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Relative homoplasy was examined between loop and stem regions.
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In these models, the contributions from tertiary interactions between loops and stems are neglected.
Besides, the additive and enhanced effects between the loop and stem sequences on the fluorescence of induced CuNPs was first proposed and investigated.
To distinguish between the loop and stem region, the loop is highlighted by a dashed underline, while the stem is highlighted by a solid underline.
As described in other studies [ 51], some small RNAs were generated from the loop or the region between the loop and stem (ssc-let-7e, ssc-miR-27a and ssc-miR-30a).
Inspection of the thermodynamic stabilities of the loop and stem region indicates that a nonlinear correlation exists between the measured binding affinity and length of aptamer duplexed region in the stem-loop architecture.
These snippets were separated into two groups according to their secondary structure: loop, and stem-loop-stem.
The other type of interaction[ 3, 17, 19, 55] is between the RNase P recognition domain (e.g., T-loop and stem) and the mRNA.
The third most abundant type of substitutions occurred between the D loop and acceptor stem, at the position of N2-methylguanosine (mG) [ 5, 6].
This region resides between stem-loop B and stem-loop C (SLC) and one strand of stem region of SLC [46].
To test the relative homoplasy between stem and loop regions, all alignments were divided into unpaired (loop) and paired (stem) positions according to a consensus secondary structure.
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