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Academic literature on the topic 'DNA binding studies'

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Published: 10 December 2022
Last updated: 28 January 2023

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Journal articles on the topic "DNA binding studies"

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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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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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Mehd, K. M., K. Soheila, R. Hamideh, and P. Hossein. "DNA binding studies of Chloridazon." New Biotechnology 25 (September 2009): S366—S367. http://dx.doi.org/10.1016/j.nbt.2009.06.978.

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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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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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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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WILLIAMS, JOHN S., JACK E. DIXON, and OURANIA M. ANDRISANI. "Binding Constant Determination Studies Utilizing Recombinant ΔCREB Protein." DNA and Cell Biology 12, no. 2 (March 1993): 183–90. http://dx.doi.org/10.1089/dna.1993.12.183.

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Bentley, Emily P., Peter E. Wright, and Ashok A. Deniz. "Mechanistic Studies of CREB-DNA Binding." Biophysical Journal 120, no. 3 (February 2021): 310a—311a. http://dx.doi.org/10.1016/j.bpj.2020.11.1971.

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Sampath, K., and C. Jayabalakrishnan. "Ruthenium(III) Thiosemicarbazone Complexes: Synthesis, Characterization, DNA Binding, Antibacterial, In vitro Anticancer and Antioxidant Studies." DJ Journal of Engineering Chemistry and Fuel 1, no. 1 (January 2, 2016): 40–53. http://dx.doi.org/10.18831/djchem.org/2016011004.

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Roviello, Giovanni N., Domenica Musumeci, Maria Moccia, Mariangela Castiglione, Roberto Sapio, Margherita Valente, Enrico M. Bucci, Giuseppe Perretta, and Carlo Pedone. "dabPna: Design, Synthesis, And Dna Binding Studies." Nucleosides, Nucleotides and Nucleic Acids 26, no. 10-12 (November 26, 2007): 1307–10. http://dx.doi.org/10.1080/15257770701530640.

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Janjua, Naveed Kausar, Amber Shaheen, Azra Yaqub, Fouzia Perveen, Sana Sabahat, Misbah Mumtaz, Claus Jacob, Lalla Aicha Ba, and Hamdoon A. Mohammed. "Flavonoid–DNA binding studies and thermodynamic parameters." Spectrochimica Acta Part A: Molecular and Biomolecular Spectroscopy 79, no. 5 (September 2011): 1600–1604. http://dx.doi.org/10.1016/j.saa.2011.05.018.

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Dissertations / Theses on the topic "DNA binding studies"

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Umurtak, H. B. "Studies on DNA-binding peptides]." Thesis, University of Southampton, 1989. http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.235192.

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Rodríguez, Armando Chapin. "Structure-function studies of DNA-binding motors." Thesis, University of Cambridge, 2003. http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.619565.

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Komori, Hirofumi. "Structural studies on DNA-binding proteins : DNA replication initiator and DNA photolyase." 京都大学 (Kyoto University), 2002. http://hdl.handle.net/2433/150005.

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Daly, Colette Lynn. "Binding studies using membrane electrodes." Thesis, University of Salford, 1989. http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.252942.

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The research embodied within this thesis has contributed to the development and application of a novel electrode technique. The electrodes fabricated herein consist of a thin PVC/Poly (vinylchloride) membrane which is made sensitive to a particular organic cation, for example Acridine Orange. The only requirements necessary to make an electrode were that the substance to be incorporated into the membrane be cationic, water soluble and surface active. These membrane electrodes gave an emf directly proportional to the log of the ( concentration of organic cations present in solution.
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Menderin, Nathan. "Studies on the Human Sp1 DNA-Binding Domain." Thesis, University of Exeter, 2009. http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.507135.

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Hill, G. R. "NMR studies of DNA and RNA binding proteins." Thesis, University of Cambridge, 2005. http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.604060.

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HMG-D is a 112-residue, non-histone chromosomal protein from Drosophila melanogaster and is a member of the class of non-sequence specific HMGB proteins. The present project was based on the observation that other HMGB complexes that had been solved by NMR had a phenylalanine residue at a key interfacial location (corresponding to position 12 in HMG-D), whereas those like HMG-D that gave few intermolecular NOE cross peaks generally had a tyrosine at this location. This tyrosine was known to be involved in hydrogen-bonding to the DNA in a related complex that had been solved crystallographically. The Y12F mutant of full-length HMG-D was expressed and purified in isotope-labelled form suitable for NMR spectroscopy, and a set of multidimensional triple resonance experiments used to derive assignments for the backbond resonances of the protein both free and in complex with the dA2 bulge DNA. Sidechain assignments for the protein were obtained by a combination of “CCH”-transfer-based experiments and NOE spectra, while nearly complete assignments for the DNA in the complex were obtained from a combination of homonuclear 2D NOESY and TOCSY experiments together with filtered NOESY experiments where just cross peaks between protons both of which were not coupled to heteronuclei were selected. Filtered NOESY-based experiments were used to observe intermolecular NOE cross peaks in isolation, and, in contrast to the case of the wild-type complex, these experiments yielded around 50 intermolecular interactions. Together with an extensive set of assigned intramolecular NOE constraints, these formed the basis for a calculation of the structure of the complex starting from random conformations of both protein and DNA chains, which resulted in an NMR structure for the complex that had good precision over the structured region (residues 3-70 of the protein and stem 1 of the DNA).
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Maynard, Allister J. "NMR studies of protein folding and DNA binding." Thesis, University of Nottingham, 1999. http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.313244.

