We want to get a 20 nucleotide sequence, but your website recommends a max length of 15 nucleotides for pure BNA. How should we distribute normal DNA bases through the sequence to maximize binding affinity?
Example 1 of BNA probe:
C+TGG+C CG+TCG +TGG+CC C+GCA
Estimated melting temperature: 87 to 90 °C (DNA-Tm) / 90 to 96 °C (RNA-Tm).
Example 2 of BNA probe:
C+T+GGC CG+TCG +TGG+CC C+G+CA
Estimated melting temperature: 90 to 95 °C (DNA-Tm) / 92 to 97 °C (RNA-Tm).
Less modifications are needed if a lower melting temperature is desired.