Target-mediated self-assembly of DNA networks for sensitive detection and intracellular imaging of APE1 in living cells

Abstract

We designed two functionalized tetrahedral DNA nanostructures (f-TDN1 and f-TDN2), which could assemble into giant DNA networks triggered by APE1, achieving sensitive detection and intracellular imaging of APE1 as well as gene therapy.

Chimeric d/l-DNA Probes of Base Excision Repair Enable Real-Time Monitoring of Thymine DNA Glycosylase Activity in Live Cells

“…We anticipate that future sequence and structural optimization of these probes will lead to improved response kinetics and signal over background, allowing for monitoring of endogenous TDG activity, possibly within whole organisms. While the current chimeric probe design will certainly benefit from further optimization, the intracellular performance of FU-7 in terms of imaging is comparable to several recently reported nucleic acid based BER probes, which employ more complex designs and/or signal amplification strategies. ,− We also note that the chimeric design provides the unique opportunity for integration with robust l -DNA-based catalytic systems (e.g., catalytic hairpin assembly) through straightforward strand-displacement mechanisms, which would greatly improve the sensitivity of BER detection . Finally, beyond BER, we expect that the chimeric probe design could be exploited for sensing and imaging other classes of DNA-modifying enzymes, or even those that act on RNA.…”

Endogenous Enzyme-Powered DNA Nanomotor Operating in Living Cells for microRNA Imaging

“…The target recognition region on L was designed to contain 6-nt toehold length because 6-nt toehold length could trigger the toehold strand displacement reactions based on previous reports. 36,37 A shorter inhibition domain of the L probe would produce a severe background signal, but a longer inhibition domain would reduce the reaction dynamics of L release from W. The inhibition domain length of the L probe was designed with 3 nt (lock-3), 4 nt (lock-4), 5 nt (lock-5), 6 nt (lock-6), and 7 nt (lock-7) (Table S1) to perform the EEPDN. A maximum F/F0 value was obtained when lock-6 was used in the EEPDN system (Figure . 2B).…”

“…The locking strand (L) is designed to silence the walking strands and respond to the target miRNA, which consists of a target recognition region and an inhibition region that prevents hybridization of W to R. An ideal L would effectively suppress the recognition of W to R when the target miRNA was absent, but it would quickly activate the recognition between W and R when the target was present. The target recognition region on L was designed to contain 6-nt toehold length because 6-nt toehold length could trigger the toehold strand displacement reactions based on previous reports. , A shorter inhibition domain of the L probe would produce a severe background signal, but a longer inhibition domain would reduce the reaction dynamics of L release from W. The inhibition domain length of the L probe was designed with 3 nt (lock-3), 4 nt (lock-4), 5 nt (lock-5), 6 nt (lock-6), and 7 nt (lock-7) (Table S1) to perform the EEPDN. A maximum F/F0 value was obtained when lock-6 was used in the EEPDN system (Figure.…”

“…APE1 is a DNA damage repair enzyme with the ability to remove apurinic/apyrimidinic (AP) sites from DNA, which is generally overexpressed in tumor cells . Based on the properties of APE1, APE1 has been widely used as a key biomarker to achieve disease diagnosis, − which provides us with clues that APE1 has the potential to be the driving force for constructing efficient nanomotors. For this EEPDN strategy, we employ endogenous APE1 as fuel to drive the autonomous motion of the machine for performing the task of imaging miRNA in live cells.…”

Homogeneous Dual Fluorescence Count of CD4 in Clinical HIV-Positive Samples via Parallel Catalytic Hairpin Assembly and Multiple Recognitions

“…To simplify the procedure, reduce costs, and realize homogeneous detection, isothermal enzyme-free amplification is preferable. Enzyme-free isothermal amplifications such as hybridization chain reaction, CHA, and DNAzyme have shown great potential, creating no need for a thermal cycler and strict conditions for enzymatic reactions. ,− Particularly, CHA, which utilizes two complementary DNA hairpins to initiate cyclic signal amplification, is a promising tool in biosensing. − CHA possesses several advantages, such as high catalytic efficiency, a simple design, and a stable system. − In addition, applying two luminescent materials as signal reporters led to more resistance toward interference. Two signal reporters might supplement each other, potentially enhancing the sensitivity, which cannot be otherwise achieved by a single signal. , …”