Label-Free Catalytic and Molecular Beacon Containing an Abasic Site for Sensitive Fluorescent Detection of Small Inorganic and Organic Molecules

Abstract

In this work, two methods with complementary features, catalytic and molecular beacon (CAMB) and label-free fluorescent sensors using abasic site, have been combined into new label-free CAMB sensors that possess advantages of each method. The label-free method using dSpacer-containing molecular beacon makes CAMB more cost-effective and less interfering to the catalytic activity, while the CAMB allows the label-free method to use true catalytic turnovers for signal amplifications, resulting in a new label-free CAMB sensor for Pb2+ ion, with a detection limit of 3.8 nM while maintaining the same selectivity. Furthermore, by using CAMB to overcome the label-free method’s limitation of the requiring excess enzyme strand, a new label-free CAMB sensor using aptazyme is also designed to detect adenosine down to 1.4 μM, with excellent selectivity over other nucleosides.

DNA as Sensors and Imaging Agents for Metal Ions

“…130,132,134,135 We took advantage of the specific binding between ATMND and AP sites (dSpacer or vacant sites) in a DNAzyme-substrate duplex to control the binding sites of fluorophores in the label-free metal ion sensor design (Figure 6E). 121,123,127 The more defined binding sites (AP sites) of ATMND in a DNA duplex compared to non-specific binding of intercalating dyes to DNA can help in the rational design of the sensors and minimize the risk of activity reduction due to the binding of dyes to the active cores of DNAzymes. In the presence of target metal ions such as Pb 2+ and UO 2 2+ , the cleavage of substrates by the DNAzymes caused the deformation of duplex regions and released ATMND from the binding site, because ATMND cannot bind to ssDNA.…”

“…(E) Single Pb 2+ ion detection using a unimolecular DNA-catalytic probe. Adapted from Refs 112, 127, 130, 94 and 136.…”

A label-free and sensitive fluorescent method for the detection of uracil-DNA glycosylase activity

“…1A). A dSpacer [28][29][30][31][32][33] (1 0 ,2 0 -dideoxyribose, an artificial non-base spacer in DNA, abbreviated as ''dSp'' and …”

“…1A). A dSpacer [28][29][30][31][32][33] (1 0 ,2 0 -dideoxyribose, an artificial non-base spacer in DNA, abbreviated as ''dSp'' and a Department of Chemistry, Beijing Key Laboratory for Microanalytical Methods and shown in the blue structure in Fig. 1A) binding fluorophore, named 2-amino-5,6,7-trimethyl-1,8-naphthyridine (ATMND), is allowed to bind the dSpacer opposite to a uracil site in the DNA duplex (DNA-U/DNA-X) through 3 complementary hydrogen bonds and p-p stacking.…”

Colorimetric assay of lead using unmodified gold nanorods

“…Even with sensitivity and accuracy, there also share some disadvantages, such as timeconsuming, expensive, and/or require sophisticated equipment, etc. To overcome these limitation and drawbacks, a variety of sensors have been developed to rapidly detect lead with high selectivity and sensitivity [12][13][14][15][16][17][18][19][20][21][22][23][24][25][26]. Among them, colorimetric sensors offer a promising approach for facile tracking of metal ions in biological, toxicological, and environmental samples.…”