We used only vertebrate motifs that are most conserved from the top 10% of the most conserved regions (minimum conservation 70%).
Primers and probes were designed to detect specific sequences on the most conserved regions of the S segment.
Sequences were piled up from the most conserved regions of these geographically diverse isolates and TaqMan® primers and probes were designed, targeting the regions with 100% sequence identity.
When applied to comparisons of two distantly related proteins, near-optimal alignments reveal that the most conserved regions among the near-optimal alignments are the highly structured regions in the proteins.
One of the most conserved regions includes cysteine 18 and its environment: position 15 is exclusively occupied by lysine or arginine, position 19 is preferentially occupied by glutamic and aspartic acid and position 17 by leucine, placing C18 in a peculiar hydrophobic but polarized environment.
We first screened for the most active shRNA molecules against the most conserved regions in the HCV genome, which were then used to generate asymmetric anti-HCV shRNAs that produce biologically active RNAi specifically directed against the genomic or antigenomic HCV sequences.
However, some sequence divergence has been observed even within the most conserved regions of the viral genome.
The 5′- and 3′-UTRs are the most conserved regions of HCV RNA among the different genotypes and isolates.
In Fig. 3, the most conserved regions are shaded.
RT polymerase domains are generally the most conserved regions of retrotransposons [37].
The most conserved regions are the central DBL3X and DBL4ε domains.
