Fluorescence detection of cytosine/guanine transversion based on a hydrogen bond forming ligand

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.…”

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

“…[8][9][10][11][12][13][14] We have recently proposed a new method for SNPs typing based on fluorescent ligands with hydrogen-bond ability in combination with the use of an apurinic or apyrimidinic site, i.e. an AP site, as a molecular recognition field.…”

“…an AP site, as a molecular recognition field. [9][10][11][12][13][14] While naturally occurring AP sites are one of the most common forms of DNA damage, 15 we intentionally constructed an AP site in an ODN duplex so as to orient the AP site toward a target nucleobase, by which a hydrophobic microenvironment is provided for ligands to recognize nucleotides through hydrogen-bonding.…”

Ratiometric Fluorescence Detection of Pyrimidine/Purine Transversion by Using a 2-Amino-1,8-naphthyridine Derivative

“…[8][9][10][11][12][13][14][15][16][17][18] We have recently discovered a series of small aromatic ligands that can bind to a nucleobase opposite an abasic site (AP site) in DNA duplexes, and have proposed a new strategy of ligand-based fluorescence assay for SNPs typing. [11][12][13][14][15][16][17][18] Our method is based on the construction of the AP site in DNA duplexes, which allows small synthetic and/or biotic ligands to bind to target nucleotides, accompanied by fluorescence signaling: an AP site-containing probe DNA is hybridized with a target DNA so as to place the AP site toward a target nucleotide, by which hydrophobic microenvironments are provided for ligands to recognize target nucleobases. Highly selective bindings toward target nucleobases were indeed obtained with the binding affinity up to the micromolar range, as has been demonstrated in AMND (2-amino-7-methyl-1,8-naphthyridine)-cytosine, 11,13 pterin-guanine, 12 vitamin B2-thymine, 15,16 and amiloride-thymine 17 bindings.…”

“…[11][12][13][14][15][16][17][18] Our method is based on the construction of the AP site in DNA duplexes, which allows small synthetic and/or biotic ligands to bind to target nucleotides, accompanied by fluorescence signaling: an AP site-containing probe DNA is hybridized with a target DNA so as to place the AP site toward a target nucleotide, by which hydrophobic microenvironments are provided for ligands to recognize target nucleobases. Highly selective bindings toward target nucleobases were indeed obtained with the binding affinity up to the micromolar range, as has been demonstrated in AMND (2-amino-7-methyl-1,8-naphthyridine)-cytosine, 11,13 pterin-guanine, 12 vitamin B2-thymine, 15,16 and amiloride-thymine 17 bindings. Our method was effectively applicable to the analysis of PCR (polymerase chain reaction) amplification products, 17 for which a complexation-induced fluorescence quenching of these AP sitebinding ligands was utilized to detect the single base mutation.…”