Versatile RNA-sensing transcriptional regulators for engineering genetic networks

Lucks, Julius B.; Qi, Lei S.; Mutalik, Vivek K.; Wang, Denise; Arkin, Adam P.

doi:10.1073/pnas.1015741108

Cited by 234 publications

(367 citation statements)

References 38 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%

Synthetic biology devices for in vitro and in vivo diagnostics

Slomovic

Pardee

Collins

2015

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

289

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%

Synthetic biology devices for in vitro and in vivo diagnostics

Slomovic

Pardee

Collins

2015

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

289

228

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“…25 ) or trans-regulation of transcription. 26 One advantage of riboswitches acting at the transcriptional level is that each expression platform represents an independent functional unit.…”

Section: Tandem Arrangement Allows Fast and Easy Enhancement Of Activmentioning

confidence: 99%

Design criteria for synthetic riboswitches acting on transcription

et al. 2015

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Riboswitches are RNA-based regulators of gene expression composed of a ligand-sensing aptamer domain followed by an overlapping expression platform. The regulation occurs at either the level of transcription (by formation of terminator or antiterminator structures) or translation (by presentation or sequestering of the ribosomal binding site). Due to a modular composition, these elements can be manipulated by combining different aptamers and expression platforms and therefore represent useful tools to regulate gene expression in synthetic biology. Using computationally designed theophylline-dependent riboswitches we show that 2 parameters, terminator hairpin stability and folding traps, have a major impact on the functionality of the designed constructs. These have to be considered very carefully during design phase. Furthermore, a combination of several copies of individual riboswitches leads to a much improved activation ratio between induced and uninduced gene activity and to a linear dose-dependent increase in reporter gene expression. Such serial arrangements of synthetic riboswitches closely resemble their natural counterparts and may form the basis for simple quantitative read out systems for the detection of specific target molecules in the cell.

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“…They also can specifically recognize folded RNAs [64] and small molecules [65], regulate pathway expression [66,67], and contribute to programmable genetic circuitry [68][69][70].…”

Section: Introductionmentioning

confidence: 99%

Engineered RNA Nanodesigns for Applications in RNA Nanotechnology

Afonin¹,

Lindsay²,

Shapiro³

2013

DNA and RNA Nanotechnology

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IntroductionThe physical world presents a very different landscape at the nanometer scale. Physical phenomena such as inertia and gravity vanish from view; instead the interactions of matter and energy are dominated by other phenomena like wave-particle duality, uncertainty, and quantum electrodynamics. Nanotechnology is the engineering of functional systems at this scale, where the axioms that govern material and device design differ dramatically from those found at the macroscale level. More precisely, "nanotechnology" typically encompasses both the miniaturization of existing technologies to the nanoscale, and the discipline of engineering molecular-scale systems from the bottom up, producing constructs with fundamentally new qualities that revolutionize human engineering, from materials and manufacturing, electronics, and information technology, to medicine, biotechnology, energy, and even security. The array of goals and applications in nanotechnology intersects with an equally wide array of techniques and materials with their own emergent properties in the field. One such branch is concerned with the re-engineering of biological mechanisms, systems, and molecules in new forms with new utilities, broadly termed bio-nanotechnology.The field of nanotechnology taking advantage of nucleic acids has its origins in the work of Nadrian Seeman and coworkers who have, over the past 30 years, spearheaded the development of DNA nano-object fabrication utilizing DNA self-assembly [1][2][3][4][5][6]. Briefly, DNA nanotechnology uses the nature of DNA complementarity for the construction of DNA tiles with discrete secondary structure by canonical WatsonCrick interactions (G-C and A-T base pairing), using a relatively small number of structural rules fundamentally based on Holliday junction motifs. The use of these rules has resulted in the engineering and characterization of numerous DNA 3D nanoscaffolds with different connectiviities [7][8][9][10][11][12][13][14][15][16][17][18] and the ability for some of them to promote targeted delivery by functioning as DNA nano-capsules [19][20][21] or DNA nano-carriers for other functionialities [22]. Another powerful technique called DNA "origami", developed by Paul Rothemund [23], has been extended from its original scope for designing different 2D DNA shapes [24] and functional templates [25][26][27][28] Abstract Nucleic acids have emerged as an extremely promising platform for nanotechnological applications because of their unique biochemical properties and functions. RNA, in particular, is characterized by relatively high thermal stability, diverse structural flexibility, and its capacity to perform a variety of functions in nature. These properties make RNA a valuable platform for bio-nanotechnology, specifically RNA Nanotechnology, that can create de novo nanostructures with unique functionalities through the design, integration, and re-engineering of powerful mechanisms based on a variety of existing RNA structures and their fundamental biochemical properties. This review...

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Versatile RNA-sensing transcriptional regulators for engineering genetic networks

Cited by 234 publications

References 38 publications

Synthetic biology devices for in vitro and in vivo diagnostics

Synthetic biology devices for in vitro and in vivo diagnostics

Design criteria for synthetic riboswitches acting on transcription

Engineered RNA Nanodesigns for Applications in RNA Nanotechnology

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