PNA Tool

Enter PNA sequence (e.g., CAGTCCAGTT):

Enter amino acid sequence and O linker (e.g., KFFKFFXBO, O for AEEA, or eg1 linker):

PNA Tool is designed to give information about the property of PNA oligos for optimal design.

The calculated Tm is for the PNA-DNA hybrid at a PNA concentration of 5 uM and the target nucleic acid in significant excess. In real experimental settings, the actual Tm may be lower by approximately 5-10 °C, depending on the specific conditions. The Tm will be slightly higher for PNA-RNA and PNA-PNA hybrid by a few degrees. For most applications, PNA with the calculated Tm of 70~80 °C is desired.

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%)
  • Complementary sequence (>7 bp)

PNA with a high purine content (>50%), a high proportion of G bases (>35%), long purine stretch (>7 bp), or a longer length (>30bp) may exhibit reduced solubility in aqueous solutions. If the PNA is intended for applications such as FISH or others that can include organic solvents, you can ignore these warnings.

For applications that require aqueous solutions such as PNA clamping, it is recommended to consider modifying the sequences or adding solubility enhancers such as 2 Lysines or O linkers. Most PNA will be soluble if organic solvents such as formamide, 20% DMSO, 0.1% TFA, or 10-20% acetonitrile can be added during stock preparation (10-100 uM). Additionally, for unlabeled PNAs, heating up to 85 °C can help dissolution.

Self-complementary of 5 bp (total 10 bp) or less are generally not a concern.

Please call us at 805) 277-0227 or email to info@pnabio.com if you have any question.