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Povey, Jane. "Structural studies of the DNA-binding protein GAL4." Thesis, University of Cambridge, 1990. http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.385462.

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Scarpantonio, Luca. "Studies of DNA binding of lanthanide platinum complexes." Thesis, University of Birmingham, 2011. http://etheses.bham.ac.uk//id/eprint/2860/.

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Using supramolecular principles, we have been designing luminescent lanthanide complexes with a defined hairpin bis-interlacator in order to obtain luminescent probes able to recognise DNA. The complexes are comprised of Platinum(II) terpyridine, which acts as a DNA recognition site and is brought together with a "remote" luminescent lanthanide unit. All the synthetic approaches were based on the accessibility of the lanthanide-platinum complexes by the self-assembly of different components in a one pot reaction. Thus, we have been able to isolate a water soluble heterometallic complex based on thiophenal linkage named [LnPt\(_2\)]Cl\(_2\). The complex has a relatively weak lanthanide luminescence, which increases upon addition of DNA. Photophysical and DNA binding properties of the lanthanide-platinum complex were investigated by UV-vis absorption, luminescent studies and circular and linear dichroism. Oligonucleotides of twelve bases were also used to investigate the intercalation [LnPt\(_2\)]Cl\(_2\) and the mono-intercalator AATP used as control compound. Using bidimensional NMR techniques, we investigated the binding site for [LnPt\(_2\)]Cl\(_2\) and AATP upon interaction with Dickerson-Drew sequence. The sulphur lanthanide-platinum linkage in [LnPt\(_2\)]Cl\(_2\) was replaced with an acetylide one in order to introduce new photophysical features. Thus the self-assembly procedures based on DTPA-bis(amido-acetylide) and a platinum(II) terpyridine led us to isolate a new lanthanide-platinum complex named [LnC\(\equiv\)CPt\(_2\)] (CH\(_3\)SO\(_3\))\(_2\). The photophysical properties and the DNA binding properties toward interaction with CT-DNA were investigated. The complex named LnC\(\equiv\)CPt\(_2\)](CH\(_3\)S)\(_3\))\(_2\) exhibited a relatively strong lanthanide luminescence that increased upon addition of DNA. The bi-functional metal complex [EuLPt](PF\(_6\)) (where Pt=platinum-2,2':6'2"-terpyridine and L=assymmetric DTPA bisamide ligand with a thiopheno pendant arm and a quinoline moiety) was synthesised and the interaction of [EuLPt](PF\(_6\)) with CT-DNA was examined by luminescence spectroscopy, linear and circular dichroism studies and thermal denaturation studies. The [EuLPt](PF\(_6\)) retained the ability to increase its luminescence upon the addition of CT-DNA. The binding properties of the complexes were tested toward interaction with plasmid DNA by gel electrophoresis and properties such as the unwinding angle were measured. The bis-intercalators [LnPt\(_2\)]Cl\(_2\) and [LnC\(\equiv\)CPt\(_2\)](CH\(_3\)SO\(_3\))\(_2\) showed the ability to uncoil DNA almost as well as cisplatin and at low concentrations, while almost double the amount of mono-intercalators, such as [EuLPt](PF\(_6\)) is required to observe the same uncoiling effect.
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Mack, Lynsey A. "Studies of extremophilic single-stranded DNA-binding proteins." Thesis, University of Edinburgh, 2005. http://hdl.handle.net/1842/12512.

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In this study, 6 bacterial SSBs are investigated which have been obtained from 4 different Shewanella strains, from Aquifex aeolicus and from E. coli. The 4 Shewanella SSBs have been taken from strains isolated at different depths of the ocean, from sea-level down to 8600m. These organisms therefore differ in their growth pressure optima. By comparing the characteristics of each of these proteins, differences will lead to clues which relate to the pressure differences. In order to highlight the different adaptations of these proteins, the thermophilic SSB from Aquifex aeolicus and the mesophilic SSB from E. coli were used as benchmarks to the piezophilic Shewanella SSBs. Circular dichroism was used to determine proportions of secondary structure present in each SSB and these were compared to the values obtained from previous crystallography work on the E. coli, in order to get some preliminary details about each structure. Further biophysical work was carried out using ITC and DSC which provided thermodynamic data regarding the binding between ssDNA and SSB, and also probed the denaturation temperatures of each protein. Exhaustive crystallisation trials were carried out on each Shewanella SSB but unfortunately did not produce any crystals of sufficient quality. As AqSSB had previously been crystallised, the structure determination is described in this study. To complement the binding data, a crystal of AqSSB in complex with ssDNA was produced and its structure determined. The structure showed great similarities with the several previously published structures of EcoSSB. Therefore this study is focussed on SSB proteins from bacteria isolated form very different habitats. By comparing their various structural and biophysical properties, further clues as to how piezophilic proteins are able to survive extreme pressures may be gained.
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Books on the topic "DNA binding studies"

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Tang, Shaojun. Studies on the DNA binding activity of HOX11 protein. Ottawa: National Library of Canada, 1994.

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Steitz, Thomas A. Structural studies of protein-nucleic acid interaction: Thesources of sequence-specific binding. Cambridge: Cambridge University Press, 1993.

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Steitz, Thomas A. Structural studies of protein-nucleic acid interaction: The sources of sequence-specific binding. New York, NY, USA: Cambridge University Press, 1993.

