Closed Cyclic DNA Machine for Sensitive Logic Operation and APE1 Detection

Abstract

systems usually require abundant inputs to guarantee equivalent output signals that can be detected or distinguished, the strategies that are able to convert weak inputs to strong outputs are highly desired for high order logic operations and highly sensitive sensing. In recent years, researchers have made, and continue to make efforts to develop advanced synthetic DNA circuit systems for biological engineering. Dynamic DNA assembly which is concerned primarily with the construction of DNA circuits or nanostructures based on DNA hybridization attracted increasing research interests. [7][8][9] Especially, the dynamic and isothermal cyclic reactions such as hybridization chain reaction (HCR) and catalytic hairpin assembly (CHA) have been extensively utilized as robust strategies of enzymefree signal amplification in molecular recognition and sensing. [10,11] HCR is an established technique to obtain duplex DNA nanowires via the initiator-triggered cross-opening of hairpin reactants, which usually contributed to significant signal amplification and ease of operation in bio/chemosensing. [12][13][14] CHA is realized through initiator-catalyzed hybridizations of different DNA hairpins and thus result in the accumulation of short duplex DNA products. [15,16] Despite the advantages and achievements in signal amplification, these unitary DNA assembly strategies usually suffer from the signal leakage and limited amplification depth, which greatly hindered their applications in precisely sensing and profiling biomarkers with trace amounts.The advanced HCR and CHA, as well as the cascade integration of them are anticipated to theoretically offer improved amplification depth and stronger anti-interference capacity to break through the primary obstacles of their widely applications in sensing. For instance, compared to typical linear HCR, the nonlinear HCR and hyperbranched HCR were developed to program assembly systems with higher-order growth kinetics and amplification depth. [17][18][19] Apart from short linear DNA product, branched DNA products such as Y-shaped, X-shaped structures were obtained through CHA pathway, which could effectively reduce the signal leakage in some degree. [20][21][22] What's more, rational combination of HCR and CHA could achieve cascade amplification and enabled ultrasensitive homogeneous detection of target. [23][24][25][26][27] It is worthy noting that most of these assembly pathways were programmed to amplify DNA self-assembly has been developed as a kind of robust signal amplification strategy, but most of reported assembly pathways are programmed to amplify signal in one direction. Herein, based on mutual-activated cascade cycle of hybridization chain reaction (HCR) and catalytic hairpin assembly (CHA), a closed cycle circuit (CCC) based DNA machine is developed for sensitive logic operation and molecular recognition. Benefiting from the synergistically accelerated signal amplification, the closed cyclic DNA machine enabled the logic computing with strong and significant output signals even...

DNA Walker-Driven Mass Nanotag Assembly System for Simultaneously Profiling Dual Markers of Oxidative Stress at Different Cellular Locations

“…By setting the incremental relative intensity of 0.5 as the threshold value, the phenotype was defined to be MUC1-positive and APE1-positive for MCF-7 cells, MUC1-positive and APE1-negative for HeLa cells, MUC1-negative and APE1-positive for HepG2 cells, and double-negative for L02 cells (Figure c). All these results coincide well with the previous reports on the relative abundance of the two targets in the four classic cell lines, ,− highlighting the capability of the presented w-MNT-AS coupled MS method in distinguishing cell lines in terms of MUC1 and APE1 expression levels.…”

“…34−36 Moreover, the APE1-specific w-MNT-AS was further utilized to test the relative activity of APE1 in cell lysates. As desired, the APE1hyperactivated A549 37 and HepG2 cells 22 demonstrated largest elevation of the signature MT signals, while almost no response was observed in the lysate of L02 cells with APE1 inactivated (Figure S8). The apparent differences in relative intensity demonstrated the ability of w-MNT-AS to monitor APE1 at the cell lysate level.…”

Fluorogenic Aptamer-Based Hybridization Chain Reaction for Signal-Amplified Imaging of Apurinic/Apyrimidinic Endonuclease 1 in Living Cells

“…In comparison, another glioma cell line, U251, which is reported to have a lower APE1 expression level, which is responsible for the radiotherapy sensitivity [ 35 ], displayed a weak fluorescence signal. Also, the HEK-293T, a normal human cell that was used as the control [ 36 , 37 ], did not display an obvious fluorescence signal. To further confirm that the fluorescence signal was caused by APE1 rather than other nucleases, a control ARP probe without an AP site (ARP-C) was also delivered into the three cell lines along with the FAC-H1 and H2.…”

DNA Nanotechnology-Empowered Fluorescence Imaging of APE1 Activity

“…Especially, the cascade integration of different amplification modes can improve amplification depth and strengthen anti-interference capacity. As shown in Figure 4b, Chai et al employed a probe containing an AP site and triggering T1, which was complementary to the 5 -toehold of H1 [70]. APE1 could cleave the AP site and release T1.…”