A Spinach molecular beacon triggered by strand displacement

Bhadra, Sanchita; Ellington, Andrew D.

doi:10.1261/rna.045047.114

Cited by 57 publications

(58 citation statements)

References 72 publications

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“…Like proteins, RNA molecules can serve as biological catalysts and genetic regulatory elements. Examples of the latter occur naturally (18)(19)(20) and have, more recently, become the target of engineering efforts to harness RNA-based sensing through riboregulators and Spinach RNA for small molecules and target RNA sequences (21)(22)(23)(24)(25). RNA sensing for diagnostics recently took a leap forward with the development of a new class of RNA sensors called toehold switches (26).…”

Section: Whole-cell Biosensingmentioning

confidence: 99%

“…Incorporating transcription-only gene circuits would result in simpler and faster systems. These systems could include using fluorescent Spinach RNA as a direct gene circuit reporter, Spinach RNA sensors that activate in the presence of their programmed target molecule, and Spinach.ST RNA for the detection of DNA and RNA sequences (21,22,24).…”

Section: In Vitro Diagnosticsmentioning

confidence: 99%

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Synthetic biology devices for in vitro and in vivo diagnostics

Slomovic

Pardee

Collins

2015

Proc. Natl. Acad. Sci. U.S.A.

296

228

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There is a growing need to enhance our capabilities in medical and environmental diagnostics. Synthetic biologists have begun to focus their biomolecular engineering approaches toward this goal, offering promising results that could lead to the development of new classes of inexpensive, rapidly deployable diagnostics. Many conventional diagnostics rely on antibody-based platforms that, although exquisitely sensitive, are slow and costly to generate and cannot readily confront rapidly emerging pathogens or be applied to orphan diseases. Synthetic biology, with its rational and short design-to-production cycles, has the potential to overcome many of these limitations. Synthetic biology devices, such as engineered gene circuits, bring new capabilities to molecular diagnostics, expanding the molecular detection palette, creating dynamic sensors, and untethering reactions from laboratory equipment. The field is also beginning to move toward in vivo diagnostics, which could provide near real-time surveillance of multiple pathological conditions. Here, we describe current efforts in synthetic biology, focusing on the translation of promising technologies into pragmatic diagnostic tools and platforms.synthetic biology | diagnostics | biosensing | synthetic gene networks | nanobiotechnology

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Section: Whole-cell Biosensingmentioning

confidence: 99%

Section: In Vitro Diagnosticsmentioning

confidence: 99%

Synthetic biology devices for in vitro and in vivo diagnostics

Slomovic

Pardee

Collins

2015

Proc. Natl. Acad. Sci. U.S.A.

296

228

View full text Add to dashboard Cite

show abstract

“…It has been demonstrated that fluorescent RNA molecules, named Spinach and Broccoli, can be employed as genetically encoded reporters for RNAimaging. 20–22 Spinach and Broccoli are RNA aptamers that can bind and activate the fluorescence of small-molecule dyes, such as 3,5-difluoro-4-hydroxybenzylidene-1-trifluoroethyl-imidazolinone (DFHBI-1T). 23–25 Recently, the Ellington group has successfully demonstrated that Spinach can function as a reporter in an RNA-based CHA reaction in vitro.…”

Section: Introductionmentioning

confidence: 99%

Genetically Encoded Catalytic Hairpin Assembly for Sensitive RNA Imaging in Live Cells

et al. 2018

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DNA and RNA nanotechnology has been used for the development of dynamic molecular devices. In particular, programmable enzyme-free nucleic acid circuits, such as catalytic hairpin assembly, have been demonstrated as useful tools for bioanalysis and to scale up system complexity to an extent beyond current cellular genetic circuits. However, the intracellular functions of most synthetic nucleic acid circuits have been hindered by challenges in the biological delivery and degradation. On the other hand, genetically encoded and transcribed RNA circuits emerge as alternative powerful tools for long-term embedded cellular analysis and regulation. Herein, we reported a genetically encoded RNA-based catalytic hairpin assembly circuit for sensitive RNA imaging inside living cells. The split version of Broccoli, a fluorogenic RNA aptamer, was used as the reporter. One target RNA can catalytically trigger the fluorescence from tens-to-hundreds of Broccoli. As a result, target RNAs can be sensitively detected. We have further engineered our circuit to allow easy programming to image various target RNA sequences. This design principle opens the arena for developing a large variety of genetically encoded RNA circuits for cellular applications.

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“…The complementary oligo can also be an extension of the aptamer sensor, which similarly ensures a rapid and reversible response. 93, 94 Regulation by a linked short complementary sequence results in a more sensitive assay because the apparent K d of the aptamer is less impacted than with longer complementary oligos.…”

Section: Analytical Applications Of Aptamersmentioning

confidence: 99%

Aptamers in analytics

İlgü

Nilsen-Hamilton

2016

Analyst

198

113

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Nucleic acid aptamers are promising alternatives to antibodies for analytics. They are generally obtained through an iterative SELEX protocol that enriches a population of synthetic oligonucleotides to a subset that can recognize the chosen target molecule specifically and avidly. A wide range of targets is recognized by aptamers. Once identified and optimized for performance, aptamers can be reproducibly synthesized and offer other key features, like small size, low cost, sensitivity, specificity, rapid response, stability, reusability. This makes them excellent options for sensory units on a variety of analytical platforms including those with electrochemical, optical, and mass sensitive transduction detection. Many novel sensing strategies have been developed by rational design to take advantage of the tendency of aptamers to undergo conformational changes upon target/analyte binding and employing the principles of base complementarity that can drive nucleic acid structure. Despite their many advantages over antibodies, surprisingly few aptamers have yet been integrated into commercially available analytical devices. In this review, we discuss how to select and engineer aptamers for their identified application(s), some of the challenges faced in developing aptamers for analytics and many examples of their reported successful performance as sensors in a variety of analytical platforms.

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A Spinach molecular beacon triggered by strand displacement

Cited by 57 publications

References 72 publications

Synthetic biology devices for in vitro and in vivo diagnostics

Synthetic biology devices for in vitro and in vivo diagnostics

Genetically Encoded Catalytic Hairpin Assembly for Sensitive RNA Imaging in Live Cells

Aptamers in analytics

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