Programmable intracellular DNA biocomputing circuits for reliable cell recognitions

Gong, Xue; Wei, Jie; Liu, Jing; Li, Ruomeng; Liu, Xiaoqing; Wang, Fuan

doi:10.1039/c8sc05217d

Cited by 87 publications

(76 citation statements)

References 50 publications

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“…, MCF-7 breast cancer cells, HepG2 liver cancer cells), in comparison to normal epithelial breast cells MCF-10A. The MCF-7 cells include the miRNA-21 and miRNA-155 as biomarkers, 57 and the HepG2 cells overexpress miRNA-21. 58 Accordingly, the different cells were treated with the tetrahedra composite shown in Scheme 1 that includes three quenched fluorophores, FAM, Cy5, and ROX.…”

Section: Resultsmentioning

confidence: 99%

DNA Tetrahedra Modules as Versatile Optical Sensing Platforms for Multiplexed Analysis of miRNAs, Endonucleases, and Aptamer–Ligand Complexes

et al. 2020

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The sensing modules for analyzing miRNAs or the endonucleases consist of tetrahedra functionalized with three different fluorophore–quencher pairs in spatially quenched configurations and hairpin units acting as recognition elements for the analytes. Three different miRNAs (miRNA-21, miRNA-221, and miRNA-155) or three different endonucleases (Nt.BbvCI, Eco RI, and Hin dIII) uncage the respective hairpins, leading to the switched-on fluorescence of the respective fluorophores and to the multiplex detection of the respective analytes. In addition, a tetrahedron module for the multiplexed analysis of aptamer ligand complexes (ligands = ATP, thrombin, VEGF) is introduced. The module includes edges modified with three spatially separated fluorophore–quencher pairs that were stretched by the respective aptamer strands to yield a switched-on fluorescent state. Formation of the respective aptamer ligands reconfigures the edges into fluorophore-quenched caged-hairpin structures that enable the multiplexed analysis of the aptamer–ligand complexes. The facile permeation of the tetrahedra structures into cells is used for the imaging of MCF-7 and HepG2 cancer cells and their discrimination from normal epithelial MCF-10A breast cells.

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Section: Resultsmentioning

confidence: 99%

DNA Tetrahedra Modules as Versatile Optical Sensing Platforms for Multiplexed Analysis of miRNAs, Endonucleases, and Aptamer–Ligand Complexes

et al. 2020

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“…Placing DNA gates on a tile allows for a modular approach to circuit assembling, in which logic units can be produced separately and stored for extended time before being integrated in more complex circuits [5] . In this paradigm, each NAND gate can be chemically crosslinked to minimize the risk of strand separation and mishybridization in complex mixtures of DNA strands during assembling complex circuits.…”

Section: Resultsmentioning

confidence: 99%

“…Moreover, the biocompatibility of such devices would enable analysis of complex sets of biomarkers, including those found in individual cells. This promises to advance diagnostics and the treatment of infectious diseases, genetic disorders, and cancers [4–7] …”

Section: Introductionmentioning

confidence: 99%

Manufacturing Reusable NAND Logic Gates and Their Initial Circuits for DNA Nanoprocessors

Molden

Grillo

Kolpashchikov

2020

Chemistry A European J

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DNA‐based computers can potentially analyze complex sets of biological markers, thereby advancing diagnostics and the treatment of diseases. Despite extensive efforts, DNA processors have not yet been developed due, in part, to limitations in the ability to integrate available logic gates into circuits. We have designed a NAND gate, which is one of the functionally complete set of logic connectives. The gate's design avoids stem‐loop‐folded DNA fragments, and is capable of reusable operations in RNase H‐containing buffer. The output of the gate can be translated into RNA‐cleaving activity or a fluorescent signal produced either by a deoxyribozyme or a molecular beacon probe. Furthermore, three NAND‐gate‐forming DNA strands were crosslinked by click chemistry and purified in a simple procedure that allowed ≈1013 gates to be manufactured in 16 h, with a hands‐on time of about 30 min. Two NAND gates can be joined into one association that performs a new logic function simply by adding a DNA linker strand. Approaches developed in this work could contribute to the development of biocompatible DNA logic circuits for biotechnological and medical applications.

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“…More recently, DNA motif and miRNA‐based biocomputing circuits for various cell recognition activities using fluorescence intensity were reported. [ 117 ] This research defined the biocomputation as the two modules of DNA as the sensing module and processing module that structure performed by hybridization chain reaction (HCR) that amplified the hybridization events of target with fluorescence (fluorescein amidite [FAM]‐tagged module) (Figure 4B). Other modules tagged with TAMRA quench the counterpart of the biocomputation module for signal amplification and are processed by Forster resonance energy transfer (FRET).…”

Section: Bioelectronic Devices Comprised Of Nucleic Acid Based Nanobimentioning

confidence: 99%

Nanobiohybrid Material‐Based Bioelectronic Devices

Yoon

Shin

Lim

et al. 2020

Biotechnology Journal

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Biomolecules, especially proteins and nucleic acids, have been widely studied to develop biochips for various applications in scientific fields ranging from bioelectronics to stem cell research. However, restrictions exist due to the inherent characteristics of biomolecules, such as instability and the constraint of granting the functionality to the biochip. Introduction of functional nanomaterials, recently being researched and developed, to biomolecules have been widely researched to develop the nanobiohybrid materials because such materials have the potential to enhance and extend the function of biomolecules on a biochip. The potential for applying nanobiohybrid materials is especially high in the field of bioelectronics. Research in bioelectronics is aimed at realizing electronic functions using the inherent properties of biomolecules. To achieve this, various biomolecules possessing unique properties have been combined with novel nanomaterials to develop bioelectronic devices such as highly sensitive electrochemical-based bioelectronic sensing platforms, logic gates, and biocomputing systems. In this review, recently reported bioelectronic devices based on nanobiohybrid materials are discussed. The authors believe that this review will suggest innovative and creative directions to develop the next generation of multifunctional bioelectronic devices.

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Programmable intracellular DNA biocomputing circuits for reliable cell recognitions

Abstract: A reconfigurable hybridization-based chain reaction was introduced to assemble enzyme-free DNA logic gates and advanced logic circuits for analyzing multiple endogenous miRNA expressions and discriminating different living cells.

Cited by 87 publications

References 50 publications

DNA Tetrahedra Modules as Versatile Optical Sensing Platforms for Multiplexed Analysis of miRNAs, Endonucleases, and Aptamer–Ligand Complexes

DNA Tetrahedra Modules as Versatile Optical Sensing Platforms for Multiplexed Analysis of miRNAs, Endonucleases, and Aptamer–Ligand Complexes

Manufacturing Reusable NAND Logic Gates and Their Initial Circuits for DNA Nanoprocessors

Nanobiohybrid Material‐Based Bioelectronic Devices

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