Nanotechnology Now

Our NanoNews Digest Sponsors
Heifer International



Home > Press > DNA design that anyone can do: Computer program can translate a free-form 2-D drawing into a DNA structure

MIT researchers have devised a technique that “reverse engineers” complex 3-D computer-aided design (CAD) models — breaking them down into the many individual shapes they’re made of — to make them far easier for users to customize for manufacturing and 3-D printing applications.

Courtesy of the researchers
MIT researchers have devised a technique that “reverse engineers” complex 3-D computer-aided design (CAD) models — breaking them down into the many individual shapes they’re made of — to make them far easier for users to customize for manufacturing and 3-D printing applications. Courtesy of the researchers

Abstract:
Researchers at MIT and Arizona State University have designed a computer program that allows users to translate any free-form drawing into a two-dimensional, nanoscale structure made of DNA.

DNA design that anyone can do: Computer program can translate a free-form 2-D drawing into a DNA structure

Cambridge, MA | Posted on January 4th, 2019

Until now, designing such structures has required technical expertise that puts the process out of reach of most people. Using the new program, anyone can create a DNA nanostructure of any shape, for applications in cell biology, photonics, and quantum sensing and computing, among many others.

"What this work does is allow anyone to draw literally any 2-D shape and convert it into DNA origami automatically," says Mark Bathe, an associate professor of biological engineering at MIT and the senior author of the study.

The researchers published their findings in the Jan. 4 issue of Science Advances, and the program, called PERDIX, is available online. The lead authors of the paper are Hyungmin Jun, an MIT postdoc, and Fei Zhang, an assistant research professor at Arizona State University. Other authors are MIT research associate Tyson Shepherd, recent MIT PhD recipient Sakul Ratanalert, ASU assistant research scientist Xiaodong Qi, and ASU professor Hao Yan.

Automated design

DNA origami, the science of folding DNA into tiny structures, originated in the early 1980s, when Ned Seeman of New York University proposed taking advantage of DNA's base-pairing abilities to create arbitrary molecular arrangements. In 2006, Paul Rothemund of Caltech created the first scaffolded, two-dimensional DNA structures, by weaving a long single strand of DNA (the scaffold) through the shape such that DNA strands known as "staples" would hybridize to it to help the overall structure maintain its shape.

Others later used a similar approach to create complex three-dimensional DNA structures. However, all of these efforts required complicated manual design to route the scaffold through the entire structure and to generate the sequences of the staple strands. In 2016, Bathe and his colleagues developed a way to automate the process of generating a 3-D polyhedral DNA structure, and in this new study, they set out to automate the design of arbitrary 2-D DNA structures.

To achieve that, they developed a new mathematical approach to the process of routing the single-stranded scaffold through the entire structure to form the correct shape. The resulting computer program can take any free-form drawing and translate it into the DNA sequence to create that shape and into the sequences for the staple strands.

The shape can be sketched in any computer drawing program and then converted into a computer-aided design (CAD) file, which is fed into the DNA design program. "Once you have that file, everything's automatic, much like printing, but here the ink is DNA," Bathe says.

After the sequences are generated, the user can order them to easily fabricate the specified shape. In this paper, the researchers created shapes in which all of the edges consist of two duplexes of DNA, but they also have a working program that can utilize six duplexes per edge, which are more rigid. The corresponding software tool for 3-D polyhedra, called TALOS, is available online and will be published soon in the journal ACS Nano. The shapes, which range from 10 to 100 nanometers in size, can remain stable for weeks or months, suspended in a buffer solution.

"The fact that we can design and fabricate these in a very simple way helps to solve a major bottleneck in our field," Bathe says. "Now the field can transition toward much broader groups of people in industry and academia being able to functionalize DNA structures and deploy them for diverse applications."

Nanoscale patterns

Because the researchers have such precise control over the structure of the synthetic DNA particles, they can attach a variety of other molecules at specific locations. This could be useful for templating antigens in nanoscale patterns to shed light on how immune cells recognize and are activated by specific arrangements of antigens found on viruses and bacteria.

"How nanoscale patterns of antigens are recognized by immune cells is a very poorly understood area of immunology," Bathe says. "Attaching antigens to structured DNA surfaces to display them in organized patterns is a powerful way to probe that biology."

Another key application is designing light-harvesting circuits that mimic the photosynthetic complexes found in plants. To achieve that, the researchers are attaching light-sensitive dyes known as chromophores to DNA scaffolds. In addition to harvesting light, such circuits could also be used to perform quantum sensing and rudimentary computations. If successful, these would be the first quantum computing circuits that can operate at room temperature, Bathe says.

