Enhancement of the Binding Ability of a Ligand for Nucleobase Recognition by Introducing a Methyl Group

Competitive Binding of Abasic Site-Binding Ligands and Masking Ligands to DNA Duplexes for the Analysis of Single-Base Mutation

“…It was previously found that the binding affinity of pterin with G opposite an AP site increased more than 10 times at 5 C compared to 20 C. 18 Accordingly, fluorescence measurements were carried out at 5 C using a 3 × 3 mm quartz cell. In the competitive binding assay with the masking ligands, fluorescence spectra of the ligands were obtained by subtracting the fluorescence spectra of the masking ligands measured under the identical measurement conditions.…”

Recent Progress in Abasic Site-binding Small Molecules for Detecting Single-base Mutations in DNA

“…in DNA duplexes, [10][11][12][13][14][15][16][17][18][19][20][21] and have proposed a new strategy of ligand-based fluorescence assay for SNP typing. In contrast to typical DNA-binding ligands capable of targeting double stranded DNAs by intercalation or groove binding, 22,23 it is characteristic of ligands to bind to non-Watson-Crick basepairing sites in DNA duplexes, where the binding is promoted by a pseudo-base pairing along the Watson-Crick edge of intrahelical target nucleobases, and also by stacking with two nucleobases flanking the AP site.…”

“…In contrast to typical DNA-binding ligands capable of targeting double stranded DNAs by intercalation or groove binding, 22,23 it is characteristic of ligands to bind to non-Watson-Crick basepairing sites in DNA duplexes, where the binding is promoted by a pseudo-base pairing along the Watson-Crick edge of intrahelical target nucleobases, and also by stacking with two nucleobases flanking the AP site. Useful affinity and selectivity for target nucleobases opposite the AP site has been indeed obtained by various kinds of heterocyclic planer compounds, including cytosine-selective 2-amino-1,8-naphthyridine derivatives, [10][11][12][13][14] guanine-selective pterin derivatives, [15][16][17] adenineselective 6,7-dimethyllumazine, 18 and thymine-selective 3,5-diaminopyrazine derivatives. [19][20][21] All of these ligands show a complexation-induced fluorescence signaling, and genotype of samples can be clearly distinguished by combining ligands with selectivity for respective target nucleobases.…”

A Pyrazine-based Fluorescence-enhancing Ligand with a High Selectivity for Thymine in AP Site-containing DNA Duplexes

“…[1][2][3][4] Of particular interest to us is the development of a class of ligands suitable for gene detection, especially for singlenucleotide polymorphisms (SNPs) typing. 5 We have recently found a series of aromatic ligands that can selectively bind to a nucleobase opposite to an abasic site (AP site) in DNA duplexes, [6][7][8][9][10][11][12][13][14][15][16] and have proposed a new strategy of ligand-based fluorescence assay for SNPs typing. In contrast to typical DNA-binding ligands capable of targeting doublestranded DNAs by intercalation or groove binding, 17,18 it is a characteristic of our ligands to target non-Watson-Crick basepairing sites in DNA duplexes, where the binding is promoted by a pseudo-base pairing along the Watson-Crick edge of intrahelical target nucleobases.…”