The Vital Role of Groove Geometries of DNA for the c-Myb Specific Recognition of a Pseudo-Palindromic Consensus in mim-1 Promoter

Binding of transcription factor (FT) to DNA sequences is an initial step for a regulatory gene to start function. However, how a FT recognizes a specific binding site among numerous similar ones in the promoter remains unclear. The chicken myeloid protein gene, mim-1, is one of the well-studied target genes activated by c-Myb FT exclusively in myelomonocytic cells. Here we report the specific recognition mechanism in the conformation of c-Myb binding to a pseudo-palindromic consensus AACNG with DNA sequence of TAACGG and the complement DNA sequence of AAACCG in mim-1. Results from Electrophoretic Mobility Shift Assay and 11 independent 40-ns molecular dynamics simulation studies using different biological scenarios all indicated that the helices R2 and R3 (R2R3) of c-Myb bound exclusively to TAACGG. Results from conformational fluctuation analysis and dynamics trajectories analysis using principal component analysis observed that a clamp-like motion of R2R3 leaded to the conformational perturbation of the binding DNA. The conformational analyses of nucleic acids structures discovered that the clamp-like motion of R2R3 resulted in apparently different trends of groove geometries between two complexes of R2R3 binding to DNA and to complement DNA sequence, which especially in the width of major groove. Furthermore, interaction energy analyses between protein and DNA suggested that the deformations of DNA groove played an important role in the stabilization of the interaction between TAACGG and R2R3 in the complex. Thus, the conformations of DNA groove are vital for the specific recognition of c-Myb.