Tag Archives: Hao Yan

A twist in my DNA

Professor Hao Yan’s team at Arizona State University (ASU) has created some new 2D and 3D DNA objects according to a Mar. 21, 2013 news release on EurekAlert,

In their latest twist to the technology, Yan’s team made new 2-D and 3-D objects that look like wire-frame art of spheres as well as molecular tweezers, scissors, a screw, hand fan, and even a spider web.

The Yan lab, which includes ASU Biodesign Institute colleagues Dongran Han, Suchetan Pal, Shuoxing Jiang, Jeanette Nangreave and assistant professor Yan Liu, published their results in the March 22 issue of Science.

Here’s where the twist comes in,

The twist in their ‘bottom up,’ molecular Lego design strategy focuses on a DNA structure called a Holliday junction. In nature, this cross-shaped, double-stacked DNA structure is like the 4-way traffic stop of genetics — where 2 separate DNA helices temporality meet to exchange genetic information. The Holliday junction is the crossroads responsible for the diversity of life on Earth, and ensures that children are given a unique shuffling of traits from a mother and father’s DNA.

In nature, the Holliday junction twists the double-stacked strands of DNA at an angle of about 60-degrees, which is perfect for swapping genes but sometimes frustrating for DNA nanotechnology scientists, because it limits the design rules of their structures.

“In principal, you can use the scaffold to connect multiple layers horizontally,” [which many research teams have utilized since the development of DNA origami by Cal Tech’s Paul Rothemund in 2006]. However, when you go in the vertical direction, the polarity of DNA prevents you from making multiple layers,” said Yan. “What we needed to do is rotate the angle and force it to connect.”

Making the new structures that Yan envisioned required re-engineering the Holliday junction by flipping and rotating around the junction point about half a clock face, or 150 degrees. Such a feat has not been considered in existing designs.

“The initial idea was the hardest part,” said Yan. “Your mind doesn’t always see the possibilities so you forget about it. We had to break the conceptual barrier that this could happen.”

In the new study, by varying the length of the DNA between each Holliday junction, they could force the geometry at the Holliday junctions into an unconventional rearrangement, making the junctions more flexible to build for the first time in the vertical dimension. Yan calls the backyard barbeque grill-shaped structure a DNA Gridiron.

“We were amazed that it worked!” said Yan. “Once we saw that it actually worked, it was relatively easy to implement new designs. Now it seems easy in hindsight. If your mindset is limited by the conventional rules, it’s really hard to take the next step. Once you take that step, it becomes so obvious.”

The DNA Gridiron designs are programmed into a viral DNA, where a spaghetti-shaped single strand of DNA is spit out and folded together with the help of small ‘staple’ strands of DNA that help mold the final DNA structure. In a test tube, the mixture is heated, then rapidly cooled, and everything self-assembles and molds into the final shape once cooled. Next, using sophisticated AFM and TEM imaging technology, they are able to examine the shapes and sizes of the final products and determine that they had formed correctly.

This approach has allowed them to build multilayered, 3-D structures and curved objects for new applications.

In addition to the EurekAlert version, you can find the full text, images, and video about the team’s paper in the Mar. 21, 2013 news item on ScienceDaily (a citation and link to the team’s paper is also included) or you can read the original Mar. 21, 2013 ASU news release. (Hao Yan’s work was last mentioned here in an Aug. 7, 2012 post.)

All of this talk of twists reminded me of a song by Tanita Tikaram, Twist in My Sobriety. I found this video of an acoustic performance (two guitars and a bass [the musical instrument not the fish]) which is even more sultry than original hit version,

Happy weekend!

Precision delivery of synthetic vaccines using DNA scaffolds

When reading about nanomedicine, one is struck by the focus on precision especially with the regard to drug delivery and other therapeutics. There’s almost always a reference to repairing or destroying  malfunctioning/diseased tissue or cells to the exclusion of the  healthy tissues/cells.

The latest work from Arizona State University has raised a great deal of interest not just with this latest announcement but also some previous work. From the July 27, 2012 posting by Dexter Johnson on his Nanoclast blog on the IEEE [Institute for Electrical and Electronics Engineers],

About 18 months ago, the nanotech trade press was buzzing with the work of Hongbin Yu and Hao Yan, both from Arizona State University (ASU), when they developed a method that used DNA origami as a scaffold. When the DNA scaffolding was combined with “nano islands” made from gold, it enabled the manufacturing of smaller electronic memory devices.

Now [July 2012] Yan has joined with Yung Chang, a biodesign immunologist also from ASU, to use three-dimensional DNA structures as a scaffold on which they piggybacked synthetic vaccine complexes to make the delivery of the vaccines safer and more effective.

There are more details in the July 25, 2012 news item on ScienceDaily,

DNA nanotechnology, where the molecule of life can be assembled into 2-D and 3-D shapes, has an advantage of being a programmable system that can precisely organize molecules to mimic the actions of natural molecules in the body.

