PNA has higher Tm than DNA, roughly about 1 degree per basepair. Because of high Tm, stem and loop structure of 6 bp or more can form a stable secondary structure depending on the application and may affect its performance.
Solubility of PNA can be reduced if purine content (specially G) is high or the length is too long.
PNA Tool is designed to give information about the property of PNA oligos for optimal design. You will get a "Redesign recommended" warning if your PNA sequence has one of the following potential issues:
Too long (>30mer)
Containing 6 or longer purine stretches
High purine content (>50%)
High G content (>35%)
Significant complementary sequence (>7 bp)
It is recommended to change PNA sequence with warning if possible, specially for the applications performed in aqueous solution. Most dye conjugation also reduces solubility. You can add two Lysines or O linkers to improve solubility.
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