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

Abstract

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.

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

“…The binding constants between pterin and G opposite the AP site were 1.2 × 10 4 M -1 for dSpacer and 2.6 × 10 4 M -1 for Spacer-C3, using a non-linear fitting method described previously. 9 As described in the results on the Tm measurements and fluorescence titration, we could obtain a more efficient binding ability by using Spacer-C3 as an AP site.…”

“…[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.…”

A chemical toxicity sensor based on the electrochemiluminescence quantification of apurinic/apyrimidinic sites in double-stranded DNA monolayer

“…Teramae's group has designed and synthesized a series of environmentally sensitive fluorescent probes which bind selectively to AP sites in ds-DNA. The binding was manifested by either fluorescence quenching or enhancement [9][10][11][12][13][14]. Wu et al reported an AP site selective fluorescent probe, sanguinarine with a large emission shift [15].…”

Synthesis and site-specific incorporation of a simple fluorescent pyrimidine

“…Several methods have been developed for detecting the presence of these cytotoxic DNA lesions. Most techniques require irreversible modifications of isolated DNA , whereas others use non-natural nucleobase analogs [77][78][79][80][81][82][83][84][85][86][87][88][89] and only a few use 2AP to investigate the stacking ability of a base opposite an abasic site [90][91][92] . Fluorescent nucleobase analogs that positively sense the presence of abasic sites could provide useful nondestructive tools for the detection of such important DNA defects.…”