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Signatures of specific DNA binding by the AT-rich interaction domain of BAF250a.

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