Abstracts

(In order submitted)

Team: Virtus Parva
Title: Nanogene-ear
Abstract: The world’s rhythm can be expressed through the singing of birds in the mornings, the water hitting the rocks on a stream, the laughter of friends. All these sounds are waves, travelling through air. How could we listen to slighter waves, the quietest of sounds? Nanogene-ear is a nanometric device designed to collect vibrations and transform them into electric signals. The main component for this device is DNA. Due to its mechanical and electrical properties, it allows us to create a capacitor-like arrangement whose deformations are the trigger for the signal transduction. Just like a microphone does, but this time in the nanoscale. Over a gold surface, a DNA membrane is attached in between two gold poles. The length of the gap between the gold layer and the membrane is dependent on the vibrations to which the device is exposed. Fluctuations in this spacing change the stored charges of the capacitor. The fabrication of this device involves nanotechnology techniques such as electroplating/physical vapor deposition, and relies on DNA’s self-Assembly onto gold surfaces. The thin membrane should be capable of detecting the slightest variations of pressure in the air due to the elastic properties of the DNA.

Team: HUST-China
Title: Nanofingers-live long and prosper
Abstract: Metabolism, cell apoptosis and immune syetem, all these physiological processes should be strictly regulated to sustain their homeostasis. The speed recovering to stable state directly determines the resistibility towards outer changes. To achieve this, here we build a device helping regulate a physiological process. We name it “Nanofingers”. It features like the Vulcan salute gesture, of which the two adjacent fingers can specifically capture a protein like a tweezer. With a special interaction mechanism, we can simultaneously regulate a physiological process from two aspects and remarkably enhance the regulation ability. In our case, we regulate thrombin and hirudin, two proteins with a contrary function in blood coagulation, trying to accelerate the blood coagulation when we are injured and in reverse prevent the formation of thrombus. The blood thus can maintain a stable state. “Live long and prosper”, the Nanofingers is a Vulcan salute from us towards the world.

Team: Pukyong National University
Title: dumbbell motor
Abstract: We demonstrate Janus micro motor in fluid. The motor consists of magnesium (Mg) particles deposited gold (Au) on the outmost surface. The Janus particle exhibits a directional motion due to the exposed Mg region which generates hydrogen gas in chloride-rich solutions (e.g. seawater) in a long term manner. We manipulate such particles in a way that two particles are connected using linear DNA structures. Through motile observation of the dumbbell-like objects, we identify the force and directional motion of two-particle ensembles.

Team: Team UBerCoolecular
Title: A DNA Origami-Gold Nanoparticle-Liposome Composite Nanostructure for Triggered Simultaneous Release of Multiple Drugs
Abstract: Lipid-based drug carriers have shown great potential in delivering small molecule therapeutics and macromolecules such as nucleic acids. Despite great promise, current drug carriers deliver a single therapeutic payload and lack the ability to preferentially target disease sites and subsequently release their therapeutic payload in a controlled manner. In many cases of cancer, being able to deliver multiple drugs is desirable for efficacious treatment, but to date, these drugs have to be delivered sequentially. Here we harness the stability of DNA Origami structures and the thermal expansion functionality of gold nanoparticles to develop a lipid-based nanostructure capable of carrying a synergistic combination of drugs with the ability to trigger release only at the target site. This composite is generated through immobilization of a DNA Origami platform on a liposome surface. Positively charged gold nanoparticles are then “sandwiched” between two DNA Origami-liposome particles through electrostatic interactions of the DNA phosphate and the charge on the gold particles. By enabling the simultaneous carriage and triggered release of drugs via our composite nanostructure, we can potentially increase antineoplastic effects of chemotherapeutics while reducing harmful side effects. Furthermore, the design of our system enables a high degree of adjustment and modularity. We could potentially adjust the proportion of the therapeutic payloads, the configuration of the structure, the main trigger and signal pair to adapt to various tissue environments, and all without affecting the stability of the primary drug carrying particle.

Team: Shandong University
Title: Nano-hedgehog
Abstract: We creat a vehicle that can carry various molecules of life, just like the hedgehog carrying different kinds of fruits. Iron nano-particle can be controlled easily in magnetic field, which helps us to make it to somewhere we need.Then we cover the iron with silicon dioxide. After surface carboxyl, the magnetic nano-particles has the ability to carry whatever molecules with hydroxyl groups, such as medicines, DNA, RNA or proteins. We can connect those molecules with a kind of immobilized lipase. When the molecules are connected to the nano-particle, the ester bond can be hydrolyzed to let out the molecules.

