Fig. 4: Secondary structures in the region of the light strand replication origin (OL) in the Tuatara (Sphenodon punctatus).
Top right is a stem-and-loop structure that may serve as OL but is highly unusual (presented as heavy-strand template DNA sequence). This OL-like structure overlaps 14 bases with tRNAAsn (normally no overlap) and two bases with tRNACys (normally two to four), (see arrows and lower right for OL comparison). Putative light-strand encoded tRNAs are presented to the left and are the same sequence as heavy-strand DNA except for the use of U instead of T. The Tuatara has an unusual tRNACys that lacks a D-stem and instead contains a D-arm replacement loop (arrow)19,20. Stems are as follows: AA = amino-acid acceptor stem, D = dihydrouridine stem, AC = anticodon stem, and T = TphiC stem. Consensus heavy-strand sequence of putative OL from squamate lizards is presented in the lower right. This sequence is based on representatives from the Iguanidae (nine genera), Gekkonidae (Teratoscincus), Dibamidae (Dibamus), Lacertidae (Eremias), Teiidae (Cnemidophorus), Cordylidae (Platysaurus), Anguidae (Elgaria), Xenosauridae (Xenosuurus), and Varanidae (Varanus);6,54 Dibamus novaeguineae, U71327, was previously reported as Lialis jicari6. Bases in capitals are conserved pairings and downstream sequences. Bases in lower case are often paired. Variable positions are labeled with their standard one-letter codes: R = G or A; Y = C or T; B = G, C, or T; and V = G, C, or A. The 3’-GCC-5’ heavy-strand template sequence identified as the point of light-strand elongation in mouse55 is indicated in green font (arrow). The heavy-strand sequence 3’-GBCCB-5’ in tRNACys related to the downstream 3’-GGCCG-5’ sequence found to be required for in vitro replication in humans56 is underlined. Note the OL-like stem-and-loop structure in the Tuatara (upper right) has a G-C rich heavy-strand sequence of 3’-CGG-5’ (bases in bold and arrow), which is the complement of the 3’-GCC-5’ heavy-strand template sequence identified as the point of light-strand elongation in mouse55. No obvious sequence related to the downstream 3’-GGCCG-5’ sequence found to be required for in vitro replication in humans56 is identifiable in the Tuatara.
