Applying Origami Folding Techniques to Strands of DNA to Produce Faster and Cheaper Computer Chips

"Origami", Image by David Wicks

“Origami”, Image by David Wicks

We all learned about the periodic table of elements in high school chemistry class. This involved becoming familiar with the names, symbols and atomic weights of all of the chemical occupants of this display. Today, the only thing I still recall from this academic experience was when the teacher told us on the first day of class that we would soon learn to laugh at the following:

Two hydrogen atoms walk into a bar and the first one says to the other “I’ve lost my electron”. The other one answers “Are you sure?”. The first one says “I’m positive.”

I still find this hilarious but whatever I recall today about learning chemistry would likely get lost at the bottom of a thimble. I know, you are probably thinking “Sew what”.

Facing the Elements

Besides everyone’s all-time favorites like oxygen and hydrogen that love to get mixed up with each other and most of the other 116 elements, another one stands alone as the foundation upon which the modern information age was born and continues to thrive today. Silicon has been used to create integrated circuits, much more commonly known as computer chips.

This has been the case since they were first fabricated in the late 1950’s. It has remained the material of choice including nearly all the chips running every imaginable one of our modern computing and communication devices. Through major advances in design, engineering and fabrication during the last five decades, chip manufacturers have been able to vastly shrink this circuitry and pack millions of components into smaller squares of this remarkable material.

A fundamental principle that has held up and guided the semiconductor industry, under relentlessly rigorous testing during silicon’s enduring run, is Moore’s Law. In its simplest terms, it states that the number of transistors that can be written onto a chip doubles nearly every two years. There have been numerous predictions for many years that the end of Moore’s Law is approaching and that another substrate, other than silicon, will be found in order to continue making chips smaller, faster and cheaper. This has not yet come to pass and may not do so for years to come.

Nonetheless, scientists and developers from a diversity of fields, industries and academia have remained in pursuit of alternative computing materials. This includes elements and compounds to improve or replace silicon’s extensible properties, and other efforts to research and fabricate entirely new computing architectures. One involves exploiting the spin states of electrons in a rapidly growing field called quantum computing (this Wikipedia link provides a detailed and accessible survey of its fundamentals and operations), and another involves using, of all things, DNA as a medium.

The field of DNA computing has actually been around in scientific labs and journals for several decades but has not gained much real traction as a viable alternative ready to produce computing chips for the modern marketplace. Recently though, a new advance was reported in a fascinating article posted on on March 13, 2016, entitled DNA ‘origami’ Could Help Build Faster, Cheaper Computer Chips, provided by the American Chemical Society (no author is credited). I will summarize and annotate it in order to add some more context, and then pose several of my own molecular questions.

Know When to Fold ‘Em

A team of researchers reported that fabricating such chips is possible when DNA is folded and “formed into specific shapes” using a process much like origami, the Japanese art of folding paper into sculptures. They presented their findings at the 251st American Chemical Society Meeting & Exposition held in San Diego, CA during March 13 through 17, 2016. Their paper entitled 3D DNA Origami Templated Nanoscale Device Fabrication, appears listed as number 305 on Page 202 of the linked document.  Their presentation on March 14, 2016, was captured on this 16-minute YouTube video, with Adam T. Woolley, Ph.D. of Brigham Young University as the presenter for the researchers.

According to Dr. Woolley, researchers want to use DNA’s “small size, base-pairing capabilities and ability to self-assemble” in order to produce “nanoscale electronics”. By comparison, silicon chips currently in production contain features 14 nanometers wide, which turn out to be 10 times “the diameter of single-stranded DNA”. Thus, DNA could be used to build chips on a much smaller and efficient scale.

However, the problem with using DNA as a chip-building material is that it is not a good conductor of electrical current. To circumvent this, Dr. Woolley and his team is using “DNA as a scaffold” and then adding other materials to the assembly to create electronics. He is working on this with his colleagues, Robert C. Davis, Ph.D. and John N. Harb, Ph.D, at Brigham Young University. They are drawing upon their prior work on “DNA origami and DNA nanofabrication”.

Know When to Hold ‘Em

To create this new configuration of origami-ed DNA, they begin with a single long strand of it, which is comparable to a “shoelace” insofar as it is “flexible and floppy”. Then they mix this with shorter stand of DNA called “staples” which, in turn, “use base pairing” to gather and cross-link numerous other “specific segments of the long strand” to build an intended shape.

Dr. Woolley’s team is not satisfied with just replicating “two-dimensional circuits”, but rather, 3D circuitry because it can hold many more electronic components. An undergraduate who works with Dr. Woolley named Kenneth Lee, has already build such a “3-D, tube-shaped DNA origami structure”. He has been further experimenting with adding more components including “nano-sized gold particles”. He is planning to add still more nano-items to his creations with the objective of “forming a semiconductor”.

The entire team’s lead objective is to “place such tubes, and other DNA origami structures, at particular sites on the substrate”. As well, they are seeking us use gold nanoparticles to create circuits. The DNA is thus being used as “girders” to create integrated circuits.

Dr. Woolley also pointed to the advantageous cost differential between the two methods of fabrication. While traditional silicon chip fabrication facilities can cost more than $1 billion, exploiting DNA’s self-assembling capabilities “would likely entail much lower startup funding” and yield potentially “huge cost savings”.

