Tag Archives: Ishtiaq Saaem

World’s largest DNA origami: 200nm x 300nm

Leave a reply

If the 200nm x 300nm size is the world’s largest DNA origami, what is the standard size?  Before you get the answer to that question, here’s more about the world’s largest from a Sept. 11, 2014 news item on Nanowerk,

Researchers from North Carolina State University, Duke University and the University of Copenhagen have created the world’s largest DNA origami, which are nanoscale constructions with applications ranging from biomedical research to nanoelectronics.

“These origami can be customized for use in everything from studying cell behavior to creating templates for the nanofabrication of electronic components,” says Dr. Thom LaBean, an associate professor of materials science and engineering at NC State and senior author of a paper describing the work …

A Sept. ?, 2014 North Carolina State University (NCSU) news release, which originated the news item, describes DNA origami and the process for creating it,

DNA origami are self-assembling biochemical structures that are made up of two types of DNA. To make DNA origami, researchers begin with a biologically derived strand of DNA called the scaffold strand. The researchers then design customized synthetic strands of DNA, called staple strands. Each staple strand is made up of a specific sequence of bases (adenine, cytosine, thaline and guanine – the building blocks of DNA), which is designed to pair with specific subsequences on the scaffold strand.

The staple strands are introduced into a solution containing the scaffold strand, and the solution is then heated and cooled. During this process, each staple strand attaches to specific sections of the scaffold strand, pulling those sections together and folding the scaffold strand into a specific shape.

Here’s the answer to the question I asked earlier about the standard size for DNA origami and a description for how the researchers approached the problem of making a bigger piece (from the news release,

The standard for DNA origami has long been limited to a scaffold strand that is made up of 7,249 bases, creating structures that measure roughly 70 nanometers (nm) by 90 nm, though the shapes may vary.

However, the research team led by LaBean has now created DNA origami consisting of 51,466 bases, measuring approximately 200 nm by 300 nm.

“We had to do two things to make this viable,” says Dr. Alexandria Marchi, lead author of the paper and a postdoctoral researcher at Duke. “First we had to develop a custom scaffold strand that contained 51 kilobases. We did that with the help of molecular biologist Stanley Brown at the University of Copenhagen.

“Second, in order to make this economically feasible, we had to find a cost-effective way of synthesizing staple strands – because we went from needing 220 staple strands to needing more than 1,600,” Marchi says.

The researchers did this by using what is essentially a converted inkjet printer to synthesize DNA directly onto a plastic chip.

“The technique we used not only creates large DNA origami, but has a fairly uniform output,” LaBean says. “More than 90 percent of the origami are self-assembling properly.”

For the curious, a link to and a citation for the paper,

Toward Larger DNA Origami by Alexandria N. Marchi, *Ishtiaq Saaem*, Briana N. Vogen, Stanley Brown, and Thomas H. LaBean. Nano Lett., Article ASAP DOI: 10.1021/nl502626s Publication Date (Web): September 1, 2014
Copyright © 2014 American Chemical Society

This paper is behind a paywall.

*May 10, 2021 According to a comment on my ‘About’ page, Dr. Saaem has pled guilty to obstruction of justice in a case concerning ricin (a deadly toxin). You can read a full account of Saaem’s pleading in an April 13, 2021 US Attorney’s Office, District of Massachusetts release,

…

According to court records, Saaem held a Ph.D. in biomedical engineering, resided in Massachusetts and worked as the director of advanced research at a biotechnology firm based in Massachusetts. Saaem became interested in acquiring ricin from castor beans as well as convallatoxin, a poison found in lily of the valley plants, after watching “Breaking Bad,” a popular television show. Saaem ordered online 100 packets of castor beans, each containing eight seeds. Saaem falsely told law enforcement agents that he purchased castor beans for planting at his apartment for decoration and that he had accidentally purchased 100 packets instead of one. After he spoke to agents, Saaem researched tasteless poisons that could be made at home.

The charge of obstruction of justice provides for a sentence of up to 20 years in prison, three years of supervised release and a fine of up to $250,000. Sentences are imposed by a federal district court judge based upon the Sentencing Guidelines and other statutory factors.

 

According to news reports, Dr. Saaem will be sentenced in August 2021.

