PNA-DNA Stability: Is Hybrid More or Less Stable?

[pzona]

If "unzipped" PNA and DNA combine to form a double helix, will the hybrid be more or less stable than a pure DNA double helix? This was a question on my chem homework (in a section on intermolecular forces), but I'm posting in this section as I already turned in the homework so I'm asking more out of curiosity than anything. The only real information I had on PNA was that its backbone is neutral, while I know that the phosphates in DNA give its backbone a negative (-2?) charge. I'm not sure how these really affect each other, as the base pairs are what connect the two together, but the charges seemed to be emphasized in the question, and this really confused me.

I'm not sure how common PNA (peptide nucleic acid) is, but I asked this question to some grad students in the bio lab where I work, and they weren't too sure as they hadn't worked much with PNA (a few didn't remember even learning about it actually). On my homework I guessed that it would be less stable, just because I know that DNA is pretty stable as it is, but I'm starting to think the stabilities would be about equal, and that the part about the charges was just thrown to distract me. Anyway, if anyone can even help me out with the thought process in this problem, I'd appreciate it.

 

[chemisttree]

I would say that the bonding should be stronger in PNA since all things being equal, a neutral backbone would lack charge repulsion present in both DNA and RNA. The interstrand bonding is identical to that of DNA... identical purine and pyrimidine bases are present in both classes of compounds and both form the same Watson-Crick pairs .

 

[quicknote]

I would approach this question by considering the structural and chemical differences between PNA and DNA. PNA is a synthetic nucleic acid that has a neutral backbone, while DNA has a negatively charged backbone due to the presence of phosphate groups. This difference in charge can potentially impact the stability of the hybrid formed by combining PNA and DNA.

One major factor that contributes to the stability of DNA is the formation of hydrogen bonds between the complementary base pairs. These hydrogen bonds help hold the two strands of DNA together in a double helix structure. Since PNA and DNA have different chemical structures, it is possible that the base pairing may not be as stable in the hybrid as it is in a pure DNA double helix. This could potentially make the hybrid less stable than a pure DNA double helix.

However, it is also important to consider other intermolecular forces such as van der Waals interactions and hydrophobic interactions. These forces may also play a role in stabilizing the hybrid structure. In addition, the overall stability of the hybrid may also depend on the specific sequences of PNA and DNA used.

In conclusion, it is difficult to determine whether the hybrid of PNA and DNA would be more or less stable than a pure DNA double helix without further experimental data. It is possible that the stabilities may be similar, or one may be more stable than the other depending on the specific conditions. Further studies and experiments would be needed to fully understand the stability of the PNA-DNA hybrid.