It’s not really a comprehensive interpretation of intercalation but I think a geometric interpretation can help some non-chemists understand how intercalating molecules bind to dna.
From the purely geometric model, some of the molecules you proposed have pretty large functional groups adjacent to rings which I think may make the intercalation process less efficient. That being said, if you took those molecules and gave massive doses to rats, some may comeback as carcinogenic.
I think that your multi-ring point is fair. The multi ring structure to me suggests that the more the pi orbitals are able to delocalize their electrons the higher the binding efficiency. I have tested 1-2 molecules where non-fused rings showed some affinity but not near the potency of fused ring structures. I would also say two rings with a carbon-carbon link seem to be potent binding as well. I presume that it’s also related to delocalizing pi orbitals and extra degrees of freedom in the intercalation process but I suppose that’s just speculative.
From the purely geometric model, some of the molecules you proposed have pretty large functional groups adjacent to rings which I think may make the intercalation process less efficient. That being said, if you took those molecules and gave massive doses to rats, some may comeback as carcinogenic.
I think that your multi-ring point is fair. The multi ring structure to me suggests that the more the pi orbitals are able to delocalize their electrons the higher the binding efficiency. I have tested 1-2 molecules where non-fused rings showed some affinity but not near the potency of fused ring structures. I would also say two rings with a carbon-carbon link seem to be potent binding as well. I presume that it’s also related to delocalizing pi orbitals and extra degrees of freedom in the intercalation process but I suppose that’s just speculative.