Expression, purification and DNA-binding properties of zinc finger domains of DOF proteins from Arabidopsis thaliana. Moghaddas Sani, H., Hamzeh-Mivehroud, M., Silva, A., P., Walshe, J., L., Mohammadi, S., A., Rahbar-Shahrouziasl, M., Abbasi, M., Jamshidi, O., Low, J., K., Dastmalchi, S., & Mackay, J., P. BioImpacts, 8(3):167-176, 1, 2018. ![Expression, purification and DNA-binding properties of zinc finger domains of DOF proteins from Arabidopsis thaliana [link]](https://bibbase.org/img/filetypes/link.svg "link")
Website doi abstract bibtex Introduction: DOF proteins are a family of plant-specific transcription factors with a conserved zinc finger (ZF) DNA-binding domain. Although several studies have demonstrated their specific DNA binding, quantitative affinity data is not available for the binding of DOF domains to their binding sites. Methods: ZF domains of DOF2.1, DOF3.4, and DOF5.8 from Arabidopsis thaliana were expressed and purified. Their DNA binding affinities were assessed using gel retardation assays and microscale thermophoresis with two different oligonucleotide probes containing one and two copies of recognition sequence AAAG. Results: DOF zinc finger domains (DOF-ZFs) were shown to form independently folded structures. Assessments using microscale thermophoresis demonstrated that DOF-ZFs interact more tightly (~100 fold) with double-motif probe than the single-motif probe. The overall Kd values for the DOF3.4-ZF and DOF5.8-ZF to the double-motif probe were ~2.3±1 and 2.5±1 μM, respectively. Conclusion: Studied DOF-ZF domains formed stable complexes with the double-motif probe. Although DOF3.4-ZF and DOF5.8-ZF do not dimerize with an appreciable affinity in the absence of DNA (judging from size-exclusion and multiangle laser light scattering data), it is possible that these ZFs form protein-protein contacts when bound to this oligonucleotide, consistent with previous reports that DOF proteins can homo- and hetero-dimerize.
@article{
title = {Expression, purification and DNA-binding properties of zinc finger domains of DOF proteins from Arabidopsis thaliana},
type = {article},
year = {2018},
keywords = {DNA binding affinity,DOF zinc finger domain,Gel retardation assay,Microscale thermophoresis},
pages = {167-176},
volume = {8},
websites = {http://bi.tbzmed.ac.ir/Abstract/bi-17551},
month = {1},
day = {28},
id = {dd4675dd-58e2-3545-8030-ebe4c5b425a8},
created = {2020-12-17T05:29:55.192Z},
file_attached = {false},
profile_id = {a5a2ab6f-a8b5-3db6-97bc-618752ee4386},
group_id = {bc1ab1d4-9e57-37e6-9fb5-435fca0ee9d2},
last_modified = {2020-12-17T05:29:55.192Z},
read = {false},
starred = {false},
authored = {false},
confirmed = {true},
hidden = {false},
citation_key = {MoghaddasSani2018},
source_type = {ARTICLE},
notes = {cited By 1},
private_publication = {false},
abstract = {Introduction: DOF proteins are a family of plant-specific transcription factors with a conserved zinc finger (ZF) DNA-binding domain. Although several studies have demonstrated their specific DNA binding, quantitative affinity data is not available for the binding of DOF domains to their binding sites. Methods: ZF domains of DOF2.1, DOF3.4, and DOF5.8 from Arabidopsis thaliana were expressed and purified. Their DNA binding affinities were assessed using gel retardation assays and microscale thermophoresis with two different oligonucleotide probes containing one and two copies of recognition sequence AAAG. Results: DOF zinc finger domains (DOF-ZFs) were shown to form independently folded structures. Assessments using microscale thermophoresis demonstrated that DOF-ZFs interact more tightly (~100 fold) with double-motif probe than the single-motif probe. The overall Kd values for the DOF3.4-ZF and DOF5.8-ZF to the double-motif probe were ~2.3±1 and 2.5±1 μM, respectively. Conclusion: Studied DOF-ZF domains formed stable complexes with the double-motif probe. Although DOF3.4-ZF and DOF5.8-ZF do not dimerize with an appreciable affinity in the absence of DNA (judging from size-exclusion and multiangle laser light scattering data), it is possible that these ZFs form protein-protein contacts when bound to this oligonucleotide, consistent with previous reports that DOF proteins can homo- and hetero-dimerize.},
bibtype = {article},
author = {Moghaddas Sani, Hakimeh and Hamzeh-Mivehroud, Maryam and Silva, Ana P. and Walshe, James L. and Mohammadi, S. Abolghasem and Rahbar-Shahrouziasl, Mahdyieh and Abbasi, Milad and Jamshidi, Omid and Low, Jason K.K. and Dastmalchi, Siavoush and Mackay, Joel P.},
doi = {10.15171/bi.2018.19},
journal = {BioImpacts},
number = {3}
}
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Although several studies have demonstrated their specific DNA binding, quantitative affinity data is not available for the binding of DOF domains to their binding sites. Methods: ZF domains of DOF2.1, DOF3.4, and DOF5.8 from Arabidopsis thaliana were expressed and purified. Their DNA binding affinities were assessed using gel retardation assays and microscale thermophoresis with two different oligonucleotide probes containing one and two copies of recognition sequence AAAG. Results: DOF zinc finger domains (DOF-ZFs) were shown to form independently folded structures. Assessments using microscale thermophoresis demonstrated that DOF-ZFs interact more tightly (~100 fold) with double-motif probe than the single-motif probe. The overall Kd values for the DOF3.4-ZF and DOF5.8-ZF to the double-motif probe were ~2.3±1 and 2.5±1 μM, respectively. Conclusion: Studied DOF-ZF domains formed stable complexes with the double-motif probe. Although DOF3.4-ZF and DOF5.8-ZF do not dimerize with an appreciable affinity in the absence of DNA (judging from size-exclusion and multiangle laser light scattering data), it is possible that these ZFs form protein-protein contacts when bound to this oligonucleotide, consistent with previous reports that DOF proteins can homo- and hetero-dimerize.","bibtype":"article","author":"Moghaddas Sani, Hakimeh and Hamzeh-Mivehroud, Maryam and Silva, Ana P. and Walshe, James L. and Mohammadi, S. 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