DNA nanotubes self-assemble into molecular bridges between cells

In a microscopic feat that resembled a high-wire circus act, Johns Hopkins researchers have coaxed DNA nanotubes to assemble themselves into bridge-like structures arched between two molecular landmarks on the surface of a lab dish. This self-assembling bridge process, which may someday be used to connect electronic medical devices to living cells, was reported by the team recently in the journal Nature Nanotechnology.

Assistant Prof. Rebecca Schulman, left, and postdoctoral fellow Abdul Mohammed used this single-molecule fluorescence microscope to track the nanotube bridge formation process. Photo by Will Kirk/Johns Hopkins University.

Assistant Prof. Rebecca Schulman, left, and postdoctoral fellow Abdul Mohammed used this single-molecule fluorescence microscope to track the nanotube bridge formation process. Photo by Will Kirk/Johns Hopkins University.

The ability to assemble these bridges, the researchers say, suggests a new way to build medical devices that use wires, channels or other devices that could “plug in” to molecules on a cell’s surface. Such technologies could be used to understand nerve cell communication or to deliver therapeutics with unprecedented precision. Molecular bridge-building, the researchers said, is also a step toward building networked devices and “cities” at the nanoscale, enabling new components of a machine or factory to communicate with one another.

To describe this process, senior author Rebecca Schulman, an assistant professor of chemical and biomolecular engineering in the Whiting School of Engineering and an INBT affiliated faculty member, referred to a death-defying stunt shown in the movie “Man on Wire.” The film depicted Philippe Petit’s 1974 high-wire walk between the World Trade Center’s Twin Towers.

Schulman and postdoctoral fellow Abdul Mohammed used a single-molecule fluorescence microscope to track the nanotube bridge formation process. These building blocks attached themselves to separate molecular anchor posts, representing where the connecting bridge would begin and end. The segments formed two nanotube chains, each one extending away from its anchor post. Then, like spaghetti in a pot of boiling water, the lengthening nanotube chains wriggled about, exploring their surroundings in a random fashion. Eventually, this movement allowed the ends of the two separate nanotube strands to make contact with one another and snap together to form a single connecting bridge span. This process can be seen in this video, linked here. Read the entire Johns Hopkins press release here.




Nanodevices built with DNA origami

Did you know DNA could be used for origami?

Not actual DNA origami.

Not actual DNA origami.

The precise control and organization of nanoscale devices has shown a great potential for ultimately creating “nano-devices” that can perform nanoscale biological measurements, deliver medicine in vivo, among many other applications. A recent article from Carlos E. Castro and colleauges from The Ohio State University demonstrates the use of DNA origami with programmable complex and reversible 1D, 2D and 3D motions.

By varying the DNA origami design, they were able to observe different mechanisms for the DNA origami’s 3D motion such as the crank-slider and four bar mechanism. The research team mainly utilized transmission electron microscopy (TEM) to follow the morphology changes as the origami moves.

DNAUsing a fluorescence quenching assay (attaching a fluorescent label on one arm and a quencher on the other), they have characterized the timescale of DNA origami motion. Overall, their group sees this technology as a “foundation for developing and characterizing a library of tunable DNA origami kinematic joints and using them in more complex controllable mechanisms similar to macroscopic machines, such as manipulators to control chemical reactions, transport biomolecules, or assemble nanoscale components in real time.”


Shown below are some of the videos showing the motions of the DNA origami that they have reported:

About the author: Herdeline Ann M. Ardoña is a third year graduate student at Johns Hopkins University Department of Chemistry, currently working in chemistry professor J.D. Tovar’s lab and co-advised by professor Hai-Quan Mao, in materials science and engineering.

Reference: Programmable motion of DNA origami mechanisms. (Proc. Natl. Acad. Sci. U.S.A., 2015, 112, 713-718)

For all press inquiries regarding INBT, its faculty and programs, contact Mary Spiro, mspiro@jhu.edu or 410-516-4802.

REU student profile: Rebecca Majewski

DNA, the genetic sequence that tells cells what proteins to manufacture, typically resides inside the nucleus of a cell, but not always. Rebecca Majewski is studying the uptake of DNA into cell nuclei using a different polymer chains. Rebecca is a rising senior in BioMolecular Engineering from the Milwaukee School of Engineering and is working as a summer intern in the Johns Hopkins Institute for Nanobiotechnology’s REU program.

“We are interested in how much of the DNA with the polyplex can get into the nucleus,” she said, but explains that DNA associated outside of the nucleus can cause false higher measurements.

Rebecca Majewski. Photo by Mary Spiro

Rebecca Majewski. Photo by Mary Spiro

Rebecca is washing the cells with the nuclei to get rid of DNA outside the nucleus and then comparing the measurement of uptake of the DNA by the cell versus the measurement of the uptake of DNA by the nucleus.

“We are interested in what DNA gets inserted into the nucleus because that is what is ultimately expressed. It is important to find out how much makes it to the final destination and then is expressed. The goal of this work is to test different polymer chains to see which one actually does the better job of getting the DNA into the nucleus,” she said.

Rebecca works alongside PhD students and postdoctoral fellows in the biomedical engineering lab of Jordan Green lab at the Johns Hopkins School of Medicine. She says she highly values the opportunity for a research experience through INBT’s REU because her undergraduate institution does not train graduate students.

For all press inquiries regarding INBT, its faculty and programs, contact Mary Spiro, mspiro@jhu.edu or 410-516-4802.

