The drastic kinetic difference in strand-displacement from toehold design was used to distinguish between the perfectly matched and the single-base mismatched strands.
The difference in strands is the result of the DNA sequence- and strand-specific imprint moiety installed at mat1 (Klar 1987a , 1990.
The distinct differences in strand directionalities, loop connectivities and syn/anti distribution within G·G·G·G tetrads between the thrombin-binding DNA aptamer d(G2T2G2TGTG2T2G2) quadruplex reported previously, and the d(G2T4G2CAG2GT4G2T) quadruplex reported here, reinforces the polymorphic nature of higher-order DNA architectures.
But when we compare the same two species for the levels of CA-rich (QTPHNK) and GT-rich (CVFGW) amino acids, we see large differences reflecting the differences in strand asymmetry between the mammals and the flatworms.
Seven protocols were comprehensively evaluated by researchers at the Broad Institute [ 10] and the authors found marked differences in strand specificity, library complexity, evenness and continuity of coverage, agreement with known annotations and accuracy for expression profiling.
Despite their differences in strand asymmetry, the major coding strands of the two groups encode essentially the same set of 11 conserved mitochondrial proteins including cytochrome b, three subunits of cytochrome c oxidase (subunit 1, 2, and 3), six subunits of NADH dehydrogenase (subunit 1, 2, 3, 4, 4L, and 5), and ATP synthase F0 subunit 6 (ATP6).
These patterns cannot be analyzed quantitatively because of seasonal differences in stranding rates across age classes, but the same qualitative patterns arose when yearling or adult samples were excluded from the analysis.
Thus there is, computationally, not much difference in analysing strand specific data compared to analysing non-stranded data.
DNA appeared earlier in the recipient in the i31 mutants compared to WT, and the change was not due to a difference in second strand synthesis.
When considering pairs of genes – "window 2" clusters – there was no significant difference in the strand orientations of these pairs.
