Recognition by the Thyroid Hormone Receptor of Canonical DNA Response Elements Ana Carolina Migliorini Figueira Luís Maurício T. R. Lima Leonardo H. F. Lima Americo T. Ranzani Guilherme dos Santos Mule Igor Polikarpov 10.1021/bi901282s.s001 https://acs.figshare.com/articles/journal_contribution/Recognition_by_the_Thyroid_Hormone_Receptor_of_Canonical_DNA_Response_Elements/2793280 To shed more light on the molecular requirements for recognition of thyroid response elements (TREs) by thyroid receptors (TRs), we compared the specific aspects of DNA TRE recognition by different TR constructs. Using fluorescence anisotropy, we performed a detailed and hierarchical study of TR−TRE binding. This was done by comparing the binding affinities of three different TR constructs for four different TRE DNA elements, including palindromic sequences and direct repeats (F2, PAL, DR-1, and DR-4) as well as their interactions with nonspecific DNA sequences. The effect of MgCl<sub>2</sub> on suppressing of nonselective DNA binding to TR was also investigated. Furthermore, we determined the dissociation constants of the hTRβ DBD (DNA binding domain) and hTRβ DBD-LBD (DNA binding and ligand binding domains) for specific TREs. We found that a minimum DNA recognition peptide derived from DBD (H1TR) is sufficient for recognition and interaction with TREs, whereas scrambled DNA sequences were unrecognized. Additionally, we determined that the TR DBD binds to F2, PAL, and DR-4 with high affinity and similar <i>K</i><sub>d</sub> values. The TR DBD-LBD recognizes all the tested TREs but binds preferentially to F2, with even higher affinity. Finally, our results demonstrate the important role played by LBDs in modulating TR−DNA binding. 2010-02-09 00:00:00 hTR β DBD PAL LBD DNA recognition peptide 1TR ligand binding domains DNA binding domain TRE DNA elements DNA sequences Canonical DNA Response ElementsTo thyroid response elements Thyroid Hormone Receptor DR nonselective DNA binding DNA TRE recognition