###

Bathe and three other MIT faculty members -- Gabriela Schlau-Cohen, Adam Willard, and Dirk Englund -- recently received a National Science Foundation grant to pursue this quantum sensing and computing project.

Other possible applications for the DNA structures include using them to help organize macromolecular protein assemblies found in cells, so that they can be more easily imaged with high-resolution cryo-electron-microscopy. MIT's new MIT.nano facility has two such microscopes, which can be used to reveal the fine details of tiny structures.

The research was funded by the National Science Foundation, the Office of Naval Research, the Army Research Office, and the National Institute of Allergy and Infectious Disease.

####

For more information, please click here

Contacts:
Abby Abazorius

617-253-2709

Copyright © Massachusetts Institute of Technology

If you have a comment, please Contact us.

Issuers of news releases, not 7th Wave, Inc. or Nanotechnology Now, are solely responsible for the accuracy of the content.

Bookmark:
Delicious Digg Newsvine Google Yahoo Reddit Magnoliacom Furl Facebook

Related News Press

News and information

INRS and ELI deepen strategic partnership to train the next generation in laser science:PhD students will benefit from international mobility and privileged access to cutting-edge infrastructure June 6th, 2025

Electrifying results shed light on graphene foam as a potential material for lab grown cartilage June 6th, 2025

Quantum computers simulate fundamental physics: shedding light on the building blocks of nature June 6th, 2025

A 1960s idea inspires NBI researchers to study hitherto inaccessible quantum states June 6th, 2025

Imaging

New material to make next generation of electronics faster and more efficient With the increase of new technology and artificial intelligence, the demand for efficient and powerful semiconductors continues to grow November 8th, 2024

Turning up the signal November 8th, 2024

New discovery aims to improve the design of microelectronic devices September 13th, 2024

Quantum researchers cause controlled ‘wobble’ in the nucleus of a single atom September 13th, 2024

3D & 4D printing/Additive-manufacturing

Presenting: Ultrasound-based printing of 3D materials—potentially inside the body December 8th, 2023

Fiber sensing scientists invent 3D printed fiber microprobe for measuring in vivo biomechanical properties of tissue and even single cell February 10th, 2023

3D-printed decoder, AI-enabled image compression could enable higher-res displays December 9th, 2022

Researchers design new inks for 3D-printable wearable bioelectronics: Potential uses include printing electronic tattoos for medical tracking applications August 19th, 2022

University of Houston research allows for 3D printing of 'organic electronics' Micro-scale organic electronics for use in bioelectronics via multiphoton 3D printers June 24th, 2022

Software

Visualizing nanoscale structures in real time: Open-source software enables researchers to see materials in 3D while they're still on the electron microscope August 19th, 2022

Luisier wins SNSF Advanced Grant to develop simulation tools for nanoscale devices July 8th, 2022

CEA and Spectronite Develop Software Radio For Spectrally Efficient Backhaul Solutions: Adapted for Spectronite’s X-Series Modem for 5G Systems, the Technology Enables Carrier Aggregation that Provides Radio Links with 10Gb/s Capacity March 4th, 2022

Govt.-Legislation/Regulation/Funding/Policy

INRS and ELI deepen strategic partnership to train the next generation in laser science:PhD students will benefit from international mobility and privileged access to cutting-edge infrastructure June 6th, 2025

Electrifying results shed light on graphene foam as a potential material for lab grown cartilage June 6th, 2025

Institute for Nanoscience hosts annual proposal planning meeting May 16th, 2025

Rice researchers harness gravity to create low-cost device for rapid cell analysis February 28th, 2025

Possible Futures

Ben-Gurion University of the Negev researchers several steps closer to harnessing patient's own T-cells to fight off cancer June 6th, 2025

Researchers unveil a groundbreaking clay-based solution to capture carbon dioxide and combat climate change June 6th, 2025

Cambridge chemists discover simple way to build bigger molecules – one carbon at a time June 6th, 2025

A 1960s idea inspires NBI researchers to study hitherto inaccessible quantum states June 6th, 2025

Nanomedicine

Ben-Gurion University of the Negev researchers several steps closer to harnessing patient's own T-cells to fight off cancer June 6th, 2025

Cambridge chemists discover simple way to build bigger molecules – one carbon at a time June 6th, 2025

