Both uridines are in the same RNA stem, separated by ∼ 4 Å.
For each asymmetric Y-junction, the even (odd) modes of the stem separated from the odd (even) modes evolve into the low-order modes of the wide (narrow) arm by controlling the widths of the two arms, and vice versa.
The corresponding sequence entered to mfold consistently renders a 6-bp "anticodon" stem and a 5-bp "acceptor" stem separated by a variable loop (Additional file 6, 15).
These structures have slight differences in their 5' ends, but the basic structure is the same: a long stem separated by 2 bulges at the 3' part, a loop, and a hairpin structure, representing the putative anticodon stem (Additional file 6, 13-14).
BOK CHOY WITH SHIITAKES Adapted from Charles Phan Time: 20 minutes 2 tablespoons neutral oil, like corn or canola 1 tablespoon minced garlic 4 to 6 heads baby bok choy, or 1/2 head large bok choy, leaves and stems separated and stems roughly chopped 10 small shiitake mushrooms, caps only, left whole 1 teaspoon sugar 1/2 cup or more chicken stock or water 2 tablespoons fish sauce.
Unlike the above predictions, thermodynamic models of this region are very similar across the two species: a large hairpin structure with two stems separated by a connecting loop.
Each of these stem-loop structures can be described by two stems separated by an internal loop, a K-turn motif, and a conserved ANA (generally ACA) motif at the 3' end.
Screening of the flanking genomic sequences with the SnoReport program revealed a sequence that can fold into a typical H/ACA box snoRNA structure, including two stems separated by the conserved ANANAA motif, a 3' terminal ACANNN motif, and an internal loop sequence that could direct the pseudouridylation of the 25S rRNA U1465 residue (Fig. 3b).
However, the stem branches separating these groups are long, and much more similar to the proposed pre-LUCA stem branches between (A) and (B) within SerRS, than between the bacterial and archaeal groups within the common SerRS form (A).
In sharp contrast, trees for DNA-handling enzymes, molecules associated with ribosomes [ 15], and a few others, e.g. membrane ATPase [ 16], typically place the root on a very long stem that separates archaebacteria and eubacteria into unambiguously distinct branches.