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Ray, Pampa. DNA binding studies of the transcriptional activator NifA and its C-terminal domain. Birmingham: University of Birmingham, 2000.

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Reynolds, Lindsey. DNA binding and structural studies of truncated forms of the AreA protein from Aspergillus nidulans. Portsmouth: University of Portsmouth, Dept. of Cell and Molecular Biology, 1998.

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Lnenicek-Allen, Mirna. Studies of the DNA binding and bending properties of HMG boxes using in vitro mutagenesis. Portsmouth: University of Portsmouth, School of Biological Sciences, 1998.

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Saluz, H. P. A laboratory guide for in vivo studies of DNA methylation and protein/DNA interactions. Basel: Birkhäuser Verlag, 1990.

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Garcia, Stephanie Jocelyn. New platinum(IV) molecular probes: Synthesis, characterization, and DNA binding studies. 1997.

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Pan, Guohua. Studies on the DNA-binding and strand ligation of the FLP recombinase. 1993.

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Winkle, Samina Van. Diethylnitrosamine, ethylnitrosourea, and dimethylbenz(a)anthracene DNA binding studies in the rainbow trout. 1988.

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Book chapters on the topic "DNA binding studies"

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Ryzhikov, Mikhail, and Sergey Korolev. "Structural Studies of SSB Interaction with RecO." In Single-Stranded DNA Binding Proteins, 123–31. Totowa, NJ: Humana Press, 2012. http://dx.doi.org/10.1007/978-1-62703-032-8_7.

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Bianco, Piero R., Adam J. Stanenas, Juan Liu, and Christopher S. Cohan. "Fluorescent Single-Stranded DNA-Binding Proteins Enable In Vitro and In Vivo Studies." In Single-Stranded DNA Binding Proteins, 235–44. Totowa, NJ: Humana Press, 2012. http://dx.doi.org/10.1007/978-1-62703-032-8_18.

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Srivastava, V. K. "DNA-Binding and Antimicrobial Studies of Molybdenum Complexes." In Next Generation DNA Led Technologies, 97–104. Singapore: Springer Singapore, 2015. http://dx.doi.org/10.1007/978-981-287-670-6_11.

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Maher, L. James. "Studies of Sequence-Nonspecific HMGB DNA-Binding Proteins." In Biological and Medical Physics, Biomedical Engineering, 143–62. New York, NY: Springer New York, 2010. http://dx.doi.org/10.1007/978-0-387-92808-1_7.

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Cardin, Christine J., and James P. Hall. "Chapter 8. Structural Studies of DNA-binding Metal Complexes of Therapeutic Importance." In DNA-targeting Molecules as Therapeutic Agents, 198–227. Cambridge: Royal Society of Chemistry, 2018. http://dx.doi.org/10.1039/9781788012928-00198.

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Jost, Jean-Pierre. "Exonuclease III Protection Assay for Specific DNA-Binding Proteins." In A Laboratory Guide to In Vitro Studies of Protein-DNA Interactions, 35–43. Basel: Birkhäuser Basel, 1991. http://dx.doi.org/10.1007/978-3-0348-7561-5_3.

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Steitz, T. A., L. Beese, B. Engelman, P. Freemont, J. Friedman, M. Sanderson, S. Schultz, G. Shields, and J. Warwicker. "Structural Studies of Three DNA Binding Proteins: Catabolite Gene Activator Protein, Resolvase, and the Klenow Fragment of DNA Polymerase I." In DNA—Ligand Interactions, 185–89. Boston, MA: Springer US, 1987. http://dx.doi.org/10.1007/978-1-4684-5383-6_13.

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Hughes, Melya J., Jean-Pierre Jost, and Josef Jiricny. "Purification of Sequence-Specific DNA-Binding Proteins by Affinity Chromatography." In A Laboratory Guide to In Vitro Studies of Protein-DNA Interactions, 221–31. Basel: Birkhäuser Basel, 1991. http://dx.doi.org/10.1007/978-3-0348-7561-5_17.

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Matthias, Patrick, Michael M. Müller, and Walter Schaffner. "Cloning of Sequence-Specific DNA-Binding Proteins by Screening λ cDNA Expression Libraries with Radiolabelled Binding-Site Probes." In A Laboratory Guide to In Vitro Studies of Protein-DNA Interactions, 233–44. Basel: Birkhäuser Basel, 1991. http://dx.doi.org/10.1007/978-3-0348-7561-5_18.

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Hu, Xiao-Yu, Xiang-Qun Li, and Rui Wang. "Studies on the synthesis and DNA-binding activity of zinc finger motif." In Peptides, 28–30. Dordrecht: Springer Netherlands, 1995. http://dx.doi.org/10.1007/978-94-010-9069-8_6.

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Conference papers on the topic "DNA binding studies"

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Dixon, D., W. Wilson, V. Steullet, and S. Takenaka. "Studies of Naphthalene Diimides as DNA-binding Agents." In The 1st International Electronic Conference on Synthetic Organic Chemistry. Basel, Switzerland: MDPI, 1997. http://dx.doi.org/10.3390/ecsoc-1-02060.

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Fujimoto, Bryant S., James B. Clendenning, Jeffrey J. Delrow, Patrick J. Heath, and J. M. Schurr. "Fluorescence and photobleaching studies of methylene blue binding to DNA." In OE/LASE '94, edited by Joseph R. Lakowicz. SPIE, 1994. http://dx.doi.org/10.1117/12.182780.

