Bioimpacts. 2018;8(3):167-176.
doi: 10.15171/bi.2018.19
PMID: 30211076
PMCID: PMC6128974
Scopus id: 85050667095
WOS: 000442045800003
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Original Research

Expression, purification and DNA-binding properties of zinc finger domains of DOF proteins from Arabidopsis thaliana

Hakimeh Moghaddas Sani 1,2, Maryam Hamzeh-Mivehroud 2,3, Ana P. Silva 4, James L. Walshe 4, S. Abolghasem Mohammadi 5, Mahdyieh Rahbar-Shahrouziasl 2, Milad Abbasi 2, Omid Jamshidi 2, Jason KK Low 4, Siavoush Dastmalchi 2,3,6 * , Joel P. Mackay 4

1 Faculty of Advanced Medical Sciences, Tabriz University of Medical Sciences, Tabriz, Iran
2 Biotechnology Research Center, Tabriz University of Medical Sciences, Tabriz, Iran
3 School of Pharmacy, Tabriz University of Medical Sciences, Tabriz, Iran
4 School of Life and Environmental Sciences, The University of Sydney, NSW 2006, Australia
5 School of Agriculture, University of Tabriz, Tabriz, Iran
6 Faculty of Pharmacy, Near East University, POBOX:99138, Nicosia, North Cyprus, Mersin 10, Turkey


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.
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