Alloxazine as a ligand for selective binding to adenine opposite AP sites in DNA duplexes and analysis of single-nucleotide polymorphisms

Burki Rajendar; Seiichi Nishizawa; Norio Teramae

doi:10.1039/B719786A

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Alloxazine as a ligand for selective binding to adenine opposite AP sites in DNA duplexes and analysis of single-nucleotide polymorphisms†

Burki Rajendar,‡^a Seiichi Nishizawa^ab and Norio Teramae*^ab

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* Corresponding authors

^a Department of Chemistry, Graduate School of Science, Tohoku University, Aoba-ku, Sendai 980-8578, Japan
E-mail: teramae@mail.tains.tohoku.ac.jp
Fax: +81 22 7956552
Tel: +81 22 7956549

^b CREST, Japan Science and Technology Agency (JST), Aoba-ku, Sendai 980-8578, Japan

Abstract

Alloxazine can bind to adenine selectively over other nucleobases opposite an abasic site in DNA duplexes (5′-TCC AG [X with combining low line] GCA AC-3′/3′-AGG TC [N with combining low line] CGT TG-5′, = AP site, = A, T, C, G) with a dissociation constant of 0.82 µM (pH 7.0, I = 0.11 M, at 5 °C), and it is applicable to SNPs typing of PCR amplification products based on the binding-induced fluorescence response.

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Supplementary files

Fluorescence titration curves (Fig. S1 and Fig. S2), salt dependence of binding constants (Fig. S3 and Table S1), calorimetric isothermal titration (Fig. S4), effect of flanking nucleotides on fluorescence responses of alloxazine and dissociation constants (Table S2), and preparation and analysis of PCR products PDF (296K)

Article information

DOI: https://doi.org/10.1039/B719786A
Article type: Communication
Submitted: 02 Jan 2008
Accepted: 07 Jan 2008
First published: 18 Jan 2008

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Org. Biomol. Chem., 2008,6, 670-673

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Alloxazine as a ligand for selective binding to adenine opposite AP sites in DNA duplexes and analysis of single-nucleotide polymorphisms

B. Rajendar, S. Nishizawa and N. Teramae, Org. Biomol. Chem., 2008, 6, 670 DOI: 10.1039/B719786A

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Organic & Biomolecular Chemistry

Alloxazine as a ligand for selective binding to adenine opposite AP sites in DNA duplexes and analysis of single-nucleotide polymorphisms†

Abstract

Supplementary files

Article information

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Alloxazine as a ligand for selective binding to adenine opposite AP sites in DNA duplexes and analysis of single-nucleotide polymorphisms

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