Team: Delta-Sci
Title: La Caja
Abstract: The DNA Origami technique has been widely used to design a great variety of innovative three-dimensional devices, such as nanosensors and drug delivery containers. In this project, we designed a half-box-shaped magnetic DNA device made of four scaffolds held together with oligonucleotides, named staples. These scaffolds are arranged in such a way that some of their ends overhang form the base of the structure as five single DNA strands. The purpose of these hanging single strands is to bind to aptamers, which will catch specific biomolecules. The inside of the structure is hollow, aiming to capture an Iron Oxide Nanoparticle (NP) functionalized with an amino-functional alkoxysilane (APTES). Due to the composition of the NP, the device would have magnetic properties, allowing it to be controlled with a magnetic field. In this way, the device may inspire new methods for drug delivery, biomolecule isolation or medical diagnosis.

Team: NanocANDy
Title: DNA nanocarrier for investigation of glycan-cell interactions
Abstract: The unique glycosylation pattern of biopolymers and its recognition by the cells plays a crucial role in cellular pathways and the induction of signal transduction. Recent and ongoing research has identified the importance of glycosylation in general and illuminated many particular aspects of glycan-receptor interactions, however, knowledge of specific glycosylation patterns is missing in many instances. Therefore, the goal of this project was the development of a basic tool to specifically investigate binding behaviour of a variety of cell types in response to nanometer-precise arrangements of a class of sugar molecules. DNA origami provides an ideal platform to design a nanocarrier for sugar molecules. The designed structure allows quantitative and high-throughput analysis of these interactions by being highly modifiable in three different ways: geometrically by realizing sugar patterns on the structure’s surface, chemically by altering the type of attached carbohydrates and spectroscopically by implementing differently excitable fluorophores.

Team: YOKABIO
Title: DNA New-World Translator
Abstract: We utilize a variety of electric appliances and electronic devices in diary life that are absolutely imperative for our businesses, studies, etc. The heart of them is so-called a central processing unit (CPU) in which the language of the CPU is a digital signal comprised of “high” or “low” signal. In other words, the CPU can understand and speak the “digital language”. In the BIOMOD2015, we are interested in the “digital language”. The computer recognizes all information on a combination of “1”-“0” processes. In our projects, we try to create an analog-to-digital (A/D) converter that translates an analog signal (concentration of a DNA strand) into the digital signal to realize the digital information processing by using DNA circuits. We strongly believe that our translator would become a bridge that enables us to connect between a biochemical system and an electronic system. Furthermore, it would convert all internal signals of human into digital signals, sharing digital language between both systems in the future.

Team: Tianjin
Title: Droplets and cell-free protein synthesis
Abstract: In the past one hundred years, molecular biology has developed fast. We discovered the structures of DNA, RNA and proteins. Based on these works, we know how to change and use them. Moreover, we can create a completely new biomolecule and get fresh novel features following through on our idea. This is also the purpose of BIOMOD. Let’s consider it further, whether we could create a more complex system——“cell”. We built a large number of cell-like containers called droplets and imported DNA into them. Then we tried to make it realize the cell-free protein synthesis or in vitro transcription and translation (IVTT). Now it works and as you think of, we have created a simple but significant “life”. This “life” can be seen as an efficient means of simplifying a cell, just like a mathematician can simplify mathematics by mathematical formulas. It offers several advantages over traditional cell-based expression methods, and provides a more accurate way to study cell’s activities through this simplification, and in the future, we will achieve a programmable cell operation. Furthermore, a numerical system model was built. Compared with experiment data, we prove that our modeling is precise and reliable.

Team: St. John's University
Title: Virus-Binding Origami II : “Claw Wars: Revenge of the Polymers”
Abstract: We describe a DNA origami designed to bind viruses; it is a three-armed ‘claw’ displaying sticky-ended DNA strands complementary to the surface of a sticky-end-modified capsid ( bacteriophage MS2). Due to low levels of claw binding to capsid (despite many optimization attempts), binding was improved by increasing the number of sticky-end binding sites on the claw from 1 to 5 per arm. ssDNA tethers were then attached between arms in an effort to limit the mobility of the claw and stop unwanted polymerization; efforts to minimize polymerization while retaining binding are ongoing; FRET and TEM studies will follow. We also made an Fab’ -DNA conjugate for attachment to the claw to bind a wild-type virus surface. Extensive synthesis optimization always resulted in a low yield; too low to make testable amounts of conjugate for attachment to claw. We are currently pursuing aptamer recognition of virus surfaces.