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Kanchanadevi, S., S. Parveen, and V. Mahalingam. "Synthesis, characterization, crystal structure and DNA-binding studies of transition metal hydrazone complexes." In 9TH NATIONAL CONFERENCE ON THERMOPHYSICAL PROPERTIES (NCTP-2017). Author(s), 2018. http://dx.doi.org/10.1063/1.5031734.

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Kenneally, D. A., P. J. Thurlow, and J. M. Cornellan. "MONOCLONAL ANTIBODY (ANTI-2B6D4) TO PLASMA FIBRONECTIN INHIBITS COLLAGEN AND THROMBIN INDUCED AGGREGATION OF WASHED PLATELETS." In XIth International Congress on Thrombosis and Haemostasis. Schattauer GmbH, 1987. http://dx.doi.org/10.1055/s-0038-1643861.

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Fibronectins(Fns) constitute a family of large glycoproteins which are known to bind to a wide range of biological molecules eg.collagen, gelatin, fibrin, heparin and DNA,and to many cells including platelets via discrete structural domains. A murine monoclonal antibody (anti-2B6D4) produced by imnunizing BALB/c mice with plasma fn, was used to study the structure and function of fn and its platelet interaction Anti-2B6D4 reacted specifically with plasma fn was unreactive with FVIII/vWF,BTG,PF4 collagen and fibrinogen nor was it reactive with platelets (unstiraulated), human PBLs or a range of tumour cell lines. Iirmuno-blotting studies( 8% SDS-PAGE) using thermolysin-digested plasma fn with anti-2B6D4 indicated that the 2B6D4 epitope was present on only 2 of the 7 fragments detected by Indian ink. The 2 fragments had an Mr of 145 and 155 K dal tons and have been reported to each contain domains which bind cells, DNA and heparin. These fragments were studied further by examining the effect of anti-2B6D4 (Fabs) on the binding of 125I-fn to thrombin-stimulated platelets and demonstrated that anti-2B6D4 binding was inhibited by 50% thus implicating the 2B6D4 epitope as a platelet binding site within the two cell binding domains. Competitive binding analysis of 125I-fn to solid-phase macromolecules i.e.collagen, gelatin, fibrin, heparin, DNA and Con A demonstrated that anti-2B6D4 (Fabs) inhibited the binding of fn to DNA by 50%,but not to the other macromolecules. Therefore, either the DNA and platelet binding sites are shared or the inhibition is due to steric hindrance. However, as Fab fragments of anti-2B6D4 were used, it is more likely that the binding sites are shared. Functional studies were performed to investigate the role of 2B6D4 in platelet-platelet interaction. Anti-2B6D4 totally blocked the aggregation of washed platelets stimulated by low dose collagen (1.6ug/ml) and thrombin (0.05U/ml), partially inhibited arachidonic acid (250ugs/ml) induced platelet aggregation and had no effect on aggregation induced by A23187 (30uM). One other report had demonstrated that fn is a requirement for A23187 and low dose thrombin induced platelet aggregation. We conclude that fn plays an essential role in platelet aggregation induced by low dose collagen and thrombin.
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Guillén, Ma José, Oscar Cataluña, Mandy Palomares, Raquel Lopez, Carmen Cuevas, and Pablo M. Aviles. "Abstract 3538: In vivo combination studies of PM01183 with alkylating, antimetabolites, DNA-topoisomerase inhibitors and tubulin binding agents." In Proceedings: AACR 102nd Annual Meeting 2011‐‐ Apr 2‐6, 2011; Orlando, FL. American Association for Cancer Research, 2011. http://dx.doi.org/10.1158/1538-7445.am2011-3538.

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Matić, Sanja, Snežana Stanić, Nevena Tomašević, Rino Ragno, and Milan Mladenović. "DISCLOSING THE TRUE NATURE OF HESPERETIN’S ANTIGENOTOXICITY „IN VIVO“ WITHIN THE „DROSOPHILA MELANOGASTER“ SOMATIC CELLS THROUGH THE EXTENSIVE GENOTOXICAL AND STRUCTURE-BASED STUDIES." In 1st INTERNATIONAL Conference on Chemo and BioInformatics. Institute for Information Technologies, University of Kragujevac, 2021. http://dx.doi.org/10.46793/iccbi21.427m.

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Previously unreported genotoxic and antigenotoxic potentials of hesperetin (Hes) were revealed by treating the Drosophila melanogaster (dm) whose DNA has been altered by means of O6-ethylguanine (dmGO6-Et) and O4-ethylthymine (dmTO4-Et) lesions appearance, caused by ethyl methanesulfonate (EMS), a proven alkylating agent and mutagen. Therefore, Hes potencies were determined by means of the comet assay on somatic cells level, where compound exerted no genotoxic effects but acted genotoxically as a Topoisomerase IIα (dmTopIIα) catalytic inhibitor by invading the Binding and Cleavage Domain and stabilizing the noncovalent dmTopIIα-plasmid DNA (dmPDNA) complex, as verified by the kinetoplast DNA (dmK-DNA) decatenation assays. Hes’s structure-based alignment caused compound’s A and C rings to occupy the area normally invaded by EMS, thus making a spatial barrier for the dmGO6-Et or dmTO4-Et lesions formation: the A ring C7-OH group formed hydrogen bonds (HBs) with either dmGO6 (dHB = 2.576 Å) or guanine’s N7 nitrogen (dmGN7, dHB = 2.737 Å), whereas the A ring C5-OH group formed an HB with dmTO4 (dHB = 3.548 Å). Furthermore, Hes likewise acted as a mixed-type competitive inhibitor of dmATPase, as verified by the catalytic, FRET, and structure-based studies where it affected the dmATPase dimerization and the hydrolysis of ATP, denying the metabolic energy for the catenation of ethylated G-dmDNA segment, the formation of dmTO4-Et-G-dmDNA phosphotyrosine intermediate (dmTO4-Et-G- dmDNA-PTyr785I), and the passage of ethylated T-dmDNA segment through the temporarily broken dmTO4-Et-G-dmDNA-PTyr785I, processes seen as comets. Conclusively, Hes may be used in anticancer therapy controlling the effects of alkylating agents.
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Koutts, K., and T. Exner. "HIGH INCIDENCE OF CARDIOLIPIN-BINDING ANTIBODIES IN PATIENTS TAKING ORAL ANTICOAGULANTS." In XIth International Congress on Thrombosis and Haemostasis. Schattauer GmbH, 1987. http://dx.doi.org/10.1055/s-0038-1644239.

