Table 1 Stability of a sample transcript – full length target and sheared fragments Folding ?G of target transcript and fragment molecules shown in Figure 8, at hybridization temperatures commonly used for long oligomer arrays.
From: Secondary structure in the target as a confounding factor in synthetic oligomer microarray design
Molecule | 2G, kcal/mole | |||
|---|---|---|---|---|
42°C | 52°C | |||
DNA | RNA | DNA | RNA | |
70-mer Probe | - 6.8 | N/A | - 4.2 | N/A |
Full Length Target | - 85.9 | - 188.4 | -56.6 | - 140.2 |
200-mer sheared Target | - 25.5 | - 58.6 | -15.9 | - 41.6 |
100-mer sheared Target | -14.2 | - 25.7 | -9.6 | -18.0 |
50-mer sheared Target (not shown) | - 6.1 | -10.5 | - 4.2 | -7.3 |