Logic Gates Based on DNA Aptamers

Andrianova, Mariia; Kuznetsov, Alexander

doi:10.3390/ph13110417

Cited by 19 publications

(9 citation statements)

References 176 publications

Supporting

Mentioning

Contrasting

Order By: Relevance

“…299 The versatility of the DNA nanotechnology toolbox has enabled DNA logic gate operations using a variety of inputs including nucleic acid strands, 300 or the binding of substrates to aptamer sequences. 301 Not surprisingly, the engineering of photoresponsive ONB-containing DNA strands has also been exploited in the design of such systems, where light either uncages the reactivity of the strands to stimulate the logic gate operation, allowing spatiotemporal activation of the DNA computational event, or acts itself as one of the input-stimuli of the DNA-based logic gate module. Photocaged single-stranded DNA was directed toward the construction of DNA logic gates (Figure 27).…”

Section: Onb-functionalized Nucleic Acids For Logic Gate Operations A...mentioning

confidence: 99%

“…The precise and programmable nature of nucleic acids has enabled these biopolymers to function as the basis of molecular logic gates, in which preprogrammed combinations of multiple inputs leads to transduction events based on strand hybridization in order to generate an output event, such as a fluorescent signal or the release of a load from an encapsulated structure. , This has enabled the design of synthetic DNA-based computational circuitries that may be interfaced with biological machinery toward a variety of applications including the targeted delivery of payloads to cells, pH sensing and miRNA detection . The versatility of the DNA nanotechnology toolbox has enabled DNA logic gate operations using a variety of inputs including nucleic acid strands, or the binding of substrates to aptamer sequences . Not surprisingly, the engineering of photoresponsive ONB-containing DNA strands has also been exploited in the design of such systems, where light either uncages the reactivity of the strands to stimulate the logic gate operation, allowing spatiotemporal activation of the DNA computational event, or acts itself as one of the input-stimuli of the DNA-based logic gate module.…”

Section: Applications Of Photocleavable Dna Nanostructuresmentioning

confidence: 99%

See 1 more Smart Citation

Photocleavable Ortho-Nitrobenzyl-Protected DNA Architectures and Their Applications

et al. 2023

View full text Add to dashboard Cite

This review article introduces mechanistic aspects and applications of photochemically deprotected ortho-nitrobenzyl (ONB)-functionalized nucleic acids and their impact on diverse research fields including DNA nanotechnology and materials chemistry, biological chemistry, and systems chemistry. Specific topics addressed include the synthesis of the ONB-modified nucleic acids, the mechanisms involved in the photochemical deprotection of the ONB units, and the photophysical and chemical means to tune the irradiation wavelength required for the photodeprotection process. Principles to activate ONB-caged nanostructures, ONB-protected DNAzymes and aptamer frameworks are introduced. Specifically, the use of ONB-protected nucleic acids for the phototriggered spatiotemporal amplified sensing and imaging of intracellular mRNAs at the single-cell level are addressed, and control over transcription machineries, protein translation and spatiotemporal silencing of gene expression by ONB-deprotected nucleic acids are demonstrated. In addition, photodeprotection of ONB-modified nucleic acids finds important applications in controlling material properties and functions. These are introduced by the phototriggered fusion of ONB nucleic acid functionalized liposomes as models for cell–cell fusion, the light-stimulated fusion of ONB nucleic acid functionalized drug-loaded liposomes with cells for therapeutic applications, and the photolithographic patterning of ONB nucleic acid-modified interfaces. Particularly, the photolithographic control of the stiffness of membrane-like interfaces for the guided patterned growth of cells is realized. Moreover, ONB-functionalized microcapsules act as light-responsive carriers for the controlled release of drugs, and ONB-modified DNA origami frameworks act as mechanical devices or stimuli-responsive containments for the operation of DNA machineries such as the CRISPR-Cas9 system. The future challenges and potential applications of photoprotected DNA structures are discussed.

show abstract

Section: Onb-functionalized Nucleic Acids For Logic Gate Operations A...mentioning

confidence: 99%

Section: Applications Of Photocleavable Dna Nanostructuresmentioning

confidence: 99%

Photocleavable Ortho-Nitrobenzyl-Protected DNA Architectures and Their Applications

et al. 2023

View full text Add to dashboard Cite

show abstract

“…This displacement causes the origami structure to unfold and release their contents. [ 123 ] This is a process that relies on careful construction of the origami structures using computer aided design software, such as caDNAno (https://www.caDNAno.org).…”

Section: The Biomolecular Toolbox: Molecular Strategies To Achieve Sp...mentioning

confidence: 99%

A Biomolecular Toolbox for Precision Nanomotors

et al. 2023

View full text Add to dashboard Cite

Figure 2. Chemically propelled nanomotors. a) Pt/Cr coated Janus nanomotors loaded with doxorubicin and functionalized with folic acid. Reproduced with permission. [54] Copyright 2014, John Wiley and Sons; b) pH-responsive ZIF-L nanomotors encapsulated with catalase and succinylated β-lactoglobulin, reproduced with permission. [55] Copyright 2019, John Wiley and Sons; c) vertically driven pH-responsive ZIF-L nanomotors encapsulating catalase and PDPA. Reproduced with permission. [34] Copyright 2019, Elsevier; d) Nanomotors constructed out of heparin, folic acid, and L-arginine were loaded with doxorubicin for the nitric oxide-mediated treatment of solid tumors. Reproduced under terms of the CC-BY license. [45] Copyright 2022, John Wiley and Sons; e) ZIF-8-coated up-conversion nanoparticles functionalised with glucose oxidase and catalase for photodynamic and oxygen starvation therapy of cancer cells. Reproduced with permission. [43] Copyright 2019, Elsevier; f) A jellyfish-shaped multi-metallic shell micromotor for DNA detection. Reproduced with permission. [57] Copyright 2014, John Wiley and Sons. g) Magnesium-based micromotor coated with titanium, PLGA embedded with clarithromycin and chitosan for the treatment of a stomach infection. Reproduced under terms of the CC-BY license. [59] Copyright 2017, Springer Nature; h) Mesoporous silica nanoparticles functionalized with urease and anti-FGFR3 for bladder treatment. Reproduced with permission. [60]

show abstract

“…[4][5][6][7][8][9] Among various nanodevices, DNA aptamerbased sensors have drawn extensive attention due to their high specicity and affinity. 4,10 Despite these achievements, the single-function nature and uncontrollability of the sensors limit their further application. On one hand, the recognition of multiple analytes is very important for diagnosis and treatment because it is oen not sufficient to make a diagnosis only by monitoring a single target under some condition.…”

Section: Introductionmentioning

confidence: 99%