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Small. 2009 Nov;5(21):2418-23. doi: 10.1002/smll.200900494.

Micrometer-sized DNA-single-fluorophore-DNA supramolecule: synthesis and single-molecule characterization.

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Department of Chemistry, Stanford University, Stanford, CA 94305-5080, USA.


The synthesis of single-fluorophore-bis(micrometer-sized DNA) triblock supramolecules and the optical and structural characterization of the construct at the single-molecule level is reported. A fluorophore-bis(oligodeoxynucleotide) triblock is synthesized via the amide-coupling reaction. Subsequent protocols of DNA hybridization/ligation are developed to form the supramolecular triblock structure with lambda-DNA fragments on the micrometer length scale. The successful synthesis of the micrometer-sized DNA-single-fluorophore-DNA supramolecule is confirmed by agarose gel electrophoresis with fluorescence imaging under UV excitation. Single triblock structures are directly imaged by combined scanning force microscopy and single-molecule fluorescence microscopy, and provide unambiguous confirmation of the existence of the single fluorophore inserted in the middle of the long DNA. This type of triblock structure is a step closer to providing a scaffold for single-molecule electronic devices after metallization of the DNAs.

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