Controlled formation of a supramolecular polymer network driven by heterometallic coordination interactions

Tian, Yu-Kui; Chen, Long; Tian, Yangchao; Wang, Xiaoyu; Wang, Rui

doi:10.1039/c2py20984e

Cited by 66 publications

(35 citation statements)

References 45 publications

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“…Aptamers have been shown to undergo liganddependent conformational changes and can be joined to ribozymes to create allosteric ribozymes (aptazymes). 86,87 To date almost all of these aptamer and aptazyme biosensors have been generated by empirical design 88,89 or in vitro selection, 21,86,90 however, algorithms for the prediction of nucleic acid secondary structure have advanced to the point where nucleic acid secondary structures can be rapidly enumerated based on nucleic acid sequence. 91 Therefore, the computational design methods for the generation of biosensors would be extremely valuable for a variety of reasons.…”

Section: Discussionmentioning

confidence: 99%

Aptamer-based optical switch for biosensors

Lee¹,

Cho²,

Cho³

2014

Analytical Science and Technology

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Abstract:In this review, we will discuss aptamer technologies including in vitro selection, signal transduction mechanisms, and designing aptamers and aptazyme for label-free biosensors and catalysts. Dye-displacement, a typical label-less method, is described here which allows avoiding relatively complex labeling steps and extending this application to any aptamers without specific conformational changes, in a more simple, sensitive and cost effective way. We will also describe most recent and advanced technologies of signaling aptamer and aptazyme for the various analytical and clinical applications. Quantum dot biosensor (QDB) is explained in detail covering designing and adaptations for multiplexed protein detection. Application to aptamer array utilizing self-assembled signaling aptamer DNA tile and the novel methods that can directly select smart aptamer or aptazyme experimentally and computationally will also be finally discussed, respectively.

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Section: Discussionmentioning

confidence: 99%

Aptamer-based optical switch for biosensors

Lee¹,

Cho²,

Cho³

2014

Analytical Science and Technology

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“…[ 85,89 ] An aptazyme is basically a self‐cleaving ribozyme (e.g., hammerhead, hepatitis delta virus, or twister ribozyme) whom a key helix is fused to and placed under the control of a structure‐switching aptamer (Figure 2H), a concept already introduced by the Breaker lab 5 years before the discovery of natural riboswitches. [ 90 ] Introducing such a construct in 3′ untranslated region of a target mRNA allows to trigger its cleavage on‐demand by adding the small molecule ligand which leads to the rapid degradation of the mRNA and gene extinction. First demonstrated in yeast, by the Smolke lab, [ 91 ] aptazymes allow the precise control of gene expression and are now used in synthetic biology programs aiming at generating yeast strains able to produce large amounts of natural plant products.…”

Section: Development and Use Of Synthetic Riboswitchesmentioning

confidence: 99%

Structure‐Switching RNAs: From Gene Expression Regulation to Small Molecule Detection

2021

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RNA is instrumental to cell life in many aspects, especially gene expression regulation. Among the various known regulatory RNAs, riboswitches are particularly interesting cis‐acting molecules as they do not need cellular factor to achieve their function and are therefore highly portable from one organism to the other. These molecules usually found in the 5′ untranslated region of bacterial messenger RNAs are able to specifically sense a target ligand via an aptamer domain prior to transmitting this recognition event to an expression platform that turns on, or off, the expression of downstream genes. In addition to their obvious scientific interest, these modular molecules can also serve for the development of synthetic RNA devices with applications ranging from the control of transgene expression in gene therapy to the specific biosensing of small molecules. The engineering of such nanomachines is greatly facilitated by the proper understanding of their structure as well as the introduction of new technologies. Herein, a general overview of the current knowledge on natural riboswitches prior to explaining the main strategies used to develop new synthetic structure‐switching molecules (riboswitches or biosensors) controlled by small molecules is given.

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“…Hammerhead ribozyme (HHR) is a well‐studied ribozyme with RNA‐cleaving ability. A ligand‐dependent HHR has been created through the conjugation of an aptamer (a member of another class of functional RNAs that recognize specific ligands) . We focused on the tertiary structure of HHR as a potential target for our molecular glue.…”

Section: Activation Of Hammerhead Ribozyme Through Tertiary Structurementioning

confidence: 99%

Molecular Glue for RNA: Regulating RNA Structure and Function through Synthetic RNA Binding Molecules

Dohno

Nakatani

2019

ChemBioChem

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We introduce the concept of molecular glues for RNA, in which specific RNA‐binding small molecules induce designed structural changes in target functional RNAs, resulting in modulation of the functions. (Z)‐NCTS is an RNA‐mismatch‐binding small molecule that recognizes 5′‐r(XGG)‐3′/5′‐r(XGG)‐3′ sequences (X=U or A) and acts as a molecular glue for RNA. The binding of (Z)‐NCTS brings two distinct 5′‐r(XGG)‐3′ domains into contact with each other, and this can result in higher‐order structural changes of target RNAs. We applied (Z)‐NCTS to induce the formation of a proposed tertiary structure of a ribozyme together with activation of RNA‐cleaving ability. The concept of a molecular glue could inspire new small‐molecule‐based strategies for regulating biological functions: a synthetic small molecule targeting functional RNAs could regulate the RNA structure and function.

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Controlled formation of a supramolecular polymer network driven by heterometallic coordination interactions

Cited by 66 publications

References 45 publications

Aptamer-based optical switch for biosensors

Aptamer-based optical switch for biosensors

Structure‐Switching RNAs: From Gene Expression Regulation to Small Molecule Detection

Molecular Glue for RNA: Regulating RNA Structure and Function through Synthetic RNA Binding Molecules

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