DNA Logic Gates
Brainard Burrus, Alex Austell, Jimmy Bueno, Jonny Clark
The DNA tic-tac-toe project known as MAYA’s aim was to use a somewhat basic design to illustrate an important
concept. Joanne Macdonald, Darko Stefanovic, and Milan Stojanovic wanted to demonstrate a use for DNA (~2 nm)
outside of its traditional biological use as a sort of memory storage device. It has already been recorded by other
researchers and scientists that DNA could be used to do computations but the team wanted to demonstrate how these
computational abilities might be used to sense certain conditions and react accordingly. Their approach was to design a
system of logic gates- the basic components of any computer.
There are two basic components which they used to build these logic gates. The first
is an enzyme made entirely out of DNA called Deoxyribozyme. Deoxyribozyme
functions by attaching to specific substrate- a complementary band of DNA- and
cleaving it if half. This can be observed by attaching a fluorescent molecule to one
side of the substrate and a “quencher” molecule to the other side that keeps the
fluorescent molecule from fluorescing when it is in range. When the enzyme cleaves
the substrate in half, the fluorescent side is separated from the “quencher” side and
consequently lights up. This fluorescence serves as the output, the 1- but another
special device is needed to turn this enzyme into a working logic gate. The
researchers turned to DNA stem-loops, merely a strand of DNA wrapped around and
bonded to its self. Stem loops will pull apart when another DNA strand
complementary to the ring portion is introduced into the mix; the complex 3D
double helices’ will only fit together geometrically when straight, so as a
complementary DNA strand zips itself to the ring section of a closed stem-loop
it pulls the already bonded section part apart. Using these stem loops, in
conjunction with deoxyribozyme, allows one to build simple logic gates.
A simple YES gate, one that will receive and input 0 or 1 and output the same – essentially a sensor – is made by
replacing one side of the active bonding site of deoxyribozyme with a closed stem loop. This prevents the enzyme from
bonding to the substrate DNA strand, and thus no fluorescence occurs- a 0. However, when a strand of DNA
complementary to the back of the stem-loops is injected into the mix, it opens the stem loop, freeing the allosteric site
and allowing Deoxyribozyme to cleave the substrate and induce fluorescence- a 1. To make and AND gate, one simply
throws another stem loop on the other side of the enzyme binding site- fluorescence will occur if the molecule which
opens stem loop 1 AND the molecule that opens stem loop 2 are present. An AND-AND-NOT gate is similarly made by
attaching a stem-loop on the back of the enzyme. When the correct DNA strand bonds with it, it opens and deforms the
enzyme, preventing it from working altogether.
Sensor YES Gate
1
AND Gate
AND-AND-NOT Gate
Now comes that task of integrating these gates into a “medium scale integrated circuit,” in this case a tick-tacktoe playing computer. The tick-tack-toe board is made out of nine wells, labeled 1-9. The fluorescing DNA substrates are
in each well, along with the necessary YES, AND, and AND-AND-NOT gates to play a game of tick-tack-toe. The players
moves are signaled by different strands of DNA , each labeled by the well the player wishes to move in and what number
move it is- i91, for instance, would signal it is the players first move and he wishes to mark square nine. This specific
DNA sequence will signal a sensor gate in square nine to light up green, signaling his move, and another square to light
up red indicating the computers move. In other squares, the humans input strand might bond to loops on the back of
AND-AND-NOT enzymes making sure they never light up. Many YES, AND, and AND-AND-NOT gates, each responding to
different input strands, are arranged in the wells such that the computer plays a perfect game of tick-tack-toe.
Not surprisingly, inventing a machine that will never lose at tic-tac-toe was not the ultimate goal for researching
and experimenting with the new uses for DNA presented in this project. The team’s purpose was to design a nanoscopic
machine which could operate on very specific elements within the human body. The implications for such a device in the
medical field could be huge, the idea being that this machine could target very specific cells, killing the malicious ones
and leaving the good ones unharmed.
What makes this design special?
Current medications are not always able to target sites with the specificity necessary to take down disease effectively.
For example, chemotherapy, in its effort to cure cancer, leaves patients weak and comes with many unwanted side
effects. This is because the medication used currently is only specific enough to search out a specific marker and attack
when it is found. Unfortunately, large numbers of healthy white blood cells may also exhibit these same marked
characteristics. The drug is unable to further discriminate its attack and wipes out huge subpopulations of white blood
cells which are necessary for the immune system to function properly. The DNA system designed for MAYA hopes to
provide a method to help drugs discriminate very specifically and in that way act as a sort of artificially intelligent doctor
that travels with the drug. If the drug is able to seek out cells that exhibit marker “A” and marker “B” but then only
destroy the ones that do not have marker “C,” we can see just how specific a drug could become. MAYA has
demonstrated the functionality of these DNA ‘AND’ and ‘NOT’ gates and the new task will be applying these capabilities
with the medical field.
