A5062069511- Advanced biosensing and bioanalysis techniques
- RNA Interference and Gene Delivery
- DNA and Nucleic Acid Chemistry
- DNA and Biological Computing
- Modular Robots and Swarm Intelligence
- Supramolecular Self-Assembly in Materials
- Bacteriophages and microbial interactions
- Molecular Junctions and Nanostructures
- Gene Regulatory Network Analysis
- Nanopore and Nanochannel Transport Studies
- Molecular Communication and Nanonetworks
- Origins and Evolution of Life
- RNA and protein synthesis mechanisms
- Advanced Materials and Mechanics
- Diffusion and Search Dynamics
- Biosensors and Analytical Detection
- bioluminescence and chemiluminescence research
- Micro and Nano Robotics
- Advanced Fluorescence Microscopy Techniques
- Electrowetting and Microfluidic Technologies
- 3D Printing in Biomedical Research
- Innovative Microfluidic and Catalytic Techniques Innovation
- Topic Modeling
- Diatoms and Algae Research
- SARS-CoV-2 detection and testing
Johns Hopkins University
2015-2024
Johns Hopkins Medicine
2024
Interface (United States)
2024
University of Baltimore
2017-2022
California Institute of Technology
2004-2015
University of California, Berkeley
2010-2012
University of Washington
2009
Stanford University
2007
Massachusetts Institute of Technology
2003
DNA molecules direct the swelling of cross-linked hydrogels with shape changes in response to different biomolecular signals.
Self-assembly creates natural mineral, chemical, and biological structures of great complexity. Often, the same starting materials have potential to form an infinite variety distinct structures; information in a seed molecule can determine which is grown as well where when. These phenomena be exploited program growth complex supramolecular structures, demonstrated by algorithmic self-assembly DNA tiles. However, lack effective seeds has limited reliability yield crystals. Here, we present...
Relating the macroscopic properties of protein-based materials to their underlying component microstructure is an outstanding challenge. Here, we exploit computational design specify size, flexibility, and valency de novo protein building blocks, as well interaction dynamics between them, investigate how molecular parameters govern viscoelasticity resultant hydrogels. We construct gel systems from pairs symmetric homo-oligomers, each comprising 2, 5, 24, or 120 individual components, that...
A central goal of chemistry is to fabricate supramolecular structures defined function and composition. In biology, control synthesis often achieved through precise over nucleation growth processes: seed molecule initiates a structure, but this kinetically inhibited in the seed's absence. Here we show how such can be systematically designed into self-assembling made DNA tiles. These structures, “zig-zag ribbons,” are have fixed width grow arbitrarily long. Under slightly supersaturated...
Peptides or peptide conjugates capable of assembling into one-dimensional (1D) nanostructures have been extensively investigated over the past two decades due to their implications in human diseases and also interesting applications as biomaterials. While many these filamentous assemblies contain a β-sheet-forming sequence key design element, eventual morphology could assume variety shapes, such fibrils, ribbons, belts, cylinders. Deciphering factors that govern stacking fashion individual...
Understanding how a simple chemical system can accurately replicate combinatorial information, such as sequence, is an important question for both the study of life in universe and development evolutionary molecular design techniques. During biological sequence replication, nucleic acid polymer serves template enzyme-catalyzed assembly complementary sequence. Enzymes then separate complement before next round replication. Attempts to understand replication could occur more simply, without...
Abstract Soft materials that swell or change shape in response to external stimuli show extensive promise regenerative medicine, targeted therapeutics, and soft robotics. Generally, a stimulus for must interact directly with the material, limiting types of may be used necessitating high concentrations. Here, we how DNA strand-displacement controllers within hydrogels can mediate size by interpreting, amplifying, integrating releasing signals direct response. These tune time scale degree...
