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

Literature Information

Publication Date 2019-05-16
DOI 10.1039/C9OB00946A
Impact Factor 3.876
Authors

Hiromu Kashida, Yuta Kokubo, Koki Makino, Hiroyuki Asanuma


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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.

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Organic & Biomolecular Chemistry

Organic & Biomolecular Chemistry
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