Structure of ribozyme constructs used in this study.

<p>The 5′-terminus of the ribozyme (green) is in close contact with the primer (red) and template (orange). The P2 oligo (dark blue) is base paired to a complementary region on the ribozyme (light blue), forming the P2 helix. (<b>A</b>) Secondary structure of the polymerase ribozyme <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0025030#pone.0025030-Johnston1" target="_blank">[7]</a> with the 5′-duplexes and the P2 duplex that were used to attach arginine or amino cofactors. The length of the 5′-duplex is indicated. “X” denotes the position of the chemical modification. The P2 oligo is truncated, and the internal mismatch was removed <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0025030#pone.0025030-Yao1" target="_blank">[12]</a>. (<b>B</b>) 3D structure of the ligase domain in the polymerase ribozyme, based on the crystal structure of the ligase <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0025030#pone.0025030-Shechner1" target="_blank">[27]</a>. Atoms that do not appear in the polymerase ribozyme were deleted. The asterisk denotes the position of the catalytic site. The positions where the 5′-duplex and the accessory domain are attached to the ligase domain are indicated, as well as the 5′-terminus and 3′-terminus of the P2 oligo.