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It is known that patients with thrombosis in autoimmune disease often suffer recurrent thrombotic episodes on withdrawl of oral anticoagulants, frequently have raised ACA and may require long term therapy. In view of the association between lupus inhibitors, phospholipid binding antibodies and thrombotic episodes we investigated a broad group of patients (n=140) taking oral anticoagulants for anti-cardiolipin antibodies (ACA).The incidence of raised ACA (defined here as more than 5 S. D. above normal) was 10%, in comparison with less than 2% in both healthy volunteers and randomized hospital patients. Analysis of patients with raised ACA indicated an approximately equal distribution among those with artifical valves and patients treated for thrombotic episodes. ANF and DNA binding studies were negative in most cases and a lupus inhibitor (KCT mixing test) was detectable only in 1/15. APTT/PT ratios were not significantly high in comparison with other clinic patients. The-ACA were predominantly IgG (12/15) in contrast to those fpund in females with recurrent abortions which are frequently IgM's. The binding antibodies appeared to be much weaker in the presence of calcium than in phosphate buffered saline.The patients having high ACA had no excess thrombotic or bleeding complications during their treatment compared with others in this group. This suggests that thrombotic or occlusive events associated with ACA may be adequately treated with oral anti-coagulants.
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Leyte, A., R. F. Evers, and M. Ph Verbeet. "EPITOPE MAPPING OF HUMAN COAGULATION FACTOR VIII WITH IN VITRO SYNTHESIZED FRAGMENTS OF THE PROTEIN." In XIth International Congress on Thrombosis and Haemostasis. Schattauer GmbH, 1987. http://dx.doi.org/10.1055/s-0038-1644043.

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We have used recombinant DNA techniques to map the epitopes of the coagulation Factor VIII for several monoclonal antibodies, raised against this protein. For this purpose, we cloned full- length- and partial Factor VIII cDNA sequences in the vector pSP64. Corresponding RNA fragments were synthesized in vitro with SP6 RNA polymerase and translated in a rabbit reticulocyte lysate system. The resulting Factor VII. I polypeptide fragments were immunoprecipitated. We have located the binding sites of a panel of monoclonal anti-Factor VIII antibodies. Two examples are shown in the figure below. The epitopes for anti-Factor VIII CLB-9 and CLB-65 have been confined to areas of 29 (711-740) and 142 (1635-1777) amino acids, respectively. The results of these studies will be useful in determining structure-function relationships of Factor VIII
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Spitzer, S. G., P. Usharani, A. D. Roser, C. K. Kasper, and S. G. Bajaj. "THE CATALYTIC TRIAD RESIDUES (HIS221, ASP269, SER365) AND THE BINDING POCKET RESIDUE (ASP359) IN FACTOR IXBm ELSINORE (IXBmLE) ARE NOT ALTERED." In XIth International Congress on Thrombosis and Haemostasis. Schattauer GmbH, 1987. http://dx.doi.org/10.1055/s-0038-1644071.

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Previous studies suggested that the defect in IXBmLE (a nonfunctional variant of human IX) is either in the catalytic triad or at the site(s) of interaction with the macromolecular substrates (antithrombin III, factor VII or factor X). To distinguish between these possibilities, we isolated a complete IX cDNA clone from a human liver cDNA library. We also constructed a genomic library (in phage EMBL3) using DNA of the BmLE patient. The library was screened with normal IX cDNA and with synthetic oligonucleotides. The positive clones containing the exons coding for IX were plaque purified. Two clones which contained the coding sequence of the catalytic domain, i.e., His221 (exon VII), and Asp269, Asp359, and Ser365 (exon VIII) were selected for further studies. The phage containing exon VIII was first digested with Sail and EcoRI and a 2-Kb fragment, which hybridized with the segment of cDNA containing exon VIII, was gel purified. The 2-Kb fragment was further digested and the subfragments were cloned into M13; the length and direction of the fragments used in sequencing are shown below:The phage containing exon VII was digested with PstI and SalI, and a 1-Kb fragment that hybridized with the 19-mer His221 probe was subcloned into M13 phage for sequencing. The sequence starting with residue Vall96 through residue Arg403 was found to be normal. Thus, none of the residues in the catalytic domain of IXBmLE are different from that of normal IX. These data provide strong indirect evidence that the noncatalytic aminoterminal portion of IX plays a significant role in the structural recognition of the macromolecular substrates. The sequence of this region of IXBmLE should provide information about the putative residue(s) essential for this recognition.
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Milović, Emilija, Nenad Janković, Jelena Petronijević, and Nenad Joksimović. "CHEMICO-BIOLOGICAL INTERACTION OF SELECTED TETRAHYDROPYRIMIDINES." In 1st INTERNATIONAL Conference on Chemo and BioInformatics. Institute for Information Technologies, University of Kragujevac, 2021. http://dx.doi.org/10.46793/iccbi21.347m.

