Can any structural features be identified for the binding affinity and what could be the reason for that?
To the best of my knowledge Rh-polypyridyl complexes are AT-rich and Ru-polypyridyl are GC rich binders.
in general groove binders will prefer AT sequences (distamycin A, netropsin, DAPI), due to steric obstruction of the GC minor groove by the guanine amino group, model intercalators (ethidium bromide, daunomycin, for example) will show no preference for either. Therefore GC binding small molecules are more rare and usually are synthesized for the job, from naturaly ocurring, mithramycin springs to mind. check the ref bellow for the molecular recognition if you want to dig deeper, there is plenty of refs on small mols targeting specific sequences.
Dervan, Bioorganic & Medicinal Chemistry 9 (2001) 2215–2235
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