Biology subjects

Scalise, D.

Publications and source records attributed to Scalise, D..

3 recordsLinked to original sources

bioRxiv2025

Adverse Effects of UV-Exposure on DNA Strand Displacement Reactions

DNA strand displacement (DSD) reactions are widely used in molecular computing and nanotechnology due to their programmability and precise control over molecular interactions. However, experimental DSD systems often underperform relative to theoretical models, due in part to poorly characterized sources of reactant impurities. Here, we identify UV-shadowing (a standard technique for visualizing DNA during PAGE purification) as a previously overlooked cause of DSD circuit errors. Counterintuitively, existing purification protocols with UV-shadowing can increase impurities that disrupt circuit behavior. Specifically, we demonstrate that UV exposure (i) reduces DSD reaction percent yield and (ii) leads to a phenomenon we call "negative leak," where high-concentration double-stranded complexes that are designed to be inert can sequester functional signal strands and thus disrupt circuit performance. Additionally, we find that UV damage is sequence-dependent, with adjacent pyrimidine-pair-rich strands being more susceptible to errors. To circumvent these errors, we introduce a simple and practical purification protocol that avoids UV exposure, and show that the errors no longer occur. Our results highlight UV-induced damage as a critical factor in DSD circuit performance, and suggest that UV-shadowing may have contributed to significant reproducibility and scaling challenges in the broader DSD literature.

synthetic biology↗

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

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↗