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Tetrahydropyrimidines (THPMs) attracted attention as a very important class of aza heterocycles with broad pharmacological activities during the past years. In many studies have been proven that THPMs have anticancer, anti-inflammatory, antimicrobial, antioxidant, antifungal, anti-HIV activity. Bearing in mind our interest in medicinal and Biginelli chemistry, we investigated interaction with important biomacromolecules (DNA, BSA) and our earlier synthetized THPMs derivatives with proven very good cytotoxic activity.[1] Investigation of affinity of compounds A and B (Figure 1) to bind to bovine serum albumin (BSA) is based on the fact that the efficiency of drugs depends on their ability to bind for carrier protein. Binding properties were investigated by using the fluorescence emission titration of BSA with A and B. The obtained values of Ka, which are in optimum range which is considered to be 106-107M-1 indicate that both compounds have great ability to bind to BSA. In addition, Ka values for A-BSA and B-BSAshow that both compounds are suitable for drug-cell
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Reports on the topic "DNA binding studies"

1

Rastinejad, Fraydoon. Structure/Function Studies of the Androgen Receptor DNA-Binding Region. Fort Belvoir, VA: Defense Technical Information Center, April 2001. http://dx.doi.org/10.21236/ada398061.

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Hanke, Andreas. Studies of Single Biomolecules, DNA Conformational Dynamics, and Protein Binding. Fort Belvoir, VA: Defense Technical Information Center, July 2008. http://dx.doi.org/10.21236/ada483440.

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Rastinejad, Fraydoon. Structure/Function Studies of the Androgen Receptor DNA-Binding Region. Fort Belvoir, VA: Defense Technical Information Center, April 2003. http://dx.doi.org/10.21236/ada427711.

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Rastinejad, Fraydoon. Structure/Function Studies of the Androgen Receptor DNA-Binding Region. Fort Belvoir, VA: Defense Technical Information Center, April 2002. http://dx.doi.org/10.21236/ada411246.

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Fagan, Patricia A. NMR studies of DNA oligomers and their interactions with minor groove binding ligands. Office of Scientific and Technical Information (OSTI), May 1996. http://dx.doi.org/10.2172/373863.

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6

Joel, Daniel M., Steven J. Knapp, and Yaakov Tadmor. Genomic Approaches for Understanding Virulence and Resistance in the Sunflower-Orobanche Host-Parasite Interaction. United States Department of Agriculture, August 2011. http://dx.doi.org/10.32747/2011.7592655.bard.

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Oroginal Objectives: (i) identify DNA markers linked to the avirulence (Avr) locus and locate the Avr locus through genetic mapping with an inter-race Orobanche cumana population; (ii) develop high-throughput fingerprint DNA markers for genotypingO. cumana races; (iii) identify nucleotide binding domain leucine rich repeat (NB-LRR) genes encoding R proteins conferring resistance to O. cumana in sunflower; (iv) increase the resolution of the chromosomal segment harboring Or₅ and related R genes through genetic and physical mapping in previously and newly developed mapping populations of sunflower; and (v) develop high-throughput DNA markers for rapidly and efficiently identifying and transferring sunflower R genes through marker-assisted selection. Revisions made during the course of project: Following changes in O. cumana race distribution in Israel, the newly arrived virulent race H was chosen for further analysis. HA412-HO, which was primarily chosen as a susceptible sunflower cultivar, was more resistant to the new parasite populations than var. Shemesh, thus we shifted sunflower research into analyzing the resistance of HA412-HO. We exceeded the deliverables for Objectives #3-5 by securing funding for complete physical and high-density genetic mapping of the sunflower genome, in addition to producing a complete draft sequence of the sunflower genome. We discovered limited diversity between the parents of the O. cumana population developed for the mapping study. Hence, the developed DNA marker resources were insufficient to support genetic map construction. This objective was beyond the scale and scope of the funding. This objective is challenging enough to be the entire focus of follow up studies. Background to the topic: O. cumana, an obligate parasitic weed, is one of the most economically important and damaging diseases of sunflower, causes significant yield losses in susceptible genotypes, and threatens production in Israel and many other countries. Breeding for resistance has been crucial for protecting sunflower from O. cumana, and problematic because new races of the pathogen continually emerge, necessitating discovery and deployment of new R genes. The process is challenging because of the uncertainty in identifying races in a genetically diverse parasite. Major conclusions, solutions, achievements: We developed a small collection of SSR markers for genetic mapping in O. cumana and completed a diversity study to lay the ground for objective #1. Because DNA sequencing and SNPgenotyping technology dramatically advanced during the course of the study, we recommend shifting future work to SNP discovery and mapping using array-based approaches, instead of SSR markers. We completed a pilot study using a 96-SNP array, but it was not large enough to support genetic mapping in O.cumana. The development of further SNPs was beyond the scope of the grant. However, the collection of SSR markers was ideal for genetic diversity analysis, which indicated that O. cumanapopulations in Israel considerably differ frompopulations in other Mediterranean countries. We supplied physical and genetic mapping resources for identifying R-genes in sunflower responsible for resistance to O. cumana. Several thousand mapped SNP markers and a complete draft of the sunflower genome sequence are powerful tools for identifying additional candidate genes and understanding the genomic architecture of O. cumana-resistanceanddisease-resistance genes. Implications: The OrobancheSSR markers have utility in sunflower breeding and genetics programs, as well as a tool for understanding the heterogeneity of races in the field and for geographically mapping of pathotypes.The segregating populations of both Orobanche and sunflower hybrids are now available for QTL analyses.
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Fromm, A., Avihai Danon, and Jian-Kang Zhu. Genes Controlling Calcium-Enhanced Tolerance to Salinity in Plants. United States Department of Agriculture, March 2003. http://dx.doi.org/10.32747/2003.7585201.bard.

