A shorter 29 mer sequence (Sub 3) (ΔG = −1.3 kcal/mol) with 3-bp in the stem of a 7-mer loop conferred highly stable AgNC.
The postulated tRNA cloverleaf structures generally contained 7 bp in the aminoacyl stem, 2 to 5 bp in the TψC stem, 5 bp in the anticodon stem, and 0 to 4 bp in the dihydrouridine (DHU) stem.
The inferred secondary structure of the 22 tRNA genes had several uniform features: 7 bp in the aminoacyl stem, 5 bp in the TφC and anticodon stem, 4 bp in the DHU stem and 7 bp in the anticodon loop.
Accordingly, the PSec model assumes 8 bp in the aminoacyl stem and 5 bp in the T stem, a structure referred to as the 8/5 structure in contrast to the normal 7/5 structure observed in tRNAs.
Thus, the mutant pc MT-Δ31,66 MT-Δ31,66cted to produce transcripts wash a stem shortened by 1 bpredictedrly toe stem in MT-Δ30,31,66,67 was 2 bproduceer, and Mtranscripts–68 by three, withst MT-Δ27,28,69,70 wastemedicted to remove 2 bp poshortenedproximal to the loop region.
Different secondary structures proposed for Sec tRNAs (see supplementary fig. S1, Supplementary Material online) were evaluated by covariance analysis and by comparing the structure components of the scores obtained by the ε-proteobacteria Sec tRNAs with covariance models assuming 7/5, 8/5, or 9/4 bp in the aminoacyl- and T-stems.
In the corresponding regions in S. retrolateralis, the nucleotide sequence can potentially form six 10- to 29-bp hairpins with 5- to 15-bp loops supported by 1 4 GC matches in the stem.
Consistent with the traditional shRNA design [ 24], the hairpins ranging from 19 21 bp in stem length produced better knockdown activities in our new design of AGO2/shRNA co-overexpression system.
T-DNAs are inserted 137 bp and 218 bp upstream of the stem-loops of MIR156A and MIR156C, respectively.
