An aptazyme-based molecular device that converts a small-molecule input into an RNA output

Ayukawa, Shotaro; Shibata, Yoko; Kiga, Daisuke

doi:10.1039/c2cc31886e

Cited by 12 publications

(8 citation statements)

References 26 publications

(33 reference statements)

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“…The previously reported designs of aptazymes based on inserting aptamers into the DNAzymes usually involved changes in the active sites of the DNAzymes [12,13,[47][48][49][50][51][52], making the activities of the DNAzymes in the aptazymes usually difficult to predict. Therefore, one successful design by the insertion approach often required sophisticated trials and optimizations, and was very difficult to extend from using one DNAzyme to another.…”

Section: Figurementioning

confidence: 99%

“…Perhaps a major reason for this difference is that, most DNA aptazyme sensors are developed by artificial design using known DNAzymes and aptamers rather than by more efficient combinatorial techniques [46], therefore extensive trial-and-error and optimization procedures are usually required for the identification of a successful aptazyme sensor with target-dependent fluorescence switch. Moreover, many of these design strategies for aptazymes often involve changes in the active sites or binding arms of functional DNAs to introduce aptamer sequences into DNAzymes [12,13,[47][48][49][50][51][52]. Such strategies have been successfully applied for target detection, but the insertion of aptamers may interfere the activity of the DNAzymes and make it M A N U S C R I P T A C C E P T E D ACCEPTED MANUSCRIPT 3 difficult to apply the same design approach rationally to other DNAzyme and aptamer pairs, because of the dramatically different properties of each DNAzyme and aptamer [53].…”

Section: Introductionmentioning

confidence: 99%

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A general approach for rational design of fluorescent DNA aptazyme sensors based on target-induced unfolding of DNA hairpins

Zhou

Xiao

Xiang

et al. 2015

Analytica Chimica Acta

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Section: Figurementioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

A general approach for rational design of fluorescent DNA aptazyme sensors based on target-induced unfolding of DNA hairpins

Zhou

Xiao

Xiang

et al. 2015

Analytica Chimica Acta

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“…In addition, because of their high efficiency and easiness of manipulation, the RNAPs are the most commonly used enzymes for in vitro transcription [15][16][17]39]. We expect that these orthogonal pairings of RNAPs with the inhibitory aptamers will have applications in the sophisticated design of translation-free, expression regulation systems [40][41][42][43][44].…”

Section: Discussionmentioning

confidence: 99%

Evolution of an inhibitory RNA aptamer against T7 RNA polymerase

2012

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Aptamers are promising gene components that can be used for the construction of synthetic gene circuits. In this study, we isolated an RNA aptamer that specifically inhibits transcription of T7 RNA polymerase (RNAP). The 38-nucleotide aptamer, which was a shortened variant of an initial SELEX isolate, showed moderate inhibitory activity. By stepwise doped-SELEX, we isolated evolved variants with strong inhibitory activity. A 29-nucleotide variant of a doped-SELEX isolate showed 50% inhibitory concentration at 11 nM under typical in vitro transcription conditions. Pull-down experiments revealed that the aptamer inhibited the association of T7 RNAP with T7 promoter DNA.

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“…Based on this strategy, aptazymes are able to directly transduce molecular recognition into a quantitative catalytic event. Taking advantages of highly specific recognition property of aptamers and signal amplification property of NAEs via multiple‐turnover reactions, aptazymes have demonstrated their great promise in many in vitro applications …”

Section: Molecular Engineering Of Aptazyme‐based Nanomaterials Towardmentioning

confidence: 99%

Molecular Engineering of Functional Nucleic Acid Nanomaterials toward In Vivo Applications

Zhang

Lan

2019

Adv Healthcare Materials

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equally exciting and perhaps more challenging field of application is toward their in vivo applications, including living animals and human bodies, in diverse areas, [2] such as sensing, drug delivery, medical imaging, and cancer therapy. However, most of these nanomaterials lack selectivity toward targets of interests. Therefore, to employ these nanomaterials for a wider range of in vivo applications, various molecular engineering approaches have been employed to obtained nanomaterials functionalized with biomolecules to enable selective targeting. [3][4][5] Among these biomolecules, functional nucleic acids, or FNAs, have shown the most promise.FNAs are DNA or RNA molecules that can interact with or bind to a specific analyte, resulting in a conformational change and/or a catalytic reaction. [6] As their names suggested, ribozymes and deoxyribozymes (called DNAzyme hereafter) can act as enzymes in the presence of cofactors to catalyze various reactions, including cleavage and ligation of RNA/DNA, and phosphorylation and peroxidation of DNA. On the other hand, riboswitches and DNA aptamers are antibody-like receptors that can bind target molecules with high affinity and selectivity. Furthermore, the binding abilities of riboswitches and aptamers can be combined with the enzymatic function of ribozymes or DNAzymes to form aptazymes so that the binding of targets can inhibit or enhance the catalytic activities. These nucleic acids, including DNAzymes, aptamers, and aptazymes, are collectively known as FNAs to emphasize their functions beyond the traditional genetic storage and transformations roles for DNA and RNA. Unlike DNA and RNA inside biological systems, FNAs are isolated via a combinatorial technique known as in vitro selection, or a process also known as systematic evolution of ligands by exponential enrichment (SELEX). The discovery of new functions of nucleic acids has not only resulted in major advances in the fields of molecular biology and biochemistry, but also revolutionized sensors designs for both in vitro and in vivo applications. [7,8] Over the past decade, numerous FNA-based nanomaterials have been developed. [9][10][11][12] Among these FNA-based nanosystems, the functions of FNAs can be categorized into two types: diagnostic function and therapeutic function. For the diagnostic function, the FNAs serve either as the biorecognition ligands for direct sensing and imaging of the Recent advances in nanotechnology and engineering have generated many nanomaterials with unique physical and chemical properties. Over the past decade, numerous nanomaterials are introduced into many research areas, such as sensors for environmental monitoring, food safety, point-ofcare diagnostics, and as transducers for solar energy transfer. Meanwhile, functional nucleic acids (FNAs), including nucleic acid enzymes, aptamers, and aptazymes, have attracted major attention from the biomedical community due to their unique target recognition and catalytic properties. Benefiting from the recent progress of molecular engine...

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An aptazyme-based molecular device that converts a small-molecule input into an RNA output

Abstract: We describe the construction of an aptazyme-based molecular device that converts, through a cascade of reactions, a small-molecule input into output RNA strands. This device is applicable as an interface between a small molecule and a molecular system that accepts only nucleic acid input.

Cited by 12 publications

References 26 publications

A general approach for rational design of fluorescent DNA aptazyme sensors based on target-induced unfolding of DNA hairpins

A general approach for rational design of fluorescent DNA aptazyme sensors based on target-induced unfolding of DNA hairpins

Evolution of an inhibitory RNA aptamer against T7 RNA polymerase

Molecular Engineering of Functional Nucleic Acid Nanomaterials toward In Vivo Applications

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