Versatile Triple-Output Molecular Logic Gate for Cysteine and Silver (I) in Foods and the Environment Based on I-Motif DNA Modulation

Abstract

DNA-based molecular logic gates have been developed rapidly but most of them have a single output mode. This study is to develop a triple-output label-free fluorescent DNA-based multifunctional molecular logic gate with berberine as a fluorescent signal and a Ag+–aptamer as a recognition matrix. The Ag+–aptamer has been identified to switch from a random coil to an i-motif structure of C–Ag+–C from a Ag+-induced responsive conformational change. As a fluorescent probe, berberine is ultrasensitive to the changes of microenvironments, and the binding to i-motif DNA’s more rigid structure causes a significant increase in fluorescence, anisotropy, and lifetime. The addition of cysteine to the berberine/C–Ag+–C system disintegrates the i-motif DNA structure because of the strong coordination between Ag+ and cysteine, and then the triple-output signals are almost retrieved. Given this, a highly sensitive triple-output molecular logic gate for the analyses of Ag+ and cysteine is constructed with high specificity. Moreover, this simple and cost-effective molecular logic gate has been applied for the detection of cysteine and Ag+ in various real environmental samples including river water, PM2.5, soil, and food samples with satisfactory recoveries from 89.83 to 106.04%.

Recent progress in stimuli‐responsive DNA‐based logic gates: Design, working principles and biological applications

“…Lan and colleagues developed an i-motif-based INHIBIT logic gate that responded to Ag þ ions. [26] In the presence of Ag þ ions, the imotif structure was induced, resulting in luminescence signals as outputs. The concentration of Ag þ ions could be quantified by measuring the emission intensity.…”

Highly sensitive and specific detection of silver ions using a dual-color fluorescence co-localization strategy

“…28 Moreover, a triple-output label-free fluorescent DNA-based multifunctional molecular logic gate was developed and has been applied for the detection of Ag + ions in various real environmental samples. 29 These techniques for Ag + detection have extremely low LODs and high selectivity.…”

Fluorescent Detection of Two Pesticides Based on CRISPR-Cas12a and Its Application for the Construction of Four Molecular Logic Gates

“…Different input combinations will result in different outputs according to the truth table permutation . Recently, some excellent logic gates were fabricated on the basis of molecular computations, such as AND, OR, XOR, NAND, half adder, half subtractor, etc. − Most of the previously reported logic gates employed nucleic acids, , proteins, , and heavy metal ions , as inputs. There is still no report about the logic gate for pesticide applications.…”

“…In the XOR logic assay, 100 nM DNA (12) and DNA ( 14), 120 nM DNA (13) and DNA (15), 100 nM DNA (16) and DNA (17), and 200 nM DNA (3−5) were used. In the INHIBIT logic assay, 100 nM DNA (1) and DNA (18), 120 nM DNA (2) and DNA (19), and 200 nM DNA (3−5) were used. A total of 200 nM crRNA and 50 nM Cas12a were used in all of the logic operations.…”

“…Thus, the (1,0) state produces an output of 1. Similarly, in the input of (0,1), DNA ( 14 Although DNA (18) will be not blocked by DNA (19) in the presence of ATR (0,1), no domain 2 exists near domain 1 in DNA (18) to complete the toehold-mediated displacement. Thus, the output reads 0.…”