Biology subjects

Schulman, R.

Publications and source records attributed to Schulman, R..

6 recordsLinked to original sources

bioRxiv2023

Plug-and-play protein biosensors using aptamer-regulated in vitro transcription

Molecular biosensors that accurately measure protein concentrations without external equipment are critical for solving numerous problems in diagnostics and therapeutics. Modularly transducing the binding of protein antibodies, protein switches or aptamers into a useful output remains challenging. Here, we develop a biosensing platform based on aptamer-regulated transcription in which aptamers integrated into transcription templates serve as inputs to molecular circuits that can be programmed to a produce a variety of responses. We modularly design molecular biosensors using this platform by swapping aptamer domains for specific proteins and downstream domains that encode different RNA transcripts. By coupling aptamer-regulated transcription with diverse transduction circuits, we rapidly construct analog protein biosensors or digital protein biosensors with detection ranges that can be tuned over two orders of magnitude. Aptamer-regulated transcription is a straightforward and inexpensive approach for constructing programmable protein biosensors suitable for diverse research and diagnostic applications. One sentence summaryWe develop a modular platform for biosensing across a wide dynamic range using aptamer-regulated transcription to detect different proteins and molecular circuits to process the RNA transcript outputs.

bioengineering↗

bioRxiv2023

De novo design of modular protein hydrogels with programmable intra- and extracellular viscoelasticity

Relating the macroscopic properties of protein-based materials to their underlying component microstructure is an outstanding challenge. Here, we exploit computational design to specify the size, flexibility, and valency of de novo protein building blocks, as well as the interaction dynamics between them, to investigate how molecular parameters govern the macroscopic viscoelasticity of the resultant protein hydrogels. We construct gel systems from pairs of symmetric protein homo-oligomers, each comprising 2, 5, 24, or 120 individual protein components, that are crosslinked either physically or covalently into idealized step-growth biopolymer networks. Through rheological assessment and molecular dynamics (MD) simulation, we find that the covalent linkage of multifunctional precursors yields hydrogels whose viscoelasticity depends on the crosslink length between the constituent building blocks. In contrast, reversibly crosslinking the homo-oligomeric components with a computationally designed heterodimer results in non-Newtonian biomaterials exhibiting fluid-like properties under rest and low shear, but shear-stiffening solid-like behavior at higher frequencies. Exploiting the unique genetic encodability of these materials, we demonstrate the assembly of protein networks within living mammalian cells and show via fluorescence recovery after photobleaching (FRAP) that mechanical properties can be tuned intracellularly, in correlation with matching formulations formed extracellularly. We anticipate that the ability to modularly construct and systematically program the viscoelastic properties of designer protein-based materials could have broad utility in biomedicine, with applications in tissue engineering, therapeutic delivery, and synthetic biology. SignificanceProtein-based hydrogels have many applications in cellular engineering and medicine. Most genetically encodable protein hydrogels are made from naturally harvested proteins or protein-polymer hybrid constructs. Here we describe de novo protein hydrogels and systematically investigate the impact of microscopic properties of the building blocks (e.g., supramolecular interaction, valencies, geometries, flexibility) on the resultant macroscopic gel mechanics, both intra-and extracellularly. These de novo supramolecular protein assemblies, whose properties can be tuned from solid gels to non-Newtonian fluids, provide expanded opportunities for applications in synthetic biology and medicine.

bioengineering↗

bioRxiv2022

Shape-shifting microgel automata controlled by DNA sequence instructions

Controlling material shapes using information-bearing molecular signals is central to the creation of autonomous, reconfigurable soft devices. While physical and chemical stimuli can direct simple material swelling, bending, or folding, it has been challenging to direct multi-step shape-change programs crucial for complex, robotic tasks. Here, we demonstrate gel automata-- sub-millimeter, photopatterned, highly swellable DNA gels--whose parts grow or shrink in response to easily designed DNA activator sequences, allowing for precisely controlled device articulation. We design and fabricate gel automata that reversibly transform between different letter shapes, and use neural networks to design automata that transform into every even or every odd numeral via designed reconfiguration programs. This sequential and repetitive metamorphosis of materials via chemical reorganization could dramatically advance our ability to manipulate micro-particles, cells, and tissues. One-Sentence SummaryPhotopatterned microgels follow sequences of DNA instructions to transform between complex, meaningful shapes such as letters and numerals.