In addition, MAYA’s design is unique from previous organic logic gates in that it is biocompatible. Previous designs using
hydrogen ions and sodium ions would be useless within the medical field because they rely on the use of acids that
would harm a living cell. With the implementation of the DNA strand and enzyme approach, the logic gates created are
fully functional in an aqueous environment, a necessary step toward the use of logic gates in medicine.
Possible Future Uses
One can imagine a huge number of different potential uses for this technology because research on both its
possibilities and its limitations is still very young. The technology could be attached to a drug as a type of ‘smart’ monitor
that could take the place of a doctors watchful eye and automatically release medicine when the body needs it. In a
diabetic patient, for example, this might mean a drug’s output function (to release insulin) is only implemented when
blood glucose levels in the body get too low. As stated previously, it might also be used to target very specific sites or
cells in the body in order to attack disease or kill malicious cells. A very direct use of the DNA logic gates would be to
analyze DNA strands themselves in order to find and study the effects of certain mutations. It is even suggested that this
technology might be used in military operations to seek out harmful agents created by our enemies in chemical warfare.
Certainly the ability of MAYA to play a perfect game of tic-tac-toe is far from similar to any of these prospective
uses. MAYA’s creators are not going to disassemble their project and inject its parts into humans for medical use. But
the research that has gone into completing MAYA and MAYA II will be very useful as this new technology is developed.
The team of designers can already put together a DNA logic gate much more smoothly and effectively than was
originally possible. Although their tic-tac-toe game’s function has no real value on its own, the methods used to build it
and the technology created will hopefully be built upon to make new scientific and medical advances for the future.
Our Model
We are modeling several different parts MAYA-II (Molecular Array of Yes and AND NOT logic gates),
which is the second generation medium-scale integrated circuit that plays tic-tac-toe with perfect strategy. The
game was used to represent the process of DNA computing via molecular automata. The model illustrates the
process of combining three different logic gates, DNA substrates, and enzymes used to create MAYA- II and
allow it to “compute” an answer. We created a sample substrate, using an LED to indicate fluorescence when it
is cleaved in half. We also created a sample enzyme and stem-loops. Finally, we integrated these parts into
models of a YES sensor gate, an AND gate, and an AND-AND-NOT gate.
Materials:
Duck Tape – Other than the fact that duck tape has about a million uses in everyday life, we used it in order to
help illustrate the different complementary bases in the substrate.
Pipe Cleaners – The flexibility of the pipe cleaners were highly useful in explaining the importance process in
which the logic gate bends and opens to release the substrate inside. The pipe cleaner also was useful in
explaining the AND-AND-NOT gate, which deforms itself.
Poster board – Used to illustrate the logic gates in MAYA-II and how they would be connected for MAYA-II. Also
the poster board provides a brief explanation of how a typical game of tic-tac-toe on MAYA-II would be played.
Magnets- Used to complete the circuit of the fluorescent side of the substrate when it separates from the
quencher side.
LED light – Illustrates the “fluorescence” that occurs when the substrate is broken.
Magnets- To complete the circuit of the fluorescent side of the substrate when it separates from the quencher
side.
Aluminum Foil- Wrapped around the magnets so that when the connect it completes the circuit.
Battery - Used in order for the LED light to work
Wire- Also used in order for the LED light to work.
Pictures:
DNA Substrate- The substrate has both a fluorescent side and a quencher side- when the enzyme splits the
substrate, the magnets on the end of the fluorescent side (wrapped in aluminum foil) come together and
complete the circuit so that the LED lights up.
Enzyme- A model deoxyribozyme.
Stem-Loop- A model of a basic stem loop bonded to itself.
YES Gate- A basic sensor gate, deoxyribozyme with a stem-loop as one side.
AND Gate- The deoxyribozyme enzyme with a stem loop added to each side, creating an AND gate.
AND-AND-NOT Gate- The enzyme with an additional stem loop on the back, deforming the enzyme
when activated.
Pictures taken from the article Smart DNA: Programming the Molecule of Life for Work and Play , November 2008
Scientific American