Figure 3.

Sequence and secondary structure of various forms of the R3C ligase enzyme. A, The enzyme (E) adopts a three-way junction structure upon binding two oligonucleotide substrates (A and B), which become ligated (curved arrow) to form the product. Conserved nucleotides that are essential for catalytic function are shown. B, The self-replicating or cross-replicating enzyme ligates two substrates to yield a new copy of the enzyme or its cross-catalytic partner, respectively. Open boxes indicate regions of Watson-Crick pairing between enzyme and substrates that can have any complementary sequence. C, The central stem-loop of the enzyme can be replaced by an aptamer domain, configured such that binding of the corresponding ligand is required to stabilize the active structure of the enzyme. The aptamer domains for theophylline (theo) and flavin mononucleotide (FMN) are shown.