Synonymous mutations can affect the stability of mRNA secondary structure through altered base pair interactions.
The mutant tRNAs selected by the method included molecules containing novel base substitutions as well as extensively altered base combinations that would not be readily generated by rationally designed site-directed mutagenesis.
Additionally, the A-to-I conversion alters base pairing, because inosine pairs preferentially with cytidine, and this potentially affects the secondary structure of the RNA.
Our model hypothesizes that point mutations, which altered base compositions (i.e., GC-to-AT or AT-to-GC), took place before the occurrence of gBGC.
In contrast, a nonconserved mismatch that alters base pairing and structure was classified as a stem loop transition (supplementary fig. S1, Supplementary Material online).
The presence of the 7amG modification did not substantially alter base stacking interactions with either the 5′-neighboring A T base pair or with the 3′-neighboring C G base pair.
We note that mutations that alter base pairing (C G ↔ A T), which account for ~75% of mutations generated by ENU, are more easily detected by HRM than mutations that maintain nucleotide valence (A T ↔ T A; Figure 4).
Most notably, we observed that more than 70% of the genes that are identified as significantly altered based on copy number alterations (see Methods) are not annotated in current pathway databases (Additional file 1: Figure S1).
The base-excision repair process protects genomes by removing and replacing altered bases in DNA.
But "the civil nature of a confinement scheme cannot be altered based merely on vagaries in the implementation of the authorizing statute," the court said today in an opinion by Justice Sandra Day O'Connor.
