I am working on various G rich sequences which can form g quadraplex. My G rich oligo sequence is making g quadraplex and it is getting destabilized by cationic porphyrins like Tmpyp4 (CD data). Is there any other chemical which can compete with Tmpyp4 and again stabilize my oligo in the presence of Tmpyp4.
Interesting... Usually Tmpyp4 should bind and stabilize G4 (example http://www.ncbi.nlm.nih.gov/pubmed/12479216) although it has been reported that Tmpyp4 can also disrupt G4 (http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3351169/). Depending on what you are actually trying to achieve/study in your sample, you could try adding other G4 binding drugs (example, but there are more... http://www.bioorganic-chemistry.com/quadruplex_ligand_review.pdf), wait a bit (measure CD/NMR to check its ok) and then add Tmpyp4. Might work, might not... Could also be that it can't be done due to the question you are asking.
Regards.
Try adding hemin as it is well known that hemin can stack on top of the G quadruplex. While there should be an electrostatic interaction with the cationic porphyrin which might disrupt the G- quartet via an interaction with the negatively charged phosphate backbone
good luck!
Thanks a lot for your answers. I am wondering about a chemical that interacts directly with Tmpy4 and sort of neutralize it.
You can add double stranded DNA as competitor(calf thymus for example). TMPyP4 is not very specific for G4. But this will be a problem to get the CD data of your oligo.
- Badges
- Science topic
- Similar topics
- Biological Science
- Molecular Biology
- Biomolecules
- Nucleic Acids
- DNA