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The specific objectives of the proposed research were to identify, clone and characterize downstream cellular target(s) of SOS3 in Arabidopsis thaliana, to analyze the Ca2+-binding characteristics of SOS3 and the sos3-1 mutant and their interactions with SOS3 cellular targets to analyze the SOS3 cell-specific expression patterns, and its subcellular localization, and to assess the in vivo role of SOS3 target protein(s) in plant tolerance to salinity stress. In the course of the study, in view of recent opportunities in identifying Ca2+ - responsive genes using microarrays, the group at Weizmann has moved into identifying Ca2+-responsive stress genes by using a combination of aqeuorin-based measurements of cytosolic Ca and analysis by DNA microarrays of early Ca-responsive genes at the whole genome level. Analysis of SOS3 (University of Arizona) revealed its expression in both roots and shoots. However, the expression of this gene is not induced by stress. This is reminiscent of other stress proteins that are regulated by post-transcriptional mechanisms such as the activation by second messengers like Ca. Further analysis of the expression of the gene using promoter - GUS fusions revealed expression in lateral root primordial. Studies at the Weizmann Institute identified a large number of genes whose expression is up-regulated by a specific cytosolic Ca burst evoked by CaM antagonists. Fewer genes were found to be down-regulated by the Ca burst. Among the up-regulated genes many are associated with early stress responses. Moreover, this study revealed a large number of newly identified Ca-responsive genes. These genes could be useful to investigate yet unknown Ca-responsive gene networks involved in plant response to stress.
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Schutt, Timothy C., and Manoj K. Shukla. Computational Investigation on Interactions Between Some Munitions Compounds and Humic Substances. Engineer Research and Development Center (U.S.), February 2021. http://dx.doi.org/10.21079/11681/39703.

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Humic acid substances (HAs) in natural soil and sediment environments effect the retention and degradation of insensitive munitions compounds and legacy high explosives (MCs): DNAN, DNi- NH4+, nMNA, NQ, NTO (neutral and anionic forms), TNT, and RDX.A humic acid model compound has been considered using molecular dynamics, thermodynamic integration, and density functional theory to characterize the munition binding ability, ionization potential, and electron affinity compared to that in the water solution. Humic acids bind most compounds and act as both a sink and source for electrons. Ionization potentials suggest HAs are more susceptible to oxidation than the MCs studied. The electron affinity of HAs are very conformation-dependent and spans the same range as the munition compounds. When HAs and MCs are complexed the HAs tend to radicalize first thus buffering MCs against reductive as well as oxidative attacks.
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Elbaum, Michael, and Peter J. Christie. Type IV Secretion System of Agrobacterium tumefaciens: Components and Structures. United States Department of Agriculture, March 2013. http://dx.doi.org/10.32747/2013.7699848.bard.

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Objectives: The overall goal of the project was to build an ultrastructural model of the Agrobacterium tumefaciens type IV secretion system (T4SS) based on electron microscopy, genetics, and immunolocalization of its components. There were four original aims: Aim 1: Define the contributions of contact-dependent and -independent plant signals to formation of novel morphological changes at the A. tumefaciens polar membrane. Aim 2: Genetic basis for morphological changes at the A. tumefaciens polar membrane. Aim 3: Immuno-localization of VirB proteins Aim 4: Structural definition of the substrate translocation route. There were no major revisions to the aims, and the work focused on the above questions. Background: Agrobacterium presents a unique example of inter-kingdom gene transfer. The process involves cell to cell transfer of both protein and DNA substrates via a contact-dependent mechanism akin to bacterial conjugation. Transfer is mediated by a T4SS. Intensive study of the Agrobacterium T4SS has made it an archetypal model for the genetics and biochemistry. The channel is assembled from eleven protein components encoded on the B operon in the virulence region of the tumor-inducing plasmid, plus an additional coupling protein, VirD4. During the course of our project two structural studies were published presenting X-ray crystallography and three-dimensional reconstruction from electron microscopy of a core complex of the channel assembled in vitro from homologous proteins of E. coli, representing VirB7, VirB9, and VirB10. Another study was published claiming that the secretion channels in Agrobacterium appear on helical arrays around the membrane perimeter and along the entire length of the bacterium. Helical arrangements in bacterial membranes have since fallen from favor however, and that finding was partially retracted in a second publication. Overall, the localization of the T4SS within the bacterial membranes remains enigmatic in the literature, and we believe that our results from this project make a significant advance. Summary of achievements : We found that polar inflations and other membrane disturbances relate to the activation conditions rather than to virulence protein expression. Activation requires low pH and nutrient-poor medium. These stress conditions are also reflected in DNA condensation to varying degrees. Nonetheless, they must be considered in modeling the T4SS as they represent the relevant conditions for its expression and activity. We identified the T4SS core component VirB7 at native expression levels using state of the art super-resolution light microscopy. This marker of the secretion system was found almost exclusively at the cell poles, and typically one pole. Immuno-electron microscopy identified the protein at the inner membrane, rather than at bridges across the inner and outer membranes. This suggests a rare or transient assembly of the secretion-competent channel, or alternatively a two-step secretion involving an intermediate step in the periplasmic space. We followed the expression of the major secreted effector, VirE2. This is a single-stranded DNA binding protein that forms a capsid around the transferred oligonucleotide, adapting the bacterial conjugation to the eukaryotic host. We found that over-expressed VirE2 forms filamentous complexes in the bacterial cytoplasm that could be observed both by conventional fluorescence microscopy and by correlative electron cryo-tomography. Using a non-retentive mutant we observed secretion of VirE2 from bacterial poles. We labeled the secreted substrates in vivo in order detect their secretion and appearance in the plant cells. However the low transfer efficiency and significant background signal have so far hampered this approach.
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Epel, Bernard, and Roger Beachy. Mechanisms of intra- and intercellular targeting and movement of tobacco mosaic virus. United States Department of Agriculture, November 2005. http://dx.doi.org/10.32747/2005.7695874.bard.