“We wanted to test several different sizes and shapes of DNA nanostructures and attach molecules to them to see if they could trigger an immune response,” said Yan, the Milton D. Glick Distinguished Chair in the Department of Chemistry and Biochemistry and researcher in Biodesign’s Center for Single Molecule Biophysics. With their biomimicry approach, the vaccine complexes they tested closely resembled natural viral particles in size and shape.

As proof of concept, they tethered onto separate pyramid-shaped and branched DNA structures a model immune stimulating protein called streptavidin (STV) and immune response boosting compound called an adjuvant (CpG oligo-deoxynucletides) to make their synthetic vaccine complexes.

First, the group had to prove that the target cells could gobble the nanostructures up. By attaching a light-emitting tracer molecule to the nanostructures, they found the nanostructures residing comfortably within the appropriate compartment of the cells and stable for several hours — -long enough to set in motion an immune cascade.

Next, in a mouse challenge, they targeted the delivery of their vaccine cargo to cells that are first responders in initiating an effective immune response, coordinating interaction of important components, such as: antigen presenting cells, including macrophages, dendritic cells and B cells. After the cargo is internalized in the cell, they are processed and “displayed” on the cell surface to T cells, white blood cells that play a central role in triggering a protective immune response. The T cells, in turn, assist B cells with producing antibodies against a target antigen.

To properly test all variables, they injected: 1) the full vaccine complex 2) STV (antigen) alone 3) the CpG (adjuvant) mixed with STV.

Over the course of 70 days, the group found that mice immunized with the full vaccine complex developed a more robust immune response up to 9-fold higher than the CpG mixed with STV. The pyramid (tetrahedral) shaped structure generated the greatest immune response. Not only was immune response to the vaccine complex specific and effective, but also safe, as the research team showed, using two independent methods, that no immune response triggered from introducing the DNA platform alone.

Here’s a little background information that may help to explain why researchers are looking for new ways to deliver vaccines, from the July 30, 2012 essay by Carl Walkey (University of Toronto) for the Nanowerk Spotlight series,

Traditionally, vaccines were formulated using attenuated or inactivated versions of the microbes they were intended to treat. However, inactivated microbes do not often elicit a strong enough immune response to induce antibody production. Attenuated viruses, on the other hand, may revert back to an active form within the body. There are also inherent difficulties in ensuring batch-to-batch consistency of the formulations. These shortcomings have led to a progressive shift towards the development of synthetic vaccines.

Synthetic vaccines can combine a portion of the target microbe, known as an ‘antigen’ together with an adjuvant that stimulates the immune system. They are more reproducible and have the potential to induce consistent and tailored immune responses. Yet, delivering both the adjuvant and antigen together to the appropriate immune cells is challenging.

While the developments at Arizona State University are exciting, it’s still a long way before there will be any treatments, from the Walkey essay,

Although the results from this study are encouraging, they represent only a step towards the ultimate goal of making DNA nanostructure-based vaccines a clinical reality. There are still many challenges.

“A big challenge from an immunological point of view is the stability of the particles” explains Chang. The body is equipped with an array of ‘nucleases’ – enzymes designed to degrade extracellular DNA. Nucleases may degrade the nanostructures before they reach their target.”

“I think safety will also be a major hurdle for the eventual clinical translation” he continues. “That will be the major concern people will have. It may cause an adverse effect or an auto-immune response. Those are the things we need to test thoroughly before moving into clinical trials.”

The researchers believe that the simplicity, robustness, and relative economy of the DNA nanostructures will be key advantages driving further development.

“DNA nanostructures have the advantage of self-assembling. You can produce them relatively simply with good reproducibility” says Yan. “With so many of the other nanoparticle systems, you have to synthesize different components chemically. This makes them difficult to scale-up.”

The July 24, 2012 news release from Arizona State University offers this comment on the potential,

Overall, though the field of DNA is still young, the research is advancing at a breakneck pace toward translational science that is making an impact on health care, electronics, and other applications.

While Chang and Yan agree that there is still much room to explore the manipulation and optimization of the nanotechnology, it also holds great promise.  “With this proof of concept, the range of antigens that we could use for synthetic vaccine develop is really unlimited,” said Chang.

I like the idea of more precise delivery of drugs and other therapies. Intuitively, it just makes sense that you want to focus on the diseased or destroyed tissues while preserving as much of the healthy ones as possible but I keep wondering if there might be a more subtle disease process at work. The problem may not lie in the diseased cells or tissues themselves but may originate in an entirely different part of the body. If you ever watch someone who’s walking awkwardly, you may notice the problem isn’t the foot placement; the real problem is in the hips. You are in fact examining the symptom rather than the problem. In which case, more precise application of various therapies will alleviate symptoms for a time while the disease process carries on.