bioengineering↗

bioRxiv2022

Lossless end-to-end transport of small molecules through micron-length DNA nanochannels

Designed and engineered protein and DNA nanopores can sense and characterize single molecules and control transmembrane transport of molecular species. However, designed biomolecular pores are less than 100 nm in length and are used primarily for transport across lipid membranes. Nanochannels that span longer distances could be used as conduits for molecules between non-adjacent compartments or cells. Here, we design microns-long, 7 nm diameter DNA nanochannels that small molecules can traverse according to the laws of continuum diffusion. Binding DNA origami caps to channel ends eliminates transport and demonstrates that molecules diffuse from one channel end to the other rather than permeating through channel walls. These micron-length nanochannels can also grow, form interconnects, and interface with living cells. This work thus shows how to construct multifunctional, dynamic agents that control molecular transport, opening new ways of studying intercellular signaling and modulating molecular transport between synthetic and living cells. O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=130 SRC="FIGDIR/small/488239v1_ufig1.gif" ALT="Figure 1"> View larger version (22K): org.highwire.dtl.DTLVardef@fec963org.highwire.dtl.DTLVardef@157bb83org.highwire.dtl.DTLVardef@d7a274org.highwire.dtl.DTLVardef@ea961c_HPS_FORMAT_FIGEXP M_FIG C_FIG

synthetic biology↗

bioRxiv2022

The ion permeability of DNA nanotube channels

Techniques from structural DNA nanotechnology make it possible to assemble complex 3-dimensional nanostructures with virtually arbitrary control over their sizes, shapes and features at length scales of 3-100 nm, providing a flexible means for constructing nanoscale devices and machines. Here, we assemble micron-length DNA nanotubes and assess their performance as pipes for controlled ion transport. DNA nanotubes grow via assembly of DNA tiles from a seed pore, a 12-helix DNA origami cylinder functionalized with cholesterol, to form a DNA nanotube channel. The central channel of a nanotube can be obstructed via Watson-Crick hybridization of a channel cap, a second DNA origami structure, to the end of a nanotube channel or a nanotube seed pore. Single-channel electrophysiological characterization shows that both nanotube seed pores and nanotube channels display ohmic ion conductance consistent with their central channels diameters. Binding of the channel cap reduces the conductances of both DNA nanotube channels and seed pores, demonstrating control of ion-transport through these micron-length channels. Because these channels could be assembled into branched architectures or routed between specific molecular terminals, these results suggest a route to self-assembling nanofluidic devices and circuits in which transport can be controlled using dynamic biomolecular interactions.

biophysics↗

bioRxiv2022

Enabling spatiotemporal regulation within biomaterials using DNA reaction- diffusion waveguides

In multicellular organisms, cells and tissues coordinate biochemical signal propagation across length scales spanning microns to meters. Endowing synthetic materials with similar capacities for coordinated signal propagation could allow these systems to adaptively regulate themselves across space and over time. Here we combine ideas from cell signaling and electronic circuitry to design a biochemical waveguide that transmits information in the form of a concentration of a DNA species on a directed path. The waveguide can be seamlessly integrated into a soft material because there is virtually no difference between the chemical or physical properties of the waveguide and the material it is embedded within. We propose the design of DNA strand displacement reactions to construct the system and, using reaction-diffusion models, identify kinetic and diffusive parameters that enable super-diffusive transport of DNA species via autocatalysis. Finally, to support experimental waveguide implementation, we show how a sink reaction could mitigate the spurious amplification of an autocatalyst within the waveguide, allowing for controlled waveguide triggering. Chemical waveguides could facilitate the design of synthetic biomaterials with distributed sensing machinery integrated throughout their structure and enable coordinated self-regulating programs triggered by changing environmental conditions.

synthetic biology↗