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Selective binding of nucleosides to gapped DNA duplex revealed by orientation and distance dependence of FRET

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Abstract

Herein we used orientation and distance dependence of Förster resonance energy transfer (FRET) to analyze the binding of nucleosides to a gapped DNA duplex. Binding isotherms and information on the structures of the complexes were obtained by monitoring FRET between pyrene and perylene, which were introduced into the DNA through D-threoninol. FRET efficiency significantly changed upon formation of a duplex with a 1-nucleotide gap and a nucleoside. The FRET plot indicated that the complex has a double helical structure similar to a nicked duplex. Cooperative binding of two nucleosides to a duplex with a 2-nucleotide gap was also revealed using FRET. Various drug-nucleic acids interactions could be investigated using this sensitive and facile method.

Graphical abstract: Selective binding of nucleosides to gapped DNA duplex revealed by orientation and distance dependence of FRET

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Publication details

The article was received on 25 Apr 2019, accepted on 15 May 2019 and first published on 16 May 2019


Article type: Paper
DOI: 10.1039/C9OB00946A
Org. Biomol. Chem., 2019, Advance Article

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    Selective binding of nucleosides to gapped DNA duplex revealed by orientation and distance dependence of FRET

    H. Kashida, Y. Kokubo, K. Makino and H. Asanuma, Org. Biomol. Chem., 2019, Advance Article , DOI: 10.1039/C9OB00946A

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