designing-a-bio-responsive-robot-from-dna-origami

Designing a Bio-responsive Robot from DNA Origami

Nucleic acids are astonishingly versatile. In addition to their natural role as storage medium for biological information1, they can be utilized in ...

folding-characterization-bio-responsive-robot-from-dna

Folding and Characterization of a Bio-responsive Robot from DNA Origami

The DNA nanorobot is a hollow hexagonal nanometric device, designed to open in response to specific stimuli and present cargo sequestered inside. Both ...

Bar Ilan University

Bar-Ilan University

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To characterize the genetic defects associated with fundus albipunctatus (FAP) in patients in Israel.

Fundus albipunctatus: novel mutations and phenotypic description of Israeli patients.

Pour caract&eacute;riser les anomalies g&eacute;n&eacute;tiques associ&eacute;es du fundus albipunctatus (FAP) chez les patients en Isra&euml;l.

Albipunctatus fond de &oelig;il : nouvelles mutations et description ph&eacute;notypique des patients isra&eacute;liens.

Um die genetische Defekte, die zugeordnete Fundus Albipunctatus (FAP) bei Patienten in Israel zu charakterisieren.

Fundus Albipunctatus: neuartige Mutationen und ph&auml;notypische Beschreibung der israelische Patienten.

Per caratterizzare i difetti genetici associati con fundus albipunctatus (FAP) in pazienti in Israele.

Fundus albipunctatus: romanzo mutazioni e descrizione fenotipica dei pazienti israeliani.

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Para caracterizar los defectos gen&eacute;ticos asociados a albipunctatus del fondo (FAP) en pacientes en Israel.

Albipunctatus del fondo: mutaciones y descripci&oacute;n fenot&iacute;pica de pacientes israel&iacute;es.

Biological systems are collections of discrete molecular objects that move around and collide with each other. Cells carry out elaborate processes by precisely controlling these collisions, but developing artificial machines that can interface with and control such interactions remains a significant challenge. DNA is a natural substrate for computing and has been used to implement a diverse set of mathematical problems, logic circuits and robotics. The molecule also interfaces naturally with living systems, and different forms of DNA-based biocomputing have already been demonstrated. Here, we show that DNA origami can be used to fabricate nanoscale robots that are capable of dynamically interacting with each other in a living animal. The interactions generate logical outputs, which are relayed to switch molecular payloads on or off. As a proof of principle, we use the system to create architectures that emulate various logic gates (AND, OR, XOR, NAND, NOT, CNOT and a half adder). Following an ex vivo prototyping phase, we successfully used the DNA origami robots in living cockroaches (Blaberus discoidalis) to control a molecule that targets their cells.

Universal computing by DNA origami robots in a living animal.

DNA origami is a robust method for the fabrication of nanoscale 2D and 3D objects with complex features and geometries. The process of DNA origami folding has been recently studied, however quantitative understanding of it is still elusive. Here, we describe a systematic quantification of the assembly process of DNA nanostructures, focusing on the heterotypic DNA junction-in which arms are unequal-as their basic building block. Using bulk fluorescence studies we tracked this process and identified multiple levels of cooperativity from the arms in a single junction to neighboring junctions in a large DNA origami object, demonstrating that cooperativity is a central underlying mechanism in the process of DNA nanostructure assembly. We show that the assembly of junctions in which the arms are consecutively ordered is more efficient than junctions with randomly-ordered components, with the latter showing assembly through several alternative trajectories as a potential mechanism explaining the lower efficiency. This highlights consecutiveness as a new design consideration that could be implemented in DNA nanotechnology CAD tools to produce more efficient and high-yield designs. Altogether, our experimental findings allowed us to devise a quantitative, cooperativity-based heuristic model for the assembly of DNA nanostructures, which is highly consistent with experimental observations.

Cooperativity-based modeling of heterotypic DNA nanostructure assembly.

Self-assembly provides an information-economical route to the fabrication of objects at virtually all scales. However, there is no known algorithm to program self-assembly in macro-scale, solid, complex 3D objects. Here such an algorithm is described, which is inspired by the molecular assembly of DNA, and based on bricks designed by tetrahedral meshing of arbitrary objects. Assembly rules are encoded by topographic cues imprinted on brick faces while attraction between bricks is provided by embedded magnets. The bricks can then be mixed in a container and agitated, leading to properly assembled objects at high yields and zero errors. The system and its assembly dynamics were characterized by video and audio analysis, enabling the precise time- and space-resolved characterization of its performance and accuracy. Improved designs inspired by our system could lead to successful implementation of self-assembly at the macro-scale, allowing rapid, on-demand fabrication of objects without the need for assembly lines.

ArticleTotal : 2	Year
Publication title Cited by 3	2013
Publication title Cited by 6	2015

Article	Year
Fundus albipunctatus: novel mutations and phenotypic description of Israeli patients. Molecular vision\| PubMed ID: 22815624	2012
Universal computing by DNA origami robots in a living animal. Nature nanotechnology\| PubMed ID: 24705510	2014
Cooperativity-based modeling of heterotypic DNA nanostructure assembly. Nucleic acids research\| PubMed ID: 26071955	2015
Meshing complex macro-scale objects into self-assembling bricks. Scientific reports\| PubMed ID: 26226488	2015

Almogit Abu-Horowitz

Biography

JoVE Journal Publications

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