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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