Team: Team Kansai
Title: DNA Origami Chochin
Abstract: Team Kansai realized Nano-Flipbook two years ago. They expressed it by two-dimensional “DNA Origami” Nano-structures. This year, we decided to expand this idea to 3D. We chose Japanese famous Ghost Character called “Chochin Obake” as the target motif. We aimed to observe this motion of the mouth opening and sticking its tongue representing a big mouth under AFM. First, we designed “DNA Origami Chochin”, which has tube structure of 20 helices. The tube consists of top and bottom pieces connected to each other by two DNA helices. DNA Origami Chochin has a characteristic that it can repeatedly open and close its mouth by strand exchange. Successfully, it has single stranded Scaffold DNA as DNA Tongue. But the original Tongue is too small to observe DNA tongue by AFM. We try to grow and enlarge DNA Tongue with DNA tail and observe it sticking out of the inside to the outside.

Team: UTokyo-Komaba
Title: Nano-Bio-Battery
Abstract: Recently research on bio-batteries, which can generate electricity inside the body, has become popular due to the development of artificial organs. Here we propose a new kind of bio-battery, made up of two tiny water droplets joined together with alpha-hemolysin and enclosed by lipid layer. Inside one droplet, Ca2+ ions and giant anionic beads are put, while inside the other, only calcium indicators. Although both ions try to move to the other side through the hole made by alpha-hemolysin in the junction, only the smaller ones (Ca2+) can pass selectively due to the difference of the size against the hole. Consequently, electric potential difference is produced. This is our first goal. By connecting the droplets to the Mg-nanoscale-electrode, electrons flow along the electric potential difference. This is the mechanism of our Nano-Bio-Battery. In the future, Nano-Bio-Battery will be put into human bodies, resulting in practical use in the medical field.

Team: BIOMOD Hokkaido Univ.
Title: A solution to congested traffic by using a system of Self-Propelled Objects
Abstract: When an emergency such as a fire occurs, many people try to run away at once and an exit often becomes congested, which delays the evacuation. Putting pillars around the exit is known to be a way to control people’s flow. To understand the mass movement of people at the presence of pillars, experiments are needed, though it’s difficult to conducts them in real world using a lot of people. In our study, we substitute microtubules for humans and analyze the movement in micro scale. Microtubules are one of the cytoskeletons in eukaryotic cells and work as self-propelled objects connected with molecular motors. In their collective action, interactions can be seen as in human one. We construct pillars on a grass by microfabrication, observe the collective action of microtubules and analyze how pillars make an effect on the flow. We expect our study will contribute to optimization of people’s evacuation.

Team: Team NTU
Title: Nano Needle- a novel tool to tackle antibiotic-resistant bacteria
Abstract: In 2014, WHO stated that antibiotic resistance becomes a serious worldwide issue. Therefore we design a hollow tube called NanoNeedle to tackle antibiotic-resistant bacteria. This device is divided into two modules: Weak and Strong. The weak structure, more flexible and bendable, consists of 12 double-helical DNA domains. The interior of the weak structure is bound to 3 with-increasing-affinity aptamers; and the plasmid, connected by one of them, carries suicide genes. The strong structure consisting of 30 double-helical DNA domains is robust enough to penetrate the cell wall and the membrane of bacteria. When meeting target bacteria, 3 aptamers inside NanoNeedle will specifically identify and sequentially be bound to the cell wall of target bacteria. Subsequent to the weak structure bending stepwise, the strong structure protrudes centrally, penetrates the membrane and delivers the plasmid into the bacteria. After the suicide genes being expressed, they kill the bacteria by destroying the maintenance of physiological functions. NanoNeedle is a versatile device since it can change different aptamers and suicide genes for various targeted antibiotic-resistant bacteria. Eventually, we expect to eliminate bacteria by delivering NanaNeedle into patients suffered from bacterial infection, and developed to as the substitute of antibiotics.

