Table 2 Evaluation of sequencing results of three DNA hairpin constructs. Average ratio of peak height after to before the hairpin region was determined as a measure of how well the sequence read through the hairpin structure. The greater the peak height ratio, the greater the ability to sequence through the hairpin. A value of 1 indicates no loss in peak height, and a value of zero indicates a complete stop in sequence after the hairpin region. All values are the averages of at least triplicate sequencing reactions.
From: Criteria for effective design, construction, and gene knockdown by shRNA vectors
| Â | Â | DNA Plasmid | ||
|---|---|---|---|---|
| Â | Â | pHSPG-shTLR4 | pHSPG-shmutTLR4 | pHSPG-shmCNN3 |
Chemistry | DNA relaxing agent | Peak Height Ratio | Peak Height Ratio | Peak Height Ratio |
BDv1.1 | None | 0.0 | 0.4 | 0.0 |
BDv1.1 | 5% DMSO | 0.0 | 0.6 | 0.2 |
BDv1.1 | 0.83 M Betaine | 0.3 | 0.9 | 0.7 |
BDv1.1 | 1 × PCRx Enhancer | 0.1 | 0.7 | 0.3 |
BDv1.1 | 0.83 M Betaine & 1 × PCRx Enhancer | 0.6 | 0.9 | 0.5 |
20:1 BD:dGTP | None | 0.4 | 0.6 | 0.5 |
20:1 BD:dGTP | 5% DMSO | 0.6 | 0.7 | 0.6 |
20:1 BD:dGTP | 0.83 M Betaine | 0.7 | 1.0 | 0.8 |
20:1 BD:dGTP | 1 × PCRx Enhancer | 0.6 | 0.8 | 0.7 |
20:1 BD:dGTP | 0.83 M Betaine & 1 × PCRx Enhancer | 0.8 | 0.9 | 0.8 |
10:1 BD:dGTP | None | 0.5 | 0.6 | 0.6 |
10:1 BD:dGTP | 5% DMSO | 0.7 | 0.8 | 0.7 |
10:1 BD:dGTP | 0.83 M Betaine | 0.8 | 0.9 | 0.9 |
10:1 BD:dGTP | 1 × PCRx Enhancer | 0.7 | 0.8 | 0.8 |
10:1 BD:dGTP | 0.83 M Betaine & 1 × PCRx Enhancer | 0.9 | 1.0 | 0.9 |
10:1 BD:dGTP | 1 × ThermoFidelase I | 0.1 | 0.2 | 0.2 |
5:1 BD:dGTP | None | 0.6 | 0.7 | 0.7 |
3:1 BD:dGTP | None | 0.6 | 0.6 | 0.6 |
dGTP only | None | 0.7 | 0.7 | 0.8 |