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Putting DNA on autopilot

ASU and MIT researchers describe method for automation of DNA origami construction

Hao Yan directs the Biodesign Center for Molecular Design and Biomimetics and is the Milton D. Glick Distinguished Professor in the School of Molecular Sciences at ASU.

January 04, 2019

Nature has made extravagant use of a simple molecule — DNA, the floor plan of all earthly life.

Inventive researchers have used the same base-pairing properties that bond two strands of DNA into the familiar double helix to build innumerable useful structures at the nanometer scale.

One such method, known as DNA origami, has yielded rich results in recent years, enabling the construction of a rapidly growing menagerie of two- and three-dimensional objects, with far-flung applications in material science, nanoelectronics, photonics and the biomedical arena.

In new research appearing in the current issue of the journal Science Advances, Hao Yan and his colleagues, in collaboration with scientists at MIT, describe a method allowing for the automation of DNA origami construction, vastly accelerating and simplifying the process of crafting desired forms and opening the world of DNA architecture to a broader audience.

"DNA origami design has come to the time that we now can draw a form freely and ask the computer to output what is needed to build the target form," Yan said.

The variety and versatility of DNA nanoarchitectures have enabled their application for tiny logic gates and nanocomputers, advanced materials with unique properties, nanoelectronics and nanocircuitries and structures displaying dynamic properties, including nanotweezersnanowalkers and nanorobots.

In recent research, DNA origami nanostructures have demonstrated the ability to improve the effectiveness of chemotherapy, reduce therapeutic side effects and even manage drug resistance.

Yan directs the Biodesign Center for Molecular Design and Biomimetics and is the Milton D. Glick Distinguished Professor in the School of Molecular Sciences at ASU. He is joined by Biodesign researchers Fei Zhang and Xiaodong Qi, along with colleagues led by Professor Mark Bathe from the Departments of Biological and Chemical Engineering at MIT. The ASU team contributes their expertise to validate the design computed by the MIT team.

Endless forms

The power of structural DNA origami lies in the method’s capacity to design and construct a virtually limitless array of forms, which self-assemble from their component parts. The basic technique involves a length of single-stranded DNA designed to elaborately fold into desired shapes through base pairing of its four complementary nucleotides. To complete the nanoform, short DNA segments from 20-60 nucleotides in length — known as staple strands — are added, acting to pin the folded scaffold structure in place by base-pairing at preselected locations, as in this animation: 

Initially, DNA origami was used to design fairly humble 2D structures, including stars, triangles and smiley faces. These objects, measuring just billionths of a meter in diameter, can only be seen with sophisticated imaging technology, principally atomic force microscopy (AFM). The DNA origami technique has since undergone rapid expansion, permitting the design and construction of nearly any arbitrary two- or three-dimensional object a researcher may envision.

The rapid advance of such technology is due to the expanded possibilities for DNA construction via scaffolded DNA origami as well as the safety and stability of DNA in physiological environments.

But while the nanostructures self-assemble with impressive reliability, the actual design phase required to engineer the varied forms has been complex and highly labor-intensive, particularly the design of staple strands needed to fold the long scaffold strand to the target geometry.

This step is typically handled manually for each geometric form, with the aid of visualization software, presenting a significant hurdle in the process. The lack of systematic design rules for producing accurate staple strands and folded scaffolding has meant that the powerful technology of DNA origami has been largely reserved for experts in the field.

Folding made easy

The new study offers a fully automated alternative that permits the design of all DNA staple sequences needed to fold any free-form 2D scaffolded DNA origami object. Previously, researchers had devised ways of automating staple strand design for 3D polygonal structures, but the ability to replicate this with arbitrary 2D nanoforms has been elusive, until now.

For the automated process, the designer of a given 2D structure first makes a simple freehand drawing of just the outer border of the desired shape. This drawing is used as the input, with the internal structure of the design determined automatically, using the program’s specialized algorithm. In an alternate method, complete internal and external boundary geometries are drawn freehand with continuous lines.

Using either technique, the 2D line-based geometric representation is used as input for the algorithm that performs automatic scaffold and staple routings, after which, the resulting DNA sequences for the scaffold and staple strands can be ordered from commercial outlets, mixed in a test tube according to a prescribed recipe of heating and cooling and self-assembled into finished structures that can be visualized using AFM imaging. 

The two approaches provide nonexperts with the means to easily synthesize complex nanostructures, helping to advance the field.

Draw it, build it!

The study demonstrates the automated sequence design of 15 irregular-design objects, featuring triangular mesh, square and honeycomb geometries with varying shape parameters. The researchers have dubbed their algorithmic approach PERDIX (Programmed Eulerian Routing for DNA Design using X-overs), and the program is available to the research community.  

PERDIX is a deceptively simple and user-friendly means of producing 2D DNA nanostructures, which has only been made possible after many years of trial and error to flesh out complex, generalizable design rules, making design automation a reality.

The PERDIX design software can automatically convert any 2D polygonal mesh design into a blueprint for a scaffolded DNA nanoform, using simple computer-aided design. The simplicity and speed of the software empowers nonspecialists to translate virtually any 2D polygonal shape into a completed design needed to “print” a 2D nanometer-scale structure.

As the authors note, the design program permits customized nanometer-scale templating of molecules, including dyes, nucleic acids, proteins and semiconductor nanocrystals. Resulting forms may find their way into varied applications in nanophotonics, nanoscale energy transport, biomolecular sensing, intelligent drug delivery, structural studies and cell-based binding.

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