Use of Abasic Site-Containing DNA Strands for Nucleobase Recognition in Water

Nucleobase recognition in water is successfully achieved by the use of an abasic site (AP site) as the molecular recognition field. We intentionally construct the AP site in DNA duplex so as to orient the AP site toward a target nucleobase and examine the complexation of 2-amino-7-methylnaphthyridin...

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Bibliographic Details
Published in:Journal of the American Chemical Society 2003-07, Vol.125 (30), p.8982-8983
Main Authors: Yoshimoto, Keitaro, Nishizawa, Seiichi, Minagawa, Masakazu, Teramae, Norio
Format: Article
Language:English
Subjects:
Analytical, structural and metabolic biochemistry
Biological and medical sciences
DNA - chemistry
Fundamental and applied biological sciences. Psychology
Models, Molecular
Naphthyridines - chemistry
Nucleic acids
Nucleic bases, nucleotides
Thermodynamics
Water - chemistry
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Summary:Nucleobase recognition in water is successfully achieved by the use of an abasic site (AP site) as the molecular recognition field. We intentionally construct the AP site in DNA duplex so as to orient the AP site toward a target nucleobase and examine the complexation of 2-amino-7-methylnaphthyridine (AMND) with nucleobases at the AP site. AMND is found to selectively bind to cytosine (C) base with a 1:1 binding constant of >106 M-1, accompanied by remarkable quenching of its fluorescence. In addition to hydrogen bonding, a stacking interaction with nucleobases flanking the AP site seems responsible for the binding properties of AMND at the AP site. Possible use of AMND is also presented for selective and visible detection of a single-base alternation related to the cytosine base.
ISSN:0002-7863
1520-5126
DOI:10.1021/ja029786m