Polyrotaxane/DNA Conjugate by Use of Intercalation:  Bridge Formation between DNA Double Helices

Fluorene has been known as an intercalator of DNA. This paper shows that the fluorene−DNA interaction has a relatively large binding constant (ca. 107-8 M-1 at least larger than 106 M-1). This large binding constant is consistent with the experimental fact that adding fluorenone stoichiometrically ejects the ethidium bromide that had been beforehand intercalated in DNA. A polyrotaxane was made from polyethylene glycol and α-cyclodextrin, and the both ends were capped with fluorene (dF-CD-PEG). When we mixed dF-CD-PEG and DNA, atomic force microscopy showed that the DNA was interlinked with dF-CD-PEG. The present work proves that DNA intercalators can be useful for a building block to manipulate DNA when they are combined with polyrotaxanes.