Construction of Highly Reactive Probes for Abasic Site Detection by Introduction of an Aromatic and a Guanidine Residue into an Aminooxy Group

Abstract

Abasic sites (AP sites) arise from hydrolysis of glycosidic bonds of DNA that is damaged by various external and internal processes; unrepaired AP sites give rise to genetic mutations. We have constructed highly reactive AP-site-detecting probes by introducing a hydrophobic and a hydrophilic residue in an aminooxy group. Synthesized probes containing either a naphthalene or a guanidine residue conjugate effectively with AP sites. In particular, a probe containing both functional groups shows the highest reaction rate, indicating that the hydrophobic and hydrophilic interactions act cooperatively in reaction with AP sites. The guanidine residue also contributes to the solubility of the molecules in aqueous media. The biotinylated probes provide much more sensitive detection of AP sites in genomic DNA than the conventional aldehyde-reactive probe.

DNA‐Templated Synthesis of Perylenediimide Stacks Utilizing Abasic Sites as Binding Pockets and Reactive Sites

“…Whereas the abasic analogue used is chemically stable or nonreactive, an abasic site or apurinic/apyrimidinic (AP) site produced from deoxyuridine‐containing DNA by treatment with a uracil DNA glycosylase (UDG) is known to react with a primary amine to yield a Schiff base that can be used for the covalent modification of DNA . Although the reactive AP in DNA has been used for single modification of DNA, it has not been utilized for multiple modification of DNA.…”

Ultrasensitive recognition of AP sites in DNA at the single-cell level: one molecular rotor sequentially self-regulated to form multiple different stable conformations

“…9,10 Thus, developing active substrate molecules that can take part in the relevant chemical reactions induced by the AP site is immensely conducive for such site-specic recognition in a DNA sequence. 11,12 To date, combined with nuclear magnetic resonance (NMR) spectrometry, 13,14 mass spectrometry 15,16 and optical techniques, [17][18][19][20] some substrate molecules have been successfully implemented for quantifying AP sites in DNA. [13][14][15][16][17][18][19][20] NMR spectrometry for detecting AP sites is characterized by highly selective signals.…”

An assay for RNA oxidation induced abasic sites using the Aldehyde Reactive Probe

“…Thereafter several modified probes for detecting DNA abasic sites have been developed mainly utilizing the property of the aminooxy group which binds preferentially to aldehyde groups in the open-ringed abasic sugar moiety [26]. However, until now the reactivity of ARP for the RNA abasic site has not been investigated.…”