T7 RNA polymerase non-specifically transcribes and induces disassembly of DNA nanostructures

Schaffter, Samuel W.; Green, Leopold N.; Schneider, Joanna; Subramanian, Hari K. K.; Schulman, Rebecca; Franco, Elisa

doi:10.1093/nar/gky283

Cited by 25 publications

(46 citation statements)

References 71 publications

Supporting

Mentioning

Contrasting

Order By: Relevance

“…These experiments indicate that more complex genetic programs relying on RNA production and degradation may be encapsulated to control nanotube assembly 35 . A notable challenge toward sustained transcription and degradation dynamics is the accumulation of abortive and elongated transcripts, which can cause side reactions and crosstalk 70 . These undesired transcripts may bind to inactive tiles producing “waste” complexes that can no longer be activated by the correct RNA trigger 36 .…”

Section: Resultsmentioning

confidence: 99%

Dynamic self-assembly of compartmentalized DNA nanotubes

et al. 2021

Self Cite

View full text Add to dashboard Cite

Bottom-up synthetic biology aims to engineer artificial cells capable of responsive behaviors by using a minimal set of molecular components. An important challenge toward this goal is the development of programmable biomaterials that can provide active spatial organization in cell-sized compartments. Here, we demonstrate the dynamic self-assembly of nucleic acid (NA) nanotubes inside water-in-oil droplets. We develop methods to encapsulate and assemble different types of DNA nanotubes from programmable DNA monomers, and demonstrate temporal control of assembly via designed pathways of RNA production and degradation. We examine the dynamic response of encapsulated nanotube assembly and disassembly with the support of statistical analysis of droplet images. Our study provides a toolkit of methods and components to build increasingly complex and functional NA materials to mimic life-like functions in synthetic cells.

show abstract

Section: Resultsmentioning

confidence: 99%

Dynamic self-assembly of compartmentalized DNA nanotubes

et al. 2021

Self Cite

View full text Add to dashboard Cite

show abstract

“…These DNA nanotubes can grow from DNA origami templates, seeds (Figure 1c) 22 , and can reach 100 µm in length [24][25][26] . DNA nanotube growth kinetics 25,[27][28][29][30] , hierarchical assembly pathways 31 and diffusion rates 22 have also been extensively characterized, allowing kinetic control over their growth and interactions with cells. Nanotubes can be functionalized with polymers, gold nanoparticles 32 , proteins 33 and peptides 34 , and thus could be templates for constructing diverse functional devices.…”

Section: Resultsmentioning

confidence: 99%

Growth and site-specific organization of micron-scale biomolecular devices on living mammalian cells

et al. 2021

Self Cite

View full text Add to dashboard Cite

Mesoscale molecular assemblies on the cell surface, such as cilia and filopodia, integrate information, control transport and amplify signals. Designer cell-surface assemblies could control these cellular functions. Such assemblies could be constructed from synthetic components ex vivo, making it possible to form such structures using modern nanoscale self-assembly and fabrication techniques, and then oriented on the cell surface. Here we integrate synthetic devices, micron-scale DNA nanotubes, with mammalian cells by anchoring them by their ends to specific cell surface receptors. These filaments can measure shear stresses between 0-2 dyn/cm2, a regime important for cell signaling. Nanotubes can also grow while anchored to cells, thus acting as dynamic cell components. This approach to cell surface engineering, in which synthetic biomolecular assemblies are organized with existing cellular architecture, could make it possible to build new types of sensors, machines and scaffolds that can interface with, control and measure properties of cells.

show abstract

“…2d). Previous literature reported the ability of T7 RNAP to initiate promoter-independent transcription from exposed, linear ssDNA regions [30][31][32][33]. Based on these observations, we hypothesized that T7 RNAP was initiating transcription from the 3' end toehold region of the DNA signal gate, causing strand displacement and signal generation ( Fig.…”

Section: Engineering Tmsd To Be Compatible With In Vitro Transcriptionmentioning

confidence: 86%

Programming Cell-Free Biosensors with DNA Strand Displacement Circuits

Jung¹,

Kk²,

Lucks³

2021

Preprint

View full text Add to dashboard Cite

Cell-free biosensors are emerging as powerful platforms for monitoring human and environmental health. Here, we expand the capabilities of biosensors by interfacing their outputs with toehold- mediated strand displacement circuits, a dynamic DNA nanotechnology that enables molecular computation through programmable interactions between nucleic acid strands. We develop design rules for interfacing biosensors with strand displacement circuits, show that these circuits allow fine-tuning of reaction kinetics and faster response times, and demonstrate a circuit that acts like an analog-to-digital converter to create a series of binary outputs that encode the concentration range of the target molecule being detected. We believe this work establishes a pathway to create 'smart' diagnostics that use molecular computations to enhance the speed, robustness and utility of biosensors.

show abstract

T7 RNA polymerase non-specifically transcribes and induces disassembly of DNA nanostructures

Cited by 25 publications

References 71 publications

Dynamic self-assembly of compartmentalized DNA nanotubes

Dynamic self-assembly of compartmentalized DNA nanotubes

Growth and site-specific organization of micron-scale biomolecular devices on living mammalian cells

Programming Cell-Free Biosensors with DNA Strand Displacement Circuits

Contact Info

Product

Resources

About