DNA Computing by Self-Assembly

Information and algorithms appear to be central to biological organization and processes, from the storage and reproduction of genetic information to the control of developmental processes to the sophisticated computations performed by the nervous system. Much as human technology uses electronic microprocessors to control electromechanical devices, biological organisms use biochemical circuits to control molecular and chemical events. The engineering and programming of biochemical circuits, in vivo and in vitro, would transform industries that use chemical and nanostructured materials. Although the construction of biochemical circuits has been explored theoretically since the birth of molecular biology, our practical experience with the capabilities and possible programming of biochemical algorithms is still very young

Biomimetic and Biophysical Approach to Profile Metastatic Cancer Cell Migration

Honors Research ScholarshipCancer metastasis is a complex process by which cells in a primary tumor acquire an aggressive phenotype, and travel to distant, secondary sites in the body. One aspect of cancer metastasis is cell migration toward the vascular system, called invasion. Multiple modalities of single cell invasion exist, including amoeboid migration and mesenchymal migration. Amoeboid migration is less well understood, and in particular, the forces involved in amoeboid migration have yet to be fully elucidated at a subcellular scale. Cellular traction force microscopy, or CTFM, is one method used to probe migration forces. However, this approach is largely limited to two dimensions, and is limited by the size of the pillars on the substrate. To address these limitations, we developed a system using microfluidics and DNA origami capable of real-time force measurement of cell migration on a subcellular scale with a 10 pN resolution. Microfluidic devices were made using soft lithography and replica molding in our laboratory. DNA origami were made using protocols developed by Michael Hudoba and Dr. Carlos Castro in the Nanoengineering and Biodesign Laboratory. The devices were imaged using TIRF microscopy to study dwell times of the sensors in the open and closed states, and the devices were analyzed with an AFM to determine that they are best suited for measuring shear forces. Further, the presence of streptavidin protein was found to have a significant effect on DOFS binding with a p-value less than 0.05. DOFS concentrations around 1 nM were found to provide the most coverage while minimizing structure aggregation. Thus, our microfluidic devices are able to be functionalized with DNA origami force sensors with a high degree of attachment. This platform is thus capable of measuring cell migration and adhesion forces, and future work should harness this system to create 3D maps of cell migration to gain insight into invasion.Institute for Materials ResearchSecond-Year Transformational Experience Program (STEP)A one-year embargo was granted for this item.Academic Major: Biomedical Engineerin

De Novo Assembly of Nucleotide Sequences in a Compressed Feature Space

Sequencing technologies allow for an in-depth analysis of biological species but the size of the generated datasets introduce a number of analytical challenges. Recently, we demonstrated the application of numerical sequence representations and data transformations for the alignment of short reads to a reference genome. Here, we expand out approach for de novo assembly of short reads. Our results demonstrate that highly compressed data can encapsulate the signal suffi- ciently to accurately assemble reads to big contigs or complete genomes

On the Computational Power of DNA Annealing and Ligation

In [20] it was shown that the DNA primitives of Separate, Merge, and Amplify were not sufficiently powerful to invert functions defined by circuits in linear time. Dan Boneh et al [4] show that the addition of a ligation primitive, Append, provides the missing power. The question becomes, "How powerful is ligation? Are Separate, Merge, and Amplify necessary at all?" This paper proposes to informally explore the power of annealing and ligation for DNA computation. We conclude, in fact, that annealing and ligation alone are theoretically capable of universal computation

Recovering Sparse Signals Using Sparse Measurement Matrices in Compressed DNA Microarrays

Microarrays (DNA, protein, etc.) are massively parallel affinity-based biosensors capable of detecting and quantifying a large number of different genomic particles simultaneously. Among them, DNA microarrays comprising tens of thousands of probe spots are currently being employed to test multitude of targets in a single experiment. In conventional microarrays, each spot contains a large number of copies of a single probe designed to capture a single target, and, hence, collects only a single data point. This is a wasteful use of the sensing resources in comparative DNA microarray experiments, where a test sample is measured relative to a reference sample. Typically, only a fraction of the total number of genes represented by the two samples is differentially expressed, and, thus, a vast number of probe spots may not provide any useful information. To this end, we propose an alternative design, the so-called compressed microarrays, wherein each spot contains copies of several different probes and the total number of spots is potentially much smaller than the number of targets being tested. Fewer spots directly translates to significantly lower costs due to cheaper array manufacturing, simpler image acquisition and processing, and smaller amount of genomic material needed for experiments. To recover signals from compressed microarray measurements, we leverage ideas from compressive sampling. For sparse measurement matrices, we propose an algorithm that has significantly lower computational complexity than the widely used linear-programming-based methods, and can also recover signals with less sparsity

Design of DNA origami

The generation of arbitrary patterns and shapes at very small scales is at the heart of our effort to miniaturize circuits and is fundamental to the development of nanotechnology. Here I review a recently developed method for folding long single strands of DNA into arbitrary two-dimensional shapes using a raster fill technique - 'scaffolded DNA origami'. Shapes up to 100 nanometers in diameter can be approximated with a resolution of 6 nanometers and decorated with patterns of roughly 200 binary pixels at the same resolution. Experimentally verified by the creation of a dozen shapes and patterns, the method is easy, high yield, and lends itself well to automated design and manufacture. So far, CAD tools for scaffolded DNA origami are simple, require hand-design of the folding path, and are restricted to two dimensional designs. If the method gains wide acceptance, better CAD tools will be required