Question

Can anyone differentiate between the triplex end stacking and intercalation. And how does it affect the hydrophilic (or hydrophobic) molecules when binding with the triplex DNA?

Answer 1

An end stacking mode is one when the molecule is found to stack at the extremity of your nucleotide.

Intercalation is the insertion of molecules between the bases of DNA. Intercalation occurs when ligands of an appropriate size and chemical nature fit themselves in between base pairs of DNA. DNA intercalation represents an invasive, yet reversible, mode of DNA-ligand binding.

Triplex end stacking would be better when binding with the triplex dna than the intercalation since intercalation would add molecules inbwteen the which would destablize the structure.

Ligands intercalation in DNA triple helices may stabilize as well as destabilize triplex structure. The effect depends on the concentration of bound intercalators per base triplet.

Triplex end stacking mode should prefer to the intercalative one due to the less interference from the intrinsic ds-DNA binding, although intentionally designed intercalator-groove-binder conjugates can improve the triplex selectivity.