Fraley nets $500K Burroughs Wellcome Fund award for microfluidics work

Stephanie Fraley (Photo: Homewood Photography)

Stephanie Fraley (Photo: Homewood Photography)

A Johns Hopkins research fellow who is developing novel approaches to quickly identify bacterial DNA and human microRNA has won the prestigious $500,000 Burroughs Wellcome Fund (BWF) Career Award at the Scientific Interfaces. The prize, distributed over the next five years, helps transition newly minted PhDs from postdoctoral work into their first faculty positions.

Stephanie Fraley is a postdoctoral fellow working with Samuel Yang, MD, in Emergency Medicine/Infectious Disease at the Johns Hopkins School of Medicine and Jeff Wang, PhD, in Biomedical Engineering with appointments in the Whiting School of Engineering and the medical school. The goal of her work is to develop engineering technologies that can diagnose and guide treatment of sepsis, a leading cause of death worldwide, while simultaneously leading to improved understanding of how human cells and bacterial cells interact.

“Sepsis is an out of control immune response to infection,” Fraley said. “We are developing tools that are single molecule sensitive and can rapidly sort and detect bacterial and host response markers associated with sepsis. However, our devices are universal in that they can be applied to many other diseases.”

Fraley is using lab-on-chip technology, also known as microfluidics, to overcome the challenges of identifying the specific genetic material of bacteria and immune cells. Her technology aims to sort the genetic material down to the level of individual sequences so that each can be quantified with single molecule sensitivity.

“Bacterial DNA is on everything and contamination is everywhere, so trying to find the ones associated with sepsis is like the proverbial search for the needle in the haystack,” Fraley said. “With microfluidics, we can separate out all the bacterial DNA, so instead of a needle in a haystack, we have just the needles.”

Another advantage to Fraley’s novel technology is that it will assess all the diverse bacterial DNA present in a sample, without presuming which genetic material is important. “Bacteria are constantly evolving and becoming drug resistant,” she said. “With this technology, we can see all the bacterial DNA that is present individually and not just the strains we THINK we need to look for.”

Fraley’s award will follow her wherever her career takes her. The first two years of the prize fund postdoctoral training and that last three years help launch her professional career in academia. During the application process, she had to make a short presentation on her proposal to BWF’s panel of experts. “It was like the television show ‘Shark Tank’ but for scientists,” she laughs. “ The panelists gave me many helpful suggestions on my idea.”

Fraley earned her bachelor’s degree in chemical engineering from the University of Tennessee at Chattanooga and her doctorate in chemical and biomolecular engineering with Denis Wirtz, professor and director of Johns Hopkins Physical Sciences-Oncology Center. Wirtz is associate director for the Institute for NanoBioTechnology and Yang and Wang also are INBT affiliated faculty members.

BWF’s Career Awards at the Scientific Interface provides funding to bridge advanced postdoctoral training and the first three years of faculty service. These awards are intended to foster the early career development of researchers who have transitioned or are transitioning from undergraduate and/or graduate work in the physical/mathematical/computational sciences or engineering into postdoctoral work in the biological sciences, and who are dedicated to pursuing a career in academic research. These awards are open to U.S. and Canadian citizens or permanent residents as well as to U.S. temporary residents.

Shaping up nanoparticles for DNA delivery to cancer cells

Hai-Quan Mao, 2012 Johns Hopkins Nano-Bio Symposium. Photo by Mary Spiro

To treat cancer, scientists and clinicians have to kill cancer cells while minimally harming the healthy tissues surrounding them. However, because cancer cells are derived from healthy cells, targeting only the cancer cells is exceedingly difficult. According to Dr. Hai-Quan Mao of the Johns Hopkins University Department of Materials Science and Engineering, the “key challenge is between point of delivery and point of target tissue” when it comes to delivering cancer therapeutics. Dr. Mao spoke about the difficulties of specifically delivering drugs or genetic material to cancer cells at the 2012 Johns Hopkins University Nano-Bio Symposium. Scientists had originally thought they could create a “magic bullet” to patrol for cancer cells in the body. However, this has not been feasible; only 5 percent of injected nanoparticles reach the targeted tumor using current delivery techniques. Simply put, scientists need to figure out how to inject a treatment into the body and then selectively direct that treatment to cancer cells if the treatments are to work to their full potential.

With this in mind, Dr. Mao and his research team aim to optimize nanoparticle design to improve delivery to tumor cells by making the nanoparticles more stable in the body’s circulatory system. Mao’s group uses custom polymers and DNA scaffolds to create nanoparticles. The DNA serves dual purposes, as a building block for the particles and as a signal for cancer cells to express certain genes (for example, cell suicide genes). By tuning the polarity of the solvent used to fabricate the nanoparticles, the group can control nanoparticle shape, forming spheres, ellipsoids, or long “worms” while leaving everything else about the nanoparticles constant. This allows them to test the effects of nanoparticle size on gene delivery. Interestingly, “worms” appear more stable in the blood stream of mice and are therefore better able to deliver targeted DNA. Studies of this type will allow intelligent nanoparticle design by illuminating the key aspects for efficient tumor targeting.

Currently, Dr. Mao’s group is extending their fabrication methods to deliver other payloads to cancer cells. Small interfering ribonucleic acid (siRNA), which can suppress expression of certain genes, can also be incorporated into nanoparticles. Finally, Mao noted that the “worm”-shaped nanoparticles created by the group look like naturally occurring virus particles, including the Ebola and Marburg viruses. In the future, the group hopes to use their novel polymers and fabrication techniques to see if shape controls virus targeting to specific tissues in the body. This work could have important applications in virus treatment.

Story by Colin Paul, a Ph.D. student in the Department of Chemical and Biomolecular Engineering at Johns Hopkins with interests in microfabrication and cancer metastasis.