1111/j.1365-2958.1993.tb01685.x.

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45

Matsuki, H. "Specific and non-specific binding of long-chain fatty acids to firefly luciferase: cutoff at octanoate." Biochimica et Biophysica Acta (BBA) - General Subjects 1426, no. 1 (January 4, 1999): 143–50. http://dx.doi.org/10.1016/s0304-4165(98)00148-2.

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46

Shaw, Seán M., and M. James C. Crabbe. "Non-specific binding of lysine-glucose-derived Maillard products to macrophages outweighs specific receptor-mediated interactions." Food Chemistry 52, no. 4 (January 1995): 399–404. http://dx.doi.org/10.1016/0308-8146(95)93289-4.

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47

Park, Jihyun, Seonghyun Lee, Nabin Won, Eunji Shin, Soo-Hyun Kim, Min-Young Chun, Jungyeun Gu, Gun-Young Jung, Kwang-Il Lim, and Kyubong Jo. "Single-molecule DNA visualization using AT-specific red and non-specific green DNA-binding fluorescent proteins." Analyst 144, no. 3 (2019): 921–27. http://dx.doi.org/10.1039/c8an01426d.

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48

Gopi, Soundhararajan, and Athi N. Naganathan. "Non-specific DNA-driven quinary interactions promote structural transitions in proteins." Physical Chemistry Chemical Physics 22, no. 22 (2020): 12671–77. http://dx.doi.org/10.1039/d0cp01758b.

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We show strong evidence for the long-range electrostatic potential of DNA to influence the conformational status and distribution of states accessible to a protein chain well before the binding event.
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49

Pal, Soumitra, Jan Hoinka, and Teresa M. Przytycka. "Co-SELECT reveals sequence non-specific contribution of DNA shape to transcription factor binding in vitro." Nucleic Acids Research 47, no. 13 (June 21, 2019): 6632–41. http://dx.doi.org/10.1093/nar/gkz540.

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Abstract Understanding the principles of DNA binding by transcription factors (TFs) is of primary importance for studying gene regulation. Recently, several lines of evidence suggested that both DNA sequence and shape contribute to TF binding. However, the following compelling question is yet to be considered: in the absence of any sequence similarity to the binding motif, can DNA shape still increase binding probability? To address this challenge, we developed Co-SELECT, a computational approach to analyze the results of in vitro HT-SELEX experiments for TF–DNA binding. Specifically, Co-SELECT leverages the presence of motif-free sequences in late HT-SELEX rounds and their enrichment in weak binders allows Co-SELECT to detect an evidence for the role of DNA shape features in TF binding. Our approach revealed that, even in the absence of the sequence motif, TFs have propensity to bind to DNA molecules of the shape consistent with the motif specific binding. This provides the first direct evidence that shape features that accompany the preferred sequence motifs also bestow an advantage for weak, sequence non-specific binding.
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Rademaker, Ben, Klaas Kramer, Huub van Ingen, Michel Kranendonk, and Henk Timmerman. "Non-Specific Binding of the Fluorescent B-Adrenergic Receptor Probe Alprenolol-NBD." Journal of Receptor Research 5, no. 2-3 (January 1985): 121–31. http://dx.doi.org/10.3109/10799898509041874.

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