A wiring diagram specifying a system of 74 DNA molecules that constitute the largest synthetic circuit of its type ever made. The circuit computes the square root of a number up to 15 and rounds down to the nearest integer (the discrete square root of a four-bit integer). Image: Caltech/Lulu Qian |
In many ways, life is like a computer. An
organism’s genome is the software that tells the cellular and molecular
machinery—the hardware—what to do. But instead of electronic circuitry, life
relies on biochemical circuitry. Now, researchers at the California Institute
of Technology (Caltech) have built the most complex biochemical circuit ever
created from scratch, made with DNA-based devices in a test tube that are
analogous to the electronic transistors on a computer chip.
Engineering these
circuits allows researchers to explore the principles of information processing
in biological systems, and to design biochemical pathways with decision-making
capabilities. Such circuits would give biochemists unprecedented control in
designing chemical reactions for applications in biological and chemical
engineering and industries. For example, in the future a synthetic biochemical
circuit could be introduced into a clinical blood sample, detect the levels of
a variety of molecules in the sample, and integrate that information into a
diagnosis of the pathology.
“We’re
trying to borrow the ideas that have had huge success in the electronic world,
such as abstract representations of computing operations, programming
languages, and compilers, and apply them to the biomolecular world,” says
Lulu Qian, a senior postdoctoral scholar in bioengineering at Caltech and lead
author on a paper published in Science.
Along with Erik
Winfree, Caltech professor of computer science, computation and neural systems,
and bioengineering, Qian used a new kind of DNA-based component to build the
largest artificial biochemical circuit ever made. Previous lab-made biochemical
circuits were limited because they worked less reliably and predictably when
scaled to larger sizes, Qian explains. The likely reason behind this limitation
is that such circuits need various molecular structures to implement different
functions, making large systems more complicated and difficult to debug. The
researchers’ new approach, however, involves components that are simple, standardized,
reliable, and scalable, meaning that even bigger and more complex circuits can
be made and still work reliably.
“You can
imagine that in the computer industry, you want to make better and better
computers,” Qian says. “This is our effort to do the same. We want to
make better and better biochemical circuits that can do more sophisticated
tasks, driving molecular devices to act on their environment.”
To build their
circuits, the researchers used pieces of DNA to make so-called logic gates—devices
that produce on-off output signals in response to on-off input signals. Logic
gates are the building blocks of the digital logic circuits that allow a
computer to perform the right actions at the right time. In a conventional
computer, logic gates are made with electronic transistors, which are wired
together to form circuits on a silicon chip. Biochemical circuits, however,
consist of molecules floating in a test tube of salt water. Instead of
depending on electrons flowing in and out of transistors, DNA-based logic gates
receive and produce molecules as signals. The molecular signals travel from one
specific gate to another, connecting the circuit as if they were wires.
Winfree and his
colleagues first built such a biochemical circuit in 2006. In this work, DNA
signal molecules connected several DNA logic gates to each other, forming
what’s called a multilayered circuit. But this earlier circuit consisted of
only 12 different DNA molecules, and the circuit slowed down by a few orders of
magnitude when expanded from a single logic gate to a five-layered circuit. In
their new design, Qian and Winfree have engineered logic gates that are simpler
and more reliable, allowing them to make circuits at least five times larger.
Their new logic
gates are made from pieces of either short, single-stranded DNA or partially
double-stranded