Table 1.
RNA loops and binding proteins.
| RNA loop | RNA-loop binding protein | References |
|---|---|---|
| MS2-binding site (MBS) | MS2 coat protein (MCP) | Bertrand et al., 1998; Romaniuk et al., 1987 |
| Lambda boxB RNA sequence | Phage lambda N protein (λN22) | Daigle and Ellenberg, 2007 |
| QB Stem-loop | QB coating protein | Rumnieks and Tars, 2014 |
| PP7 RNA sequence | PP7 coating protein | Lim et al., 2001; Lim and Peabody, 2002 |
| Box B nut L/R | phage HK022 Nun protein | Chattopadhyay et al., 1995; Van Gilst et al., 1997 |
| Amino-terminal RNA-binding domain of U1 snRNP A (U1A) | U1A protein | Moras and Poterszman, 1995; Oubridge et al., 1994 |
| Nanos Response Elements (NRE) | NRE-specific protein e.g., Pumilio | Murata and Wharton, 1995; Wharton and Struhl, 1991 |
RNA 3D structure is highly complex, which is associated with a number of its functions. RNA loops are structures which result from base pairing and can perform multiple functions such as binding to proteins, RNA or DNA. RNA-loops have been used to tag mRNA (Figure 12B) as well as to bring transcriptional regulators to the modified gRNA-loops of CRISPR/Cas9 (see text for more details). Here, we list the stem-loop structures known to bind to specific proteins.