Team: Bioluminati
Title: Ion concentration driven bistable switching device
Abstract: DNA, the primary genetic material for most organisms, does not only exist in the well-known double helix form, but can also exhibit a myriad of secondary and tertiary structures such as DNA triple helix, cruciform etc. The stability of these structures depends on the medium conditions - pH, ion concentration in the medium, and temperature. This dependence can be utilized to design DNA based constructs that can switch conformational states in response to changes in the environment, allowing for high precision external manipulation of the structure of the construct. Further, different DNA structures can exhibit novel biological activity such as specific protein binding etc., allowing for the application of such constructs in highly controlled biological processes. Here, we propose a novel DNA device - a single-stranded circular DNA loop of 108 bases with two pairs of complementary sequences on opposite parts of the loop. The sequences are arranged such that only one pair can be Watson-Crick base paired at any given time. Thus the molecule can switch between two conformations. Further, one pair of complementary sequences can, under suitable conditions, take up secondary structures of G-quadruplex and I-motif. These secondary structures have many special properties, including the dependence of their stability on the potassium concentration of the surrounding medium. External control on the potassium concentration of the solution enables us to manipulate the stability of the G-quadruplex and I-motif secondary structures and by extension, the equilibrium constant between the two conformations of the device. Thus, the device serves as a molecular switch that can be externally “flipped”. By including a mechanism to get a read out of the number of molecules in each conformation, the device can also be used as a real-time sensitive indicator of potassium concentration. This has immense utility in imaging technology wherein it could be used to follow non-invasively, with nanosecond temporal resolution, any biological event where potassium level change is involved. The firing of neurons with the action-potential coursing down the maze of neural circuitry in the brain comes as a real possibility. Also, a slight variant of the sequence forms a 'potency-adjustable' Thrombin-binding aptamer (TBA), a much needed modification that could take the TBA experimental drug stuck in FDA phase-II clinical trial for low of potency, all the way to market in treatment of stroke and hypercoagulable disorders.

Team: Team Sendai
Title: If it ain't got that twist - Size-controllable Linear Homomultimer
Abstract: In nature, various biological functions are realized by multimeric proteins. In most cases, these proteins have intrinsic curvature and the number of monomers are determined by their circular assembly. However, controlling the number of linear assembly is difficult without additional capping mechanisms. Here, we propose a novel mechanism to control the linear assembly by using a rotating shaft as a vernier. We designed a DNA origami monomer consisting of a cylinder and a twisted shaft, where the shaft can rotate inside the cylinder. Since the shaft is slightly twisted, there is a phase shift between stacking surfaces on its both ends. As the monomers stack, the phase shift accumulates on the shaft. When the accumulated twist reaches the limit on the cylinder, the stacking is inhibited. Our design enables us to make size-controllable DNA origami complexes, which provide various possibilities for nanotechnology.

Team: Ochadai
Title: DNA based UV-cut sheet
Abstract: Gold nanoparticles have a wide range of applications due to their optical and electronics properties. In our project, we focused on the interaction of these particles with light of a specific wavelength, and designed an optical filter that cuts ultraviolet rays. To create an interference pattern with the particles, we attached them onto a rectangular DNA origami designed by Rothemund et al. We modified the design slightly so that when an additional DNA strand is added, these numerous origami bind together, forming a planar sheet. The pattern of gold nanoparticules on the sheet cuts UV while transmitting other wavelengths, and may be a novel transparent UV cut material. For future applications, we propose an eye drop that prevents diseases cased by excess exposure to sunlight. By forming this sheet on our eye, we can protect the entirety of it, not only our pupil as previously developed UV-cut contact lenses do.

Team: South China University of Technology
Title: The Magical Band-Aid
Abstract: Chronic kidney disease (CKD) has become a worldwide health concern because of its high morbidity, high mortality and disability as well as huge treatment difficulties and costs. In China, CKD is one of the common and detrimental diseases. Proteinuria, as an important clinical index of CKD, is also the main factor that worsens it. Thus, reducing or eliminating the leakage of urine protein is the key to treating CKD. The formation of proteinuria and the occurrence of CKD are closely related to the disfunction of glomerular filtration barriers. The current therapies except dialysis and transplant mainly utilize hormone and immunomodulation to control systemic co-factors in order to treat CKD. However, this therapy may cause lots of side-effects and drug resistance and can only defer the further deterioration rather than cure CKD, so repairing the damaged membrane and restoring its function are the fundamental treatment. Basing on this idea, we synthesize a size- and shape-controlled porous polymer membrane (PPM) which mimics the structure and function of glomerular filtration membrane (GFM), and couple anti-Nephrin, one of the specific antibody of GFM, with PPM, generating the PPM-anti-Nephrin with GFM repairing targeting. Additionally, we establish different nephropathy rat models and successfully make PPMs adhere to the damaged GFMs and repair them and realize the treatment to the rats with kidney diseases, which is really like a magical band-aid. The achievements we gain may offer a brand-new idea for treating CKD and can be expected to exert great impact on the future treatment.

