Table 2.
Charge state and polarity of PNA oligomers.
| PNA | Sequencea | Charge Stateb | Polarityc |
|---|---|---|---|
| 1 | H2N-G-G-A-G-G-C-G-G-G-Lys | positive | parallel |
| 2 | H2N-Glu-G-G-A-G-G-C-G-G-G-Glu-Lys | zwitterionic | parallel |
| 3 | H2N-G-G-G-C-G-G-A-G-G-Lys | positive | anti-parallel |
| 4 | H2N-Glu-G-G-G-C-G-G-A-G-G-Glu-Lys | zwitterionic | anti-parallel |
| 5 | H2N-G-G-A-X-G-C-G-X-G-Lys | positive | parallel |
| 6 | H2N-G- X-G-C-G-X-A-G-G-Lys | positive | anti-parallel |
| 7 | H2N-Glu-G-G-A-X-G-C-G-X-G-Glu-Lys | zwitterionic | parallel |
| 8 | H2N Glu-G-X-G-C-G-X-A-G-G-Glu-Lys | zwitterionic | anti-parallel |
| 9 | H2N Glu-G-X-G-C-G-X-A-G-G-Glu-Lys | zwitterionic | anti-parallel |
a
PNA oligomers are written from N terminus to C terminus. Lys = lysine, Glu = glutamic acid, X = aeg PPG residues, X = cyclopentane PPG residues.
b
The charge state is the most likely overall charge state for each oligomer at physiological pH. Positively charged sequences have primary amines (lysine side chain and N terminus) while zwitterionic oligomers also contain two acid moieties (glutamic acid side chains).
c
The polarity is defined in relation to the target sequence (5′-CCT CCG CCC-3′) where the N terminus of PNA oligomers is analogous to the 5′ end of natural nucleic acids.