Coatings that shake off bacteria and biological photocopying

Leave a reply

The American Vacuum Society (AVS) is holding its 58th International Symposium and Exhibition from Oct. 30 – Nov. 4, 2011 in Nashville, Tennessee. Presentations are not focused on vacuuming (hoovering) floors but rather on something called vacuum science and they span from a presentation on bacteria and coatings to another on photocopying DNA to more.

From the Oct. 31, 2011 news item on Nanowerk,

“Sea water is a very aggressive biological system,” says Gabriel Lopez, whose lab at Duke University studies the interface of marine bacterial films with submerged surfaces. While the teeming abundance of ocean life makes coral reefs and tide pools attractive tourist destinations, for ships whose hulls become covered with slime, all this life can, quite literally, be a big drag. On just one class of U.S. Navy destroyer, biological build-up is estimated to cost more than $50 million a year, mostly in extra fuel, according to a 2010 study performed by researchers from the U.S. Naval Academy and Naval Surface Warfare Center in Maryland. Marine biofouling can also disrupt the operation of ocean sensors, heat-exchangers that suck in water to cool mechanical systems, and other underwater equipment.

I think rather than describing sea water as ‘aggressive’  which suggests intent, I’d use ‘active’ as Lopez does later in another context (excerpted from the news item),

Lopez and his group focus on a class of materials called stimuli-responsive surfaces. As the name implies, the materials will alter their physical or chemical properties in response to a stimulus, such as a temperature change. The coatings being tested in Lopez’s lab wrinkle on the micro- or nano-scale, shaking off slimy colonies of marine bacteria in a manner similar to how a horse might twitch its skin to shoo away flies. The researchers also consider how a stimulus might alter the chemical properties of a surface in a way that could decrease a marine organism’s ability to stick.

At the AVS Symposium, held Oct. 30 – Nov. 4 in Nashville, Tenn., Lopez will present results from experiments on two different types of stimuli-responsive surfaces: one that changes its texture in response to temperature and the other in response to an applied voltage. The voltage-responsive surfaces are being developed in collaboration with the laboratory of Xuanhe Zhao, also a Duke researcher, who found that insulating cables can fail if they deform under voltages. “Surprisingly, the same failure mechanism can be made useful in deforming surfaces of coatings and detaching biofouling,” Zhao said.

“The idea of an active surface is inspired by nature,” adds Lopez, who remembers being intrigued by the question of how a sea anemone’s waving tentacles are able to clean themselves. [emphasis mine] Other biological surfaces, such as shark skin, have already been copied by engineers seeking to learn from nature’s own successful anti-fouling systems.

(I did profile some biomimicry work being done with shark skin in my comments on part 4 of the Making Stuff programmes broadcast as part of the Nova series on PBS (US Public Broadcasting Stations) in my Feb. 10, 2011 posting.)

This next presentation is in the area of synthetic biology. From the Oct. 31, 2011 news item (DNA origami from inkjet synthesis produced strands) on Nanowerk,

In the emerging field of synthetic biology, engineers use biological building blocks, such as snippets of DNA, to construct novel technologies. One of the key challenges in the field is finding a way to quickly and economically synthesize the desired DNA strands. Now scientists from Duke University have fabricated a reusable DNA chip that may help address this problem by acting as a template from which multiple batches of DNA building blocks can be photocopied. The researchers have used the device to create strands of DNA which they then folded into unique nanoscale structures.

…

“We found that we had an “immortal” DNA chip in our hands,” says Ishtiaq Saaem, a biomedical engineering researcher at Duke and member of the team. [emphasis mine] “Essentially, we were able to do the biological copying process to release material off the chip tens of times. [emphasis mine] The process seems to work even using a chip that we made, used, stored in -20C for a while, and brought out and used again.”

After releasing the DNA from the chip, the team “cooked” it together with a piece of long viral DNA. “In the cooking process, the viral DNA is stapled into a desired shape by the smaller chip-derived DNA,” explains Saaem. One of the team’s first examples of DNA origami was a rectangle shape with a triangle attached on one side, which the researchers dubbed a “nano-house.” The structure could be used to spatially orient organic and inorganic materials, serve as a scaffold for drug delivery, or act as a nanoscale ruler, Saaem says.

I’m not very comfortable with the notion of an “immortal DNA chip” but then I have many reservations about synthetic biology. Still, I think it’s important to pay attention and consider the possibility that my fears about synthetic biology might make as much sense as the fears many had about electricity in the 19th century.