Team: Team Tsukuba
Title: Self-regulated micro sensor
Abstract: We plan to create a cell-like sensor in response to external conditions. To design the micro sensor in a simple and self-regulated manner, we mimic the cellular structures, which are simply divided into two parts, a compartment in membrane structure and a chemical mixture in which biochemical reactions and regulations occur. In this study, we optimized a phospholipid bilayer structure as the container for the micro sensor, and a gene expression system reconstituted from the purified elements to proceed the reactions and regulations. Self-regulation is relied on the structural changes of the RNA sequence, which can form either a stem-loop or a pseudoknot. The transition between the two structures can be self-regulated by the downstream protein molecule S15. The functional protein molecule sensing the metal ions in the environment is co-expressed with S15. The micro sensor is supposed to be used for testing the harmful metal ions in the organisms.

Team: Primary Contact
Title: Universal Biosensor Design
Abstract: Our team has proposed a universal design for biosensors, one which can be easily adapted to create a multitude of biosensors having applications ranging from point of care diagnostics to water safety measurements. Biosensors have four major components: a core structure to hold all elements together, sensing elements to sense the target entity, a transducer to convert the sensed signal into a usable one and an output device to display the result to the user. Often these components have to be modified extensively as per the requirements of the specific target that is being sensed. Our biosensor is a mixture of two types of particles. The core structure of both is made of hollow mesoporous silica nanoparticles. The inner cavity is filled with our signalling molecule- fluorophore tagged DNA origami, each of the two types has one specific type of origami (tagged with one type of fluorophore) while the pores are gated by aptamers. The presence of the target (aptamer’s ligand) unlocks aptamer gates on both which results in release of origami from the nanoparticle. The two types of origamis interact with each other via guide strands, leading to fluorescence due to FRET. An ELISA plate based implementation can be made for the same to create a high-throughput biosensing device.

Team: OhioMOD
Title: Novel DNA origami device for protein aggregate theranostics
Abstract: Protein aggregates are associated with a variety of diseases including Alzheimer’s, Parkinson’s, and Macular Degeneration. The ability to detect the protein precursors to these aggregates, often misfolded proteins, provides critical early-stage diagnostics and monitoring to ultimately improve treatment outcomes. Furthermore, where most biosensing devices simply provide a readout of the target presence, we aim to build a device that induces a functional response that aids to clear the target protein or treat the disease. We hypothesize that aptamer-functionalized DNA origami will bind specific target proteins, undergo conformational changes, and subsequently form oligomeric complexes that elicit a functional response to clear the protein or recruit components to the site of disease. While initial goals are focused on proof of concept with a purely DNA-based system, we will achieve the long term goals through a novel approach of using cryptic binding sites initially buried in the inner part of the device and exposed after the protein-driven conformational change. The functional response will either expose signaling molecules to drive trafficking or aggregate sensors into defined geometries (inspired by the natural pentamer formation of immunoglobulin M (IgM) that recruits and activates complement, a key component of immune function). The DNA nanostructure is comprised of two plates connected by a DNA hinge referred to hereafter as “BUS” – Biosensing Unit Structure. Gel electrophoresis and transmission electron microscopy (TEM) confirmed well-folded BUS. Complementary overhangs on the BUS aid the formation of dimers and trimers, as confirmed by TEM. Future proof of principle experiments will utilize vascular endothelial growth factor (VEGF) and its corresponding aptamer to demonstrate simultaneous protein sequestration and trimer assembly. The BUS may be employed to target amyloids in addition to VEGF to ultimately become a theranostic (therapeutic diagnostic) device for the treatment of Macular Degeneration, Alzheimer’s disease, and Parkinson’s disease.

