Flexible binding of m$^{6}$A reader protein YTHDC1 to its preferred RNA motif

N$^{6}$-Methyladenosine (m$^{6}$A) is the most prevalent chemical modification in human mRNAs. Its recognition by reader proteins enables many cellular functions, including splicing and translation of mRNAs. However, the binding mechanisms of m$^{6}$A-containing RNAs to their readers are still elusive due to the unclear roles of m$^{6}$A-flanking ribonucleotides. Here, we use a model system, YTHDC1 with its RNA motif 5'-G$_{-2}$G$_{-1}$(m$^{6}$A)C$_{+1}$U$_{+2}$-3', to investigate the binding mechanisms by atomistic simulations, X-ray crystallography, and isothermal titration calorimetry. The experimental data and simulation results show that m$^{6}$A is captured by an aromatic cage of YTHDC1 and the 3' terminus nucleotides are stabilized by cation-π-π interactions, while the 5' terminus remains flexible. Notably, simulations of unbound RNA motifs reveal that the methyl group of m$^{6}$A and the 5' terminus shift the conformational preferences of the oligoribonucleotide to the bound-like conformation, thereby facilitating the association process. The binding mechanisms may help in the discovery of chemical probes against m$^{6}$A reader proteins