For example, the p Ka of the A in a sequence is ≤3.1, whereas the two A's in (loop sequence of a leadzyme) have p Ka values of 6.5 (shown in bold) and 4.3, respectively (1).
In contrast, introducing a single short loop into a long loop sequence, results in a significant increase in the T pH values, between C3T888 and the C3T833, C3T838 and C3T388 series, suggesting that the short loop could be acting to orient the intercalating strands together to enhance stability.
Interestingly, the U in (loop sequence in a U6 RNA intramolecular stem loop), which is stacked within the helix at pH 7.0, is flipped out at pH 5.7 to favor a stacking interaction between wobble A+C and Watson−Crick GC pairs flanking the U bulge (10).
The H3t gene is located in a histone cluster and has a stem-loop sequence in the 3′-UTR, similar to H3.1.
A single nucleotide insertion in a single D-loop sequence was treated as additional information, and used in pair-wise comparison.
Our study thus supports hypotheses of an association of immune system depletion with an increase in V3 loop sequence variability and with the escape of the viral sequence to distant parts of the sequence space.
Any precursor that provided a match with an expectation value less that 1× e-7 against a stem-loop sequence in miRBase was considered a true Salmo salar ortholog of an evolutionary conserved miRNA gene.
While H3mm6 H3mm18 were similar to H3.3 and their genes were scattered outside the histone gene clusters, H3t was similar to H3.1 and its gene was located in histone cluster 2. H3t also had a stem-loop sequence in its 3′-UTR (see summary in Table 1).
A change in helix position could cause a change in the (exposed) loop sequence, even though the overall amino acid sequence in the protein changes by only one amino acid (as in the Fusconaia-Pleurobema and Lemiox-Ptychobranchus M COX2e comparisons [discussed above]).
The fold of Gi alpha 1 differs from that of the homologous Gt alpha subunit in the conformation of a helix-loop sequence located in the alpha-helical domain that is characteristic of these proteins; this site may participate in effector binding.
In the last part of the study we related the location of a V3 loop sequence in sequence space to the corresponding patient CD4+ T-cell count.