Team: Berlin15
Title: Multifunctional SynBio Nanoscaffolds
Abstract: Increased surface area is a key factor for the developement of more efficient nano devices. We are introducing a multifunctional biomolecular nano scaffold with three-dimensional reactive nanostructures. Therefore, the FliC-gene - encoding for flagellin – is modified with variously designed D3-domains to integrate diverse modifications into the protein for our purpose of a multifunctional scaffold. The different D3 domains bear reagions for the incorporation of non-canonical amino acids. These add functionalities to link the designed flagellin with plastic-degrading enzymes to create the scaffold of a molecular filter system for degrading microplastics. However, by incorporating catechol derivatives into the D3-domains of FliC, these modified proteins can be used as ion catchers in nano electronics for different applications. Immobilizing functionalized flagellins on silica monoliths creates our nano device. In addition, immobilized functionalized flagellins coupled with specific antibodies on assay plates will display a third dimension which can significantly enhance the sensitivity in immunoassays.

Team: NanoLions
Title: Self-Assembling Microtubule-Polystyrene Network
Abstract: Microtubules, which are polymers of a protein called tubulin, are a key component of the cellular cytoskeleton. In vitro, microtubules readily polymerize from tubulin subunits to lengths of 5-20 microns, and are easily functionalized and imaged. These properties make microtubules ideal tools for engineering self-assembling nano-scale systems. The ability to form self-assembling physical networks on the micro-scale has potential applications in signal transduction. Functionalizing microtubules with metallic particles can potentially create pathways capable of conducting electromagnetic signals. We use microtubules to form a self-assembling microscale network, using microspheres as nodes, and microtubules as linkers. To achieve this, streptavidin-coated beads were mixed with biotinylated microtubules in a flow cell. The microtubules linked beads up to 30 microns apart (4 times the bead’s radius) and gave rise to networks. A conductive bead-microtubule network provides unique advantages over a static, prefabricated model since the microtubule-bead system can dynamically reorganize in response to stimuli.

Team: Nzymes 'R' Us
Title: Rings, trees, and forests: nanoscale optimization of metabolism using designer, multi-enzyme assemblies
Abstract: Multiple enzymes constituting a heterologously expressed metabolic pathway (“assembly line”) in microbial cells (“factories”) are now routinely used to biosynthesize various chemicals and drugs. The ability to control the nanoscale topologies of these molecular assembly lines will allow pathway optimization. However, in contrast with DNA, protein assembly design rules remain elusive and/or non-generalizable. Here, we demonstrate the capacity to build spatially controlled protein assemblies by creating supramolecular complexes of green and red fluorescent proteins (FPs) using a combined computational-experimental approach. Different types of assemblies were generated: terminating ring structures, self-propagating branched fractal formations, and irreversibly-bound scaffolding units mediated by an unnatural amino acid. Our method allows for both specificity and modularity, which enables us to substitute the FPs with enzymes of a biochemical pathway in the molecular assembly line. Furthermore, protein-protein interactions responsible for assembly can be controlled by phosphorylation to allow temporal control and responsiveness to external stimuli.

Team: Universidad Autónoma de Nuevo Léon
Title: ImaGene
Abstract: In spite of the accelerated rate at which the world is producing data in videos, music, files, etc, the need for an efficient and more practical type of storage is growing. Inspired by this particular situation we decided to replicate what nature does in the form of genes, Dna and chromatin (information storage) by mixing its basic components (nucleotides) with some familiar forms of electronic technology components (circuits); by this we will try to achieve a form of a DNA microprocessor, whose information will be stored in nucleic bases, attached to a surface, that will be interpreted with binary logic according to the existing difference on the impedance curves each base produce. There have been other attempts of determining oligonucleotides, dsDNA, and ssDNA impedance, mostly used for detection of different targets such as miRNA, SNP and a variety of metals. Never the less, our approach relies on the impedance of a specific base, so this can be useful in having a kind of bookmark when reading the information stored in this chip, having a cost-effective way to store, read and modify information integrated in a single "device".

