*3.6. Relative Average Solvent Accessibility (RASA)*

The DOT residues buriedness is analysed by the NACCESS [47] program and the RASA of each residue is calculated by using Equation (4).

$$\text{RASA} = \frac{A\_{ilbd}}{\sum\_{i=1}^{n} (A\_{ilbd})} \tag{4}$$

where *Aibd*: RASA of *i*th residue binding with RNA in DOT region; *n*: number of DOT residues in a protein–RNA complex.

#### *3.7. Secondary Structure of Protein and RNA*

Secondary structure of both proteins and RNA molecules are analysed by DSSP and DSSR programs, respectively [48,49]. The DSSR program gives dot bracket notation of secondary structure of RNA as shown in Figure S1, in which "." represents unpaired nucleotide, "(" or ")" represent paired bases, and "{" or "}" or "[" or "]" or "<" or ">" represent pseudoknot bases.
