Figure 2.

The positively charged surface and the nucleic acid binding property of A3H. (A) The positively charged surface around the Zn-active center of A3H, covering loop 1, 3, 5, 7, and helix 1 and 6 (h1, h6) and the Zn-center. The other end of the molecule is mostly neutral or negatively charged (Supplementary Figure S3C). The surface electrostatic potential colored according to calculated electrostatic potential of accessible surface area from −5 kT/e (red) to 5 kT/e (blue). The side chain of W115 was modeled based on the monomer structure. (B–E) Representative gel images of EMSA showing A3H mutants binding to 50 nt ssRNA (1 nM, B), 50 nt ssDNA (10 nM, C), 13 nt ssDNA (10 nM, D), and 8 nt ssDNA (10 nM, E). Quantification and estimate of binding affinity for each oligonucleotide are shown in Table 2.