Team: University of Calgary
Title: Nanosensor with a binary output to identify DNA single point mutations
Abstract: We have built a nanosensor that recognizes single point mutations and reports their positions in a DNA strand of a known sequence. Ultimately, the nanosensor generates a binary code for each base position along the strand of interest. This binary sequence is then interpreted to produce an unambiguous answer, clarifying whether there is a mutation at the site of interest and identifying the specific base. In order to produce the code we immobilize fluorescently labeled DNA bait strands on a chip using dip pen nanolithography. This method enables the generation of submicron-sized isles of molecules that are attached to a surface. Then, the bait strands in the isles are hybridized with the target strands from the sample. This effectively concentrates the DNA from solution into a precise localized area. Thus, very little genetic material is required for the analysis. Three separate isles with hybridized DNA molecules are needed for the identification of the base at a given position. The isles are exposed to three different treatments – we employ chemical cleavage of mismatch reactions and heat. These treatments are specific and only cleave particular mismatches along the hybridized sequence. Finally, each isle is analyzed using a confocal microscope to create a 3 digit long binary code that identifies the DNA base at the position of interest. By simplifying the interpretation of genetic diagnostics we are striving to improve early and reliable detection of point mutations which can enhance the accuracy, and efficiency of medical treatment.

Team: Jilin_China
Title: Using Simple DNA Box as a Carrier to The Drugs of Cancer
Abstract: Although many promising anti-cancer drugs have been developed over the past 50 years, effective delivery of the drugs to diseased cells remains a challenge. Recently, nanoparticles have been used as drug delivery vehicles due to their high delivery efficiencies and the possibility to circumvent cellular drug resistance. However, the lack of biocompatibility to engineer spatially addressable surfaces for multi-functional activity remains an obstacle to their widespread use. We design a novel drug carrier system based on self-assembled, spatially addressable DNA origami nanostructures that confronts these limitations. All of this DNA origami nanostructures were self-assembled by numbers of trigeminal DNA molecules. The trigeminal DNA molecules is composed of several single stranded DNA molecules. All of this DNA origami nanostructures have similar molecular size and structure. Anti-cancer drug was non-covalently attached to DNA origami nanostructures.

Team: Protomatos
Title: Expanded NanoCages - Unwrapping Nano Black Boxes
Abstract: The concept of “black box” symbolizes the abstraction of complex processes enclosed within. This inspires our project to literally build “nanoboxes” of DNA Origami, proving experimentally the functionality of a novel algorithm that flexibilize the design of polyhedral DNA nanocages. These nanostructures could be used in a large application as scaffolds to increase efficiency of enzymatic pathways by direct anchoring and encapsulation of enzymes, optimizing the molecular logistics of the catalytic reactions and potentially enzyme lifetime. Since the compartmentalized pathways could vary in length and each enzyme in size, therefore a precise control of the cage design could lead to various options for properly building the scaffolds. In a bioproduction scenario, we also explore the binding of paramagnetic particles to ease the cages separation in solution, making them renewable. These potential theoretical applications are supported by an extensive research and mathematical modelling.

Team: Team Injectimod
Title: Artificial Self-Assembly of the T3SS Needle Tip
Abstract: Self-assembly in Nature is responsible for the formation of molecular machines with a remarkable complexity and variety of functions. In Nature, scaffolding allows for precise construction and organisation of the complex supramolecular structures that exist in cellular machinery. One such system is the bacterial Type III secretion system (T3SS), a molecular syringe that injects host cell membranes with toxins, leading to infections such as Shigellosis, the Black Plague and Chlamydia. It is a complex supramolecular nanomachine which self-assembles from dozens of individual proteins. However, its mechanisms of assembly and final structure are poorly characterised. We aim to build a synthetic DNA scaffold to artificially assemble the needle-tip complex of the T3SS. This will allow for investigation of the thermodynamic and structural aspects of scaffolded self-assembly. Successful assembly of this protein complex will also provide a novel tool for artificially constructing antigenic structures, potentially providing a new basis for vaccine development.

Team: Tema member
Title: Droplets and cell-free protein synthesis
Abstract: In the past one hundred years, molecular biology has developed fast. We discovered the structures of DNA, RNA and proteins. Based on these works, we know how to change and use them. Moreover, we can create a completely new biomolecule and get fresh novel features following through on our idea. This is also the purpose of BIOMOD. Let’s consider it further, whether we could create a more complex system——“cell”. We built a large number of cell-like containers called droplets and imported DNA into them. Then we tried to make it realize the cell-free protein synthesis or in vitro transcription and translation (IVTT). Now it works and as you think of, we have created a simple but significant “life”. This “life” can be seen as an efficient means of simplifying a cell, just like a mathematician can simplify mathematics by mathematical formulas. It offers several advantages over traditional cell-based expression methods, and provides a more accurate way to study cell’s activities through this simplification, and in the future, we will achieve a programmable cell operation. Furthermore, a numerical system model was built. Compared with experiment data, we prove that our modeling is precise and reliable.

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