Control over when and where nanostructures arise is essential for the self-assembly of dynamic or multicomponent devices. We design construct a DNA origami seed control DAE-E tile nanotube assembly. Seeds greatly accelerate nucleation growth because they serve as templates. also circumference. Simulations predict rates suggest small barrier remains nanotubes grow from seeds.
Chemical circuits can coordinate elaborate sequences of events in cells and tissues, from the self-assembly biological complexes to sequence embryonic development. However, autonomously directing timing synthetic systems using chemical signals remains challenging. Here we demonstrate that a simple DNA strand-displacement circuit release target into solution at constant rate after tunable delay range hours days. The rates be tuned order 1–100 nM per day. Multiple timer different strands times...
Characterizing the relative onset time, strength, and duration of molecular signals is critical for understanding operation signal transduction genetic regulatory networks. However, detecting multiple such molecules as they are produced then quickly consumed challenging. A MER can encode information about transient events stable DNA sequences amenable to downstream sequencing or other analysis. Here, we report development a de novo event recorder that processes using strand displacement...
Algorithmic self-assembly, a generalization of crystal growth processes, has been proposed as mechanism for autonomous DNA computation and bottom-up fabrication complex nanostructures. A "program" growing desired structure consists set molecular "tiles" designed to have specific binding interactions. key challenge making algorithmic self-assembly practical is designing tile programs that make assembly robust errors occur during initiation growth. One method the controlled assembly, often...
An essential motif for the assembly of biological materials such as actin at scale hundreds nanometers and beyond is a network one-dimensional fibers with well-defined geometry. Here, we demonstrate programmed organization DNA filaments into micron-scale architectures where component are oriented preprogrammed angles. We assemble L-, T-, Y-shaped origami junctions that nucleate two or three micron length nanotubes high yields. The angles between mirror templates on junctions, demonstrating...
Algorithmic self-assembly, a generalization of crystal growth, has been proposed as mechanism for bottom-up fabrication complex nanostructures and autonomous DNA computation. In principle, growth can be programmed by designing set molecular tiles with binding interactions that enforce assembly rules. practice, however, errors during cause undesired products, drastically reducing yields. Here we provide experimental evidence made more robust to adding redundant "proofread" assembly. We...
Cells use sophisticated, multiscale spatial patterns of chemical instructions to control cell fate and tissue growth. While some types synthetic pattern formation have been well studied 1-6 , it remains unclear how design processes that can reproducibly create similar patterns. Here we describe a scalable approach for the generate such patterns, which be implemented using DNA reaction-diffusion networks 7,8 . In our method, black-box modules are connected together into integrated programs...
We demonstrate a versatile process for assembling micron-scale filament architectures by controlling where DNA tile nanotubes nucleate on origami assemblies. "Nunchucks," potential mechanical magnifiers of nanoscale dynamics consisting two connected dsDNA linker, form at yields sufficient application and consistent with models.
Self-assembled DNA nanostructures have potential applications in therapeutics, diagnostics, and synthetic biology. A challenge using biological environments or cell culture, however, is that they may be degraded by enzymes found these environments, such as nucleases. Such degradation can slowed introducing alternative substrates for nucleases, coating with membranes peptides. Here we demonstrate a means which reversed situ through the repair of nanostructure defects. To this effect, show...
The functional stability and lifetimes of synthetic molecular circuits in biological environments are important for long-term, stable sensors or controllers cell tissue behavior. DNA-based circuits, particular DNA strand-displacement provide simple effective biocompatible control mechanisms sensors, but vulnerable to digestion by nucleases present living tissues serum-supplemented culture. double-stranded single-stranded circuit components medium the corresponding effect nuclease-mediated...
Designed and engineered protein DNA nanopores can be used to sense characterize single molecules control transmembrane transport of molecular species. However, designed biomolecular pores are less than 100 nm in length primarily for across lipid membranes. Nanochannels that span longer distances could as conduits between nonadjacent compartments or cells. Here, we design micrometer-long, 7-nm-diameter nanochannels small traverse according the laws continuum diffusion. Binding origami caps...