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To cause disease, plant viruses must replicate and spread locally and systemically within the host. Cell-to-cell virus spread is mediated by virus-encoded movement proteins (MPs), which modify the structure and function of plasmodesmata (Pd), trans-wall co-axial membranous tunnels that interconnect the cytoplasm of neighboring cells. Tobacco mosaic virus (TMV) employ a single MP for cell- cell spread and for which CP is not required. The PIs, Beachy (USA) and Epel (Israel) and co-workers, developed new tools and approaches for study of the mechanism of spread of TMV that lead to a partial identification and molecular characterization of the cellular machinery involved in the trafficking process. Original research objectives: Based on our data and those of others, we proposed a working model of plant viral spread. Our model stated that MPᵀᴹⱽ, an integral ER membrane protein with its C-terminus exposed to the cytoplasm (Reichel and Beachy, 1998), alters the Pd SEL, causes the Pd cytoplasmic annulus to dilate (Wolf et al., 1989), allowing ER to glide through Pd and that this gliding is cytoskeleton mediated. The model claimed that in absence of MP, the ER in Pd (the desmotubule) is stationary, i.e. does not move through the Pd. Based on this model we designed a series of experiments to test the following questions: -Does MP potentiate ER movement through the Pd? - In the presence of MP, is there communication between adjacent cells via ER lumen? -Does MP potentiate the movement of cytoskeletal elements cell to cell? -Is MP required for cell-to-cell movement of ER membranes between cells in sink tissue? -Is the binding in situ of MP to RNA specific to vRNA sequences or is it nonspecific as measured in vitro? And if specific: -What sequences of RNA are involved in binding to MP? And finally, what host proteins are associated with MP during intracellular targeting to various subcellular targets and what if any post-translational modifications occur to MP, other than phosphorylation (Kawakami et al., 1999)? Major conclusions, solutions and achievements. A new quantitative tool was developed to measure the "coefficient of conductivity" of Pd to cytoplasmic soluble proteins. Employing this tool, we measured changes in Pd conductivity in epidermal cells of sink and source leaves of wild-type and transgenic Nicotiana benthamiana (N. benthamiana) plants expressing MPᵀᴹⱽ incubated both in dark and light and at 16 and 25 ᵒC (Liarzi and Epel, 2005 (appendix 1). To test our model we measured the effect of the presence of MP on cell-to-cell spread of a cytoplasmic fluorescent probe, of two ER intrinsic membrane protein-probes and two ER lumen protein-probes fused to GFP. The effect of a mutant virus that is incapable of cell-to-cell spread on the spread of these probes was also determined. Our data shows that MP reduces SEL for cytoplasmic molecules, dilates the desmotubule allowing cell-cell diffusion of proteins via the desmotubule lumen and reduces the rate of spread of the ER membrane probes. Replicase was shown to enhance cell-cell spread. The data are not in support of the proposed model and have led us to propose a new model for virus cell-cell spread: this model proposes that MP, an integral ER membrane protein, forms a MP:vRNAER complex and that this ER-membrane complex diffuses in the lipid milieu of the ER into the desmotubule (the ER within the Pd), and spreads cell to cell by simple diffusion in the ER/desmotubule membrane; the driving force for spread is the chemical potential gradient between an infected cell and contingent non-infected neighbors. Our data also suggests that the virus replicase has a function in altering the Pd conductivity. Transgenic plant lines that express the MP gene of the Cg tobamovirus fused to YFP under the control the ecdysone receptor and methoxyfenocide ligand were generated by the Beachy group and the expression pattern and the timing and targeting patterns were determined. A vector expressing this MPs was also developed for use by the Epel lab . The transgenic lines are being used to identify and isolate host genes that are required for cell-to-cell movement of TMV/tobamoviruses. This line is now being grown and to be employed in proteomic studies which will commence November 2005. T-DNA insertion mutagenesis is being developed to identify and isolate host genes required for cell-to-cell movement of TMV.
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