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Signatures of Specific DNA Binding by the AT-Rich Interaction Domain of BAF250a

Giri, M and Maulik, A and Singh, M (2019) Signatures of Specific DNA Binding by the AT-Rich Interaction Domain of BAF250a. In: Biochemistry, 59 (1). pp. 100-113.

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Official URL: http://dx.doi.org/10.1021/acs.biochem.9b00852

Abstract

The AT-rich interaction domain (ARID) containing BAF250a is a subunit of the BAF-A class of SWI/SNF chromatin remodeling complexes. The ARID belongs to a family of conserved DNA binding domains found in several eukaryotic proteins; however, its exact contribution to BAF250a function and the mechanism of its DNA binding are not well understood. Here we have probed the interaction of the BAF250a ARID with three different double-stranded DNA (dsDNA) sequences to understand its DNA binding properties. A comprehensive biophysical and thermodynamic study using nuclear magnetic resonance (NMR) spectroscopy and isothermal titration calorimetry revealed the complex nature of BAF250a ARID-DNA interactions. The thermodynamic signatures of the BAF250a ARID with 12 A-T bp dsDNA (AT-12) are distinct from those of 12 G-C bp dsDNA (GC-12) or 12 bp Dickerson dodecamer DNA (DD-12) sequences. We observed that the binding of the BAF250a ARID with AT-12 DNA is enthalpically driven in a tested temperature range of 5-25 °C. BAF250a ARID/AT-12 DNA interaction exhibited a larger negative calorimetric specific heat change (�Cp) compared to that of BAF250a ARID/GC-12 DNA or BAF250a ARID/DD-12 DNA interactions. In the presence of salt (NaCl), ARID/AT-12 DNA binding was less perturbed than ARID/GC-12 DNA or ARID/DD-12 DNA binding. Overall, these results show that BAF250a ARID/AT-12 DNA interaction has signatures of "specific" binding. Furthermore, using NMR chemical shift perturbation experiments, we have identified DNA binding residues on the BAF250a ARID and generated a data-driven HADDOCK model of the ARID/DNA complex that was further supported by mutating key lysine residues that were found to be important for DNA binding.

Item Type: Journal Article
Additional Information: Copyright of this article belongs to American Chemical Society
Keywords: Amino acids; Binding energy; Calorimetry; Chemical shift; Complexation; DNA; Nuclear magnetic resonance spectroscopy; Sodium chloride; Specific heat, Chromatin remodeling complex; DNA-binding properties; Double-stranded DNA (ds-DNA); Eukaryotic proteins; Isothermal titration calorimetry; NMR chemical shift perturbations; Nuclear magnetic resonance(NMR); Thermodynamic studies, DNA sequences
Department/Centre: Division of Biological Sciences > Molecular Biophysics Unit
Division of Chemical Sciences > NMR Research Centre (Formerly Sophisticated Instruments Facility)
Depositing User: Id for Latest eprints
Date Deposited: 31 Jan 2020 10:19
Last Modified: 31 Jan 2020 10:19
URI: http://eprints.iisc.ac.in/id/eprint/64361

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