Acidic conditions do facilitate the dissolving of PNA oligomers. PNAs are purified by reverse phase HPLC in the presence of trifluoroacetic acid, therefore, dissolving the lyophillisate in water results in a solution with a pH < 3. Addition of extra trifluoroacetic acid should not be necessary and is not recommended because performance of reverse transcription can be affected (potentially resulting in low yield and shorter cDNA fragments).

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The concentration of PNA solutions should be measured spectrophotometrically by reading the sample absorbance at 260 nm. To measure exclusively the PNA molecules in solution, the PNA stock should be centrifuged at 12,000 x g to first sediment any aggregated PNA molecules before diluting for OD measurement. Each PNA sequence has its own specific extinction coefficient that is different from a DNA oligomer of the same sequence due to the chemical differences.
For further details on determining PNA concentrations, refer to Appendix B of the handbook supplied with the GeneChip Globin Reduction Kit (http://media.affymetrix.com/support/downloads/manuals/globin_reduction_protocol_manual.pdf).

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In contrast to DNA oligonucleotides, PNA oligomers do not have a negatively charged backbone. Instead it is made from repeating N-(2-aminoethyl)-glycin units linked by peptide bonds. Additionally, they do not contain any pentose sugar moieties or phosphate groups. Because of these chemical characteristics, their water solubility is reduced in comparison to DNA oligonucleotides. To dissolve PNA molecules after storage below room temperature, the oligomers must first be incubated for 10 minutes at room temperature, then 10 minutes at 50 degrees C and then finally returned to room temperature before use.

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At this time we cannot recommend storage of the diluted PNA stock solutions due to the potential for the PNAs to aggregate, but we are investigating ways to do this in the future.

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Using PNAs from other vendors has not been thoroughly tested.

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