Figure 1

a, Summary of the SRA–DNA interactions; mc, main-chain-atom-mediated contacts; w, water-mediated hydrogen bonds. Black boxes represent CpG recognition sequence and K495-associated dotted lines represent weak hydrogen bonds. b, The side chains of V451 of the base flipping loop and R496 of the CpG recognition loop are in direct van der Waals contact. c, The two loops—CpG recognition and base flipping—penetrate into the DNA helix from opposite directions. d, The 5mC flips out and binds in a cage-like pocket. e, The surface charge at neutral pH is displayed as blue for positive (20 k_BT), red for negative (−20 k_BT), and white for neutral, where k_B is the Boltzmann's constant and T is the temperature.