Fig. 1

Structure of IscB protein and IscB-ωRNA-DNA ternary complex diagram[17] a. Schematic of IscB protein domains. The IscB protein primarily consists of the N-terminal PLMP domain, RuvC domain, HNH domain, WED domain, and TI domain. The PLMP domain, located at the N-terminus of the protein, is involved in protein localization. The RuvC domain and HNH domain are related to DNA cleavage. The WED domain is mainly involved in binding to both the protein and DNA. The TI domain is related to the stability of the protein. b. IscB-ωRNA-DNA ternary complex diagram. The ωRNA binds to the complementary sequence of DNA, directing the protein to recognize specific DNA sequences. The WED domain forms hydrogen bonds with the single-stranded DNA terminus through specific amino acid residues. The RuvC domain forms direct chemical bonds with the DNA backbone through its catalytic active site, participating in DNA cleavage. TI represents TAM-interacting region. TS represents target strand. NTS represents non-target strand"

Fig. 2

Structure of IsrB protein and IsrB-ωRNA-DNA ternary complex diagram[23] a. Schematic of IsrB protein domains. The IsrB protein primarily consists of the N-terminal PLMP domain, RuvC domain, WED domain, and TI domain. The PLMP domain, located at the N-terminus of the protein, is involved in protein localization; The WED domain is mainly involved in binding to both the protein and DNA; The RuvC domain is related to DNA cleavage; The TI domain is related to the stability of the protein. b. IsrB-ωRNA-DNA ternary complex diagram. The ωRNA binds to the complementary sequence of DNA, directing the protein to recognize specific DNA sequences; The WED domain forms hydrogen bonds with the single-stranded DNA terminus through specific amino acid residues; The RuvC domain forms direct chemical bonds with the DNA backbone through its catalytic active site, participating in DNA cleavage; PLL represents phosphate-lock loop. TI represents TAM-interacting region. TS represents target strand. NTS represents non-target strand"

Fig. 3

Structure of TnpB protein and TnpB-reRNA-DNA ternary complex diagram[32] a. Schematic of TnpB protein domains. The TnpB protein consists of an N-terminal recognition (Rec) lobe and a C-terminal nuclease (Nuc) lobe. The Rec lobe includes the REC and wedge (WED) domains. The Nuc lobe includes the RuvC domain and the ZnF domain. The REC domain is mainly responsible for recognizing DNA; The WED domain is primarily involved in binding to the protein and DNA; The RuvC domain is associated with DNA cleavage; The ZnF domain is related to DNA binding. b. Ternary structure of TnpB-reRNA-DNA. The reRNA binds to the complementary sequence of DNA, directing the protein to recognize specific DNA sequences; The WED domain forms hydrogen bonds with the single-stranded DNA terminus through specific amino acid residues; The RuvC domain forms direct chemical bonds with the DNA backbone through its catalytic active site, participating in DNA cleavage; The ZnF domain binds to specific DNA sequences through its zinc finger structure, making the binding more stable; TS represents target strand; NTS represents non-target strand"

Table 1

Optimization strategies and research progress for the OMEGA gene editing system"

Fig. 4

Predicted secondary structures of the guide RNAs from the IscB, IsrB and TnpB systems [23, 32, 36] a. The ωRNA of the IscB system is divided into 4 regions (R1, R2, R3, and R4);b. The ωRNA of the IsrB system is divided into 4 stems (S1-4) and 8 stem-loops (SL1-8); the adaptor PK is the junction pseudoknot structure formed by SL2 and SL5; the nexus PK is the nexus pseudoknot structure formed by the region between SL4, S2, and SL7; the Shine-Dalgarno sequence is a ribosome binding site in bacteria, located approximately 8 bases upstream of the mRNA start codon (usually AUG); c. The reRNA of the TnpB system is divided into stem 1 and 2; Triplex is triple helix structure; Stem is stem-loop structure; 5′-ss terminus is 5′ end terminal sequence; PK is pseudoknot structure; TS is target strand; NTS is non-target strand; TAM is target-adjacent motif"