Tag Archives: ASU Biodesign Institute

Electrifying DNA (deoxyribonucleic acid)

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All kinds of things have electrical charges including DNA (deoxyribonucleic acid) according to an April 15, 2015 news item on Azonano,

Electrical charges not only move through wires, they also travel along lengths of DNA, the molecule of life. The property is known as charge transport.

In a new study appearing in the journal Nature Chemistry, authors, Limin Xiang, Julio Palma, Christopher Bruot and others at Arizona State University’s Biodesign Institute, explore the ways in which electrical charges move along DNA bases affixed to a pair of electrodes.

Their work reveals a new mechanism of charge transport that differs from the two recognized patterns in which charge either tunnels or hops along bases of the DNA chain.

An April 13, 2015 Arizona State University (ASU) news release (also on EurekAlert and dated April 14, 2015), which originated the news item, explains why this ‘blue sky’ research may prove important in the future,

Researchers predict that foundational work of this kind will have important implications in the design of a new generation of functional DNA-based electronic devices as well as providing new insights into health risks associated with transport-related damage to DNA.

Oxidative damage is believed to play a role in the initiation and progression of cancer. It is also implicated in neurodegenerative disorders like Alzheimer’s, Huntington’s disease and Parkinson’s disease and a range of other human afflictions.

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An electron’s movements plays an important role in your body’s chemical reactions (from the news release),

The transfer of electrons is often regarded as the simplest form of chemical reaction, but nevertheless plays a critical role in a broad range of life-sustaining processes, including respiration and photosynthesis.

Charge transport can also produce negative effects on living systems, particularly through the process of oxidative stress, which causes damage to DNA and has been invoked in a broad range of diseases.

“When DNA is exposed to UV light, there’s a chance one of the bases– such as guanine–gets oxidized, meaning that it loses an electron,” Tao says. (Guanine is easier to oxidize than the other three bases, cytosine, thymine, and adenine, making it the most important base for charge transport.)

In some cases, the DNA damage is repaired when an electron migrates from another portion of the DNA strand to replace the missing one. DNA repair is a ceaseless, ongoing process, though a gradual loss of repair efficiency over time is one factor in the aging process. Oxidation randomly damages both RNA and DNA, which can interfere with normal cellular metabolism.

Radiation damage is also an issue for semiconductor devices, Tao notes–a factor that must be accounted for when electronics are exposed to high-energy particles like X rays, as in applications designed for outer space.

Researchers like Xiang and Tao hope to better understand charge transport through DNA, and the molecule provides a unique testing ground for observation. The length of a DNA molecule and its sequence of 4 nucleotides A, T, C and G can be readily modified and studies have shown that both alterations have an effect on how electrical charge moves through the molecule.

When the loss of an electron or oxidation occurs in DNA bases, a hole is left in place of the electron. This hole carries a positive charge, which can move along the DNA length under the influence of an electrical or magnetic field, just as an electron would. The movement of these positively charged holes along a stretch of DNA is the focus of the current study.

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The news release goes on to describe charge transport,

Two primary mechanisms of charge transport have been examined in detail in previous research. Over short distances, an electron displays the properties of a wave, permitting it to pass straight through a DNA molecule. This process is a quantum mechanical effect known as tunneling.

Charge transport in DNA (and other molecules) over longer distances involves the process of hopping. When a charge hops from point to point along the DNA segment, it behaves classically and loses its wavelike properties. The electrical resistance is seen to increases exponentially during tunneling behavior and linearly, during hopping.

By attaching electrodes to the two ends of a DNA molecule, the researchers were able to monitor the passage of charge through the molecule, observing something new: “What we found in this particular paper is that there is an intermediate behavior,” Tao says. “It’s not exactly hopping because the electron still displays some of the wave properties.”

Instead, the holes observed in certain sequences of DNA are delocalized, spread over several base pairs. The effect is neither a linear nor exponential increase in electrical resistance but a periodic oscillation. The phenomenon was shown to be highly sequence dependent, with stacked base pairs of guanine-cytosine causing the observed oscillation.

Control experiments where G bases alternated, rather than occurring in a sequential stack, showed a linear increase in resistance with molecular length, in agreement with conventional hopping behavior.

A further property of DNA is also of importance in considering charge transport. The molecule at room temperature is not like a wire in a conventional electronic device, but rather is a highly dynamic structure, that writhes and fluctuates.

The last bit about writhing and fluctuating makes this work sound fascinating and very challenging.

Here’s a link to and a citation for the paper,

Intermediate tunnelling–hopping regime in DNA charge transport by Limin Xiang, Julio L. Palma, Christopher Bruot, Vladimiro Mujica, Mark A. Ratner, & Nongjian Tao. Nature Chemistry 7, 221–226 (2015) doi:10.1038/nchem.2183 Published online 20 February 2015

This paper is behind a paywall.

A twist in my DNA

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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!