page_title: DNA-binding metallo-intercalators
section_title: Mechanism of DNA-intercalation
hierarchical_section_title: DNA-binding metallo-intercalators / Mechanism of DNA-intercalation
caption_attribution_description: English: The binding of a metallo-intercalator between adjacent base pairs of DNA.
context_page_description: DNA-binding metallo-intercalators are positively charged, planar, polycyclic, aromatic compounds that unwind the DNA double helix and insert themselves between DNA base pairs. Metallo-intercalators insert themselves between two intact base pairs without expelling or replacing the original nitrogenous bases; the hydrogen bonds between the nitrogenous bases at the site of intercalation remain unbroken. In addition to π-stacking between the aromatic regions of the intercalator and the nitrogenous bases of DNA, intercalation is stabilized by van der Waals, hydrophobic, electrostatic, and entropic interactions. This ability to bind to specific DNA base pairs allows for potential therapeutic applications of metallo-intercalators.
context_section_description: Metallo-intercalators π-stack with unbroken DNA base pairs after entering via a groove, typically the minor, (in contrast to metallo-insertors, which replace expelled base pairs after entering double stranded DNA via the minor groove). Intercalation of a metallo-intercalator creates less strain in the DNA duplex than insertion; metallo-insertors induce an untwist of the double helix and an opening of the phosphate backbone while metallo-intercalators marginally increase the rise and width of the major groove. Intercalation of metal compounds between DNA base pairs effectively stabilizes the double helix, increasing the melting temperature of the DNA duplex.
  Binding of metallo-intercalators to DNA is reversible and depends on the properties of the intercalating molecule. Metallo-intercalators with different metal centers, oxidation states, coordination geometries, and overall sizes will exhibit varying “depths of insertion”. For example, square planar complexes penetrate deeper into the DNA base pairs than octahedral or tetrahedral complexes do. Also, positive charges on the metallo-intercalator strengthen DNA-binding because of electrostatic attraction to the negatively charged sugar-phosphate backbone.
caption: Figure 2: Metallo-intercalators enter double stranded DNA via the major groove and π-stack between adjacent unbroken base pairs. Here, the phi ligand of a rhodium complex intercalates a DNA segment with the sequence 5'-G(5IU)TGCAAC-3' (PDB ID 454D).[8]
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