Recognition of DNA abasic site nanocavity by fluorophore-switched probe: Suitable for all sequence environments

Ligands for Abasic Site-containing DNA and their Use as Fluorescent Probes

Apurinic and apyrimidinic sites, also referred to as abasic or AP sites, are residues of duplex DNA in which one DNA base is removed from a Watson-Crick base pair. They are formed during the enzymatic repair of DNA and offer binding sites for a variety of guest molecules. Specifically, the AP site may bind an appropriate ligand as a substitute for the missing nucleic base, thus stabilizing the abasic site-containing DNA (AP-DNA). Notably, ligands that bind selectively to abasic sites may be employed for analytical and therapeutical purposes. As a result, there is a search for structural features that establish a strong and selective association of a given ligand with the abasic position in DNA. Against this background, this review provides an overview of the different classes of ligands for abasic site-containing DNA (AP-DNA). This review covers covalently binding substrates, namely amine and oxyamine derivatives, as well as ligands that bind to AP-DNA by noncovalent association, as represented by small heterocyclic aromatic compounds, metal-organic complexes, macrocyclic cyclophanes, and intercalator-nucleobase conjugates. As the systematic development of fluorescent probes for AP-DNA has been somewhat neglected so far, this review article contains a survey of the available reports on the fluorimetric response of the ligand upon binding to the AP-DNA. Based on these data, this compilation shall present a perspective for future developments of fluorescent probes for AP-DNA.

Fluorescently probing site-specific and self-catalyzed DNA depurination

Depurination occurs via hydrolysis of the purine-deoxyribose glycosyl bond and causes nucleic acid damage. In particular, the DNA sequences that can undergo a self-catalyzed depurination (SCD) will cause a great uncertainty in duplicating, separating, purifying, and storing the DNA samples. Therefore, there is a great demand to develop a rapid detection method for SCD events. Herein, the use of a convenient fluorescence method to follow the site-specific SCD was demonstrated. We found that the resultant apurine site (AP site) from depurination can be selectively recognized by a fluorescent probe of palmatine (PAL) with a turn-on fluorescence response. The dependence of SCD on the bases of the depurination site, pH, metal ions, and time shows that our method can be used to rapidly evaluate the depurination process. Furthermore, the depurination process can be photo-switched using a photoacid as an external initiator. Our work will find wide applications in preliminarily identifying the DNA depurination.

Target-switched triplex nanotweezer and synergic fluorophore translocation for highly selective melamine assay

This paper describes a triplex DNA nanotweezer to specifically capture melamine (MEL). The triplex-forming oligonucleotide (TFO) arm can be switched from the open state to the closed state once MEL binds to the abasic site (AP site) in duplex via the bifacial hydrogen bonding with thymines. Following this nanotweezer operation, the AP site-bound fluorophore is translocated to the terminal triplet to subsequently light up the nanotweezer. The TFO arm is found to be pivotal for permitting the AP site binding. The synergic processes of target competition and fluorophore translocation support a high selectivity for the MEL assay even against the inherent adenosine and the MEL hydrolysis products. Chelerythrine is employed as the fluorescent probe. The detection limit of MEL was estimated to be about 140 nM assuming a signal-to-noise ratio of 3. It was applied to the determination of MEL in spiked milk samples without any separation procedure. Conceivably, this method opens a new avenue towards highly selective triplex-based sensors by making use of other commercially available DNA modifications for recognizing other analytes. Graphical abstract Schematic presentation of a triplex nanotweezer with an open-to-close conversion upon the abasic site binding of melamine. The assay is based on a synergic fluorophore translocation. The corresponding duplex otherwise shows no binding with melamine. Chelerythrine (CHE) with a yellow-green emission peaking at 544 nm is employed as the fluorescent probe.

Supramolecularly Multicolor DNA Decoding Using an Indicator Competition Assay

Relative to the individual intensity-dependent strategy, the multicolor fluorescence sensor has promise to achieve a high signaling contrast. In this work, we develop a cucurbituril-based supramolecular and multicolor DNA recognition rationale via indicator competition assay (ICA). Alkaloids of coptisine (COP) and palmatine (PAL) are identified as the proof-of-principle indicators with a lighting-up fluorescence upon supramolecular complexation to cucurbit[7]uril (CB[7]). With an introduced abasic site (AP site) as the contestant, DNAs having pyrimidines opposite this site can compete for COP with CB[7] to bring an emission color change from green to yellow brown, while those having purines opposite the AP site do not compete for COP and still have the green emission, indicative of a high selectivity for the multicolor nucleotide transversion recognition. However, because of the relatively weaker binding of PAL with CB[7], the AP site-containing DNA can take away PAL from its CB[7] complex and resultantly bring a blue-to-green emission color change independent of the AP site-opposite nucleotide identity, dissimilar to the remaining blue color for the fully matched DNA without the AP site, suggesting a preferable strategy for the AP site biomarker detection. Our method demonstrates a new way to develop an ICA-based multicolor DNA sensor with the supramolecular cucurbituril complexation to ensure a highly selective performance.