Analysis of DNA-guided self-assembly of microspheres using imaging flow cytometry

Cancer Biomarker-Triggered Disintegrable DNA Nanogels for Intelligent Drug Delivery

Even though various techniques have been developed thus far for targeted delivery of therapeutics, design and fabrication of cancer biomarker-triggered disintegrable nanogels, which are exclusively composed of nucleic acid macromolecules, are still challenging nowadays. Here, we describe for the first time our creation of intelligent DNA nanogels whose backbones are sorely disintegrable by flap endonuclease 1 (FEN1), an enzymatic biomarker that is highly overexpressed in most cancer cells but not in their normal counterparts. It is the catalytic actions of intracellular FEN1 on bifurcated DNA structures that lead to the cancer-specific disintegration of our DNA nanogels and controlled release of drugs in target cancer cells. Consequently, the brand-new strategies introduced in the current report could break new ground in designing drug carriers for eliminating unwanted side effects of chemotherapeutic agents and live-cell probes for cancer risk assessment, diagnosis, and prognosis.

Purification of single-stranded DNA by co-polymerization with acrylamide and electrophoresis

Single-stranded DNA (ssDNA) oligonucleotides are useful as aptamers, hybridization probes and for emerging applications in DNA nanotechnology. Current methods to purify ssDNA require both a strand-separation step and a separate size-separation step but may still leave double-stranded DNA (dsDNA) impurities in the sample. Here, we use commercially available acrydite DNA primers to immobilize one strand of a PCR product within a polyacrylamide matrix. Electrophoresis moves the non-crosslinked DNA into the gel where the single-stranded product of desired size can be recovered. Our results show this method produces high yields of pure ssDNA.

Sequence Design for a Test Tube of Interacting Nucleic Acid Strands

We describe an algorithm for designing the equilibrium base-pairing properties of a test tube of interacting nucleic acid strands. A target test tube is specified as a set of desired "on-target" complexes, each with a target secondary structure and target concentration, and a set of undesired "off-target" complexes, each with vanishing target concentration. Sequence design is performed by optimizing the test tube ensemble defect, corresponding to the concentration of incorrectly paired nucleotides at equilibrium evaluated over the ensemble of the test tube. To reduce the computational cost of accepting or rejecting mutations to a random initial sequence, the structural ensemble of each on-target complex is hierarchically decomposed into a tree of conditional subensembles, yielding a forest of decomposition trees. Candidate sequences are evaluated efficiently at the leaf level of the decomposition forest by estimating the test tube ensemble defect from conditional physical properties calculated over the leaf subensembles. As optimized subsequences are merged toward the root level of the forest, any emergent defects are eliminated via ensemble redecomposition and sequence reoptimization. After successfully merging subsequences to the root level, the exact test tube ensemble defect is calculated for the first time, explicitly checking for the effect of the previously neglected off-target complexes. Any off-target complexes that form at appreciable concentration are hierarchically decomposed, added to the decomposition forest, and actively destabilized during subsequent forest reoptimization. For target test tubes representative of design challenges in the molecular programming and synthetic biology communities, our test tube design algorithm typically succeeds in achieving a normalized test tube ensemble defect ≤1% at a design cost within an order of magnitude of the cost of test tube analysis.

Open source and DIY hardware for DNA nanotechnology labs

A set of instruments and specialized equipment is necessary to equip a laboratory to work with DNA. Reducing the barrier to entry for DNA manipulation should enable and encourage new labs to enter the field. We present three examples of open source/DIY technology with significantly reduced costs relative to commercial equipment. This includes a gel scanner, a horizontal PAGE gel mold, and a homogenizer for generating DNA-coated particles. The overall cost savings obtained by using open source/DIY equipment was between 50 and 90%.

3D Printing with Nucleic Acid Adhesives

By relying on specific DNA:DNA interactions as a "smart glue", we have assembled microparticles into a colloidal gel that can hold its shape. This gel can be extruded with a 3D printer to generate centimeter size objects. We show four aspects of this material: (1) The colloidal gel material holds its shape after extrusion. (2) The connectivity among the particles is controlled by the binding behavior between the surface DNA and this mediates some control over the microscale structure. (3) The use of DNA-coated microparticles dramatically reduces the cost of DNA-mediated assembly relative to conventional DNA nanotechnologies and makes this material accessible for macroscale applications. (4) This material can be assembled under biofriendly conditions and can host growing cells within its matrix. The DNA-based control over organization should provide a new means of engineering bioprinted tissues.

Progress Report on the Generation of Polyfunctional Microscale Particles for Programmed Self-Assembly

A process for 3D programmed self-assembly of lithographically printable microscale polymer particles using ssDNA hybridization as the associative force is described. We report our progress in establishing the unit processes required for 3D programmed self-assembly and demonstrate the successful fabrication and sequence-specific self-assembly of covalent ssDNA-functionalized parallelepipeds with dimensions in the sub 10 μm regime characterized by optical microscopy and imaging flow cytometry. This technology has the potential to produce parallelepiped particles with different ssDNA on each facet.

The self-assembly of particles with isotropic interactions

A generic field-theoretic model for the self-assembly of particles with isotropic interactions, motivated by ideas in DNA-mediated colloidal assembly, is presented. A simplest possible system of colloids in explicit solvent is examined to determine the ability of non-connected particles to form complex nanometre or micron scale equilibrium structures in the absence of confounding kinetic effects. It is found that non-trivial morphologies are possible and that, for this effectively one component system, these parallel the phases of diblock copolymer melts for certain parameter choices, despite the absence of connectivity or packing frustration in the model. An explanation for the morphological similarity between these architecturally disparate systems is given. For other parameter choices, it is found that meta-stable and defected phases become more common, and that similarity with block copolymer morphologies decreases.

Measuring in situ primary and competitive DNA hybridization activity on microspheres

Microspheres serve as convenient substrates for studying DNA activity on surfaces. Here, in addition to employing conventional sample preparation involving multiple wash and resuspension steps prior to flow cytometry measurements, we also directly sampled the reaction volume to acquire in situ measurements of primary and competitive hybridization events. Even in the absence of post hybridization wash steps, nonspecific binding events were negligible and thus allowed for direct, quantitative assessment of hybridization events as they occurred on colloidal surfaces. The in situ results indicate that primary duplex formation between immobilized probes and soluble targets on microsphere surfaces is less favorable than predicted by solution models. The kinetics of competitive displacement of primary hybridization partners by secondary targets measured in situ or post washing also deviate from expectations based on theoretical solution thermodynamics, but are consistent with predicted kinetic trends stemming from differences in either the toehold base length or branch migration.