My Questions

  • What is the optimal range and variety in design, processing power and software that can elevate DNA chips to their highest uses? Are there only very specific applications or can they be more broadly used in commercial computing, telecom, science, and other fields?
  • Can any of the advances currently being made and widely followed in the media using the CRISPR gene editing technology somehow be applied here to make more economical, extensible and/or specialized DNA chips?
  • Does DNA computing represent enough of a potential market to attract additional researchers, startups, venture capital and academic training to be considered a sustainable technology growth sector?
  • Because of the potentially lower startup and investment costs, does DNA chip development lend itself to smaller scale crowd-funded support such Kickstarter campaigns? Might this field also benefit if it was treated more as an open source movement?

February 19, 2017 Update:  On February 15, 2017, on the NOVA science show on PBS in the US, there was an absolutely fascinating documentary shown entitled The Origami Revolution. (The link is to the full 53-minute broadcast.) It covered many of the today’s revolutionary applications of origami in science, mathematics, design, architecture and biology. It was both highly informative and visually stunning. I highly recommend clicking through to learn about how some very smart people are doing incredibly imaginative and practical work in modern applications of this ancient art.

Scientists Are Developing Massive Storage Systems Based Upon Minute Amounts of DNA and Polymers

"Yeast Helicases Unwinding DNA", Image by eLife - The Journal

“Yeast Helicases Unwinding DNA”, Image by eLife – The Journal

The world has an insatiable appetite and relentlessly growing need for more electronic memory. Those gazillions of bits and bytes created daily and being propelled forward at an ever-increasing rate need to keep on going somewhere for storage, search and retrieval. Some scientists are now looking at radically different systems that utilize DNA and highly specialized natural and synthetic substances called polymers for this.

The latest developments on these efforts, providing a new spin on the old adage “no small feat”, were reported on in an article entitled The Future of Data Storage is in Tiny Strings of Molecules 60,000 Times Thinner Than a Strand of Hair, by Dave Gershgorn of Popular Science (where this piece was first published), posted on June 10, 2015. I will sum this up, annotate and pose a few, well, small questions.

Upon a strand of polymer, approximately 60,000 times smaller than a single strand of hair, researchers at France’s Institut Charles Sadron and Aix-Marseille Universite have been able to encode some binary data. Jean-Francois Lutz, the deputy director of Institut Charles Sadron, was one of the co-authors of a paper describing this entitled Design and Synthesis of Digitally Encoded Polymers That Can be Decoded and Erased that was published in the May 26, 2015 edition of Nature. Among many other things, only 10 grams of the polymer that Lutz has synthesized would be needed to store a zettabyte of data that, using today’s systems, would require 1,000 kilogram of cobalt alloy to manufacture comparable capacity with today’s hardware.

This new polymer is processed into a memory system by using a mass spectrometer, which is normally used in sequencing DNA. After two years of work on this research by Lutz, much more work on it remains ahead. Currently, it can only hold several bytes of info which he expects to scale up to kilobytes within five years. He views similar work on using DNA for storage as a “roadmap” for the anticipated progress of his own research.

Taking the lead on the content storage work with DNA is Harvard Medical School and Technicolor. Thus far in their work, researchers have encoded “10 megabytes to a DNA sequence”, and been able to decode a few hours later. Harvard Professor George Church, who is leading this effort, has previously printed “20 million copies of his book to DNA” consisting of a single drop of liquid. This accomplishment was first introduced on The Colbert Report on October, 4, 2012.* I highly recommend clicking-through to view this 5.5 minute interview and, likewise, reading Dr. Church’s remarkable book (which I have previously had the pleasure of reading in its brain-bending entirety), entitled Regenesis: How Synthetic Biology Will Reinvent Nature and Ourselves (Basic Books, 2012). He also discussed his book in the video.

Harvard and Technicolor are examining whether and how DNA memory can be implemented for archiving “large quantities of media”. That is, since such technology can store petabytes within a single drop of liquid and last “100,000 years in the right conditions”, it might well be preferable to current storage technologies. The current constraint on DNA storage is the relative slowness in the data encoding process. However, at the current rate of progress, this might become commercially viable sometime in the future.

Lutz also believes his work on polymers will not be commercially viable for years but will nonetheless be better able as a mass storage medium than DNA in terms of its relative ease of fabrication and price.

My own questions are as follows:

  • What are the technological, economic, cultural and regulatory implications of these systems that seem to promise truly unlimited storage at a nominal price?
  • Since there is another branch of research that has been working on DNA computing for a number of years, where DNA is used for information processing, would it be advantageous to integrate this with DNA memory technology?
  • Could such DNA storage be carried around by a person within them? That is, can such memory DNA be implanted into someone such that it carries around their own information while somehow being shielded against mingling with that person’s own DNA? Let’s say a drop of this memory DNA is placed within very safe and small chip, place under a person’s skin, and then scanned to add or read data. Might this be possible and, if so, would it serve any purpose that could not be accomplished by other means?

Having nothing whatsoever to do with DNA or polymers,  but having everything to do with Steven Colbert as he prepares to take over as the host of The Late Show in just a few months, please also see this hilarious  YouTube video that went viral last week entitled The Colbeard.