Electrifying results shed light on graphene foam as a potential material for lab grown cartilage June 6th, 2025

Self-propelled protein-based nanomotors for enhanced cancer therapy by inducing ferroptosis June 6th, 2025

Quantum Computing

Quantum computers simulate fundamental physics: shedding light on the building blocks of nature June 6th, 2025

Magnetism in new exotic material opens the way for robust quantum computers June 4th, 2025

A new study provides insights into cleaning up noise in quantum entanglement:When it comes to purifying quantum entanglement, new theoretical work highlights the importance of tailoring noise-minimizing solutions to specific quantum systems May 16th, 2025

Programmable electron-induced color router array May 14th, 2025

Discoveries

Researchers unveil a groundbreaking clay-based solution to capture carbon dioxide and combat climate change June 6th, 2025

Cambridge chemists discover simple way to build bigger molecules – one carbon at a time June 6th, 2025

Electrifying results shed light on graphene foam as a potential material for lab grown cartilage June 6th, 2025

A 1960s idea inspires NBI researchers to study hitherto inaccessible quantum states June 6th, 2025

Announcements

INRS and ELI deepen strategic partnership to train the next generation in laser science:PhD students will benefit from international mobility and privileged access to cutting-edge infrastructure June 6th, 2025

Electrifying results shed light on graphene foam as a potential material for lab grown cartilage June 6th, 2025

Quantum computers simulate fundamental physics: shedding light on the building blocks of nature June 6th, 2025

A 1960s idea inspires NBI researchers to study hitherto inaccessible quantum states June 6th, 2025

Interviews/Book Reviews/Essays/Reports/Podcasts/Journals/White papers/Posters

Cambridge chemists discover simple way to build bigger molecules – one carbon at a time June 6th, 2025

Electrifying results shed light on graphene foam as a potential material for lab grown cartilage June 6th, 2025

Quantum computers simulate fundamental physics: shedding light on the building blocks of nature June 6th, 2025

A 1960s idea inspires NBI researchers to study hitherto inaccessible quantum states June 6th, 2025

Tools

Portable Raman analyzer detects hydrogen leaks from a distance: Device senses tiny concentration changes of hydrogen in ambient air, offering a dependable way to detect and locate leaks in pipelines and industrial systems April 25th, 2025

Rice researchers harness gravity to create low-cost device for rapid cell analysis February 28th, 2025

New 2D multifractal tools delve into Pollock's expressionism January 17th, 2025

New material to make next generation of electronics faster and more efficient With the increase of new technology and artificial intelligence, the demand for efficient and powerful semiconductors continues to grow November 8th, 2024

Military

Quantum engineers ‘squeeze’ laser frequency combs to make more sensitive gas sensors January 17th, 2025

Chainmail-like material could be the future of armor: First 2D mechanically interlocked polymer exhibits exceptional flexibility and strength January 17th, 2025

Single atoms show their true color July 5th, 2024

NRL charters Navy’s quantum inertial navigation path to reduce drift April 5th, 2024

Nanobiotechnology

Ben-Gurion University of the Negev researchers several steps closer to harnessing patient's own T-cells to fight off cancer June 6th, 2025

Electrifying results shed light on graphene foam as a potential material for lab grown cartilage June 6th, 2025

Self-propelled protein-based nanomotors for enhanced cancer therapy by inducing ferroptosis June 6th, 2025

Low-cost formulation reduces dose and increases efficacy of drug against worms: Praziquantel, usually administered in large tablets, is the only anthelmintic available on the market. New form of presentation uses nanotechnology and facilitates use by children and pets May 16th, 2025

Research partnerships

INRS and ELI deepen strategic partnership to train the next generation in laser science:PhD students will benefit from international mobility and privileged access to cutting-edge infrastructure June 6th, 2025

Superconductors: Amazingly orderly disorder: A surprising effect was discovered through a collaborative effort by researchers from TU Wien and institutions in Croatia, France, Poland, Singapore, Switzerland, and the US during the investigation of a special material: the atoms are May 14th, 2025

HKU physicists uncover hidden order in the quantum world through deconfined quantum critical points April 25th, 2025

SMART researchers pioneer first-of-its-kind nanosensor for real-time iron detection in plants February 28th, 2025

NanoNews-Digest
The latest news from around the world, FREE




  Premium Products
NanoNews-Custom
Only the news you want to read!
 Learn More
NanoStrategies
Full-service, expert consulting
 Learn More











ASP
Nanotechnology Now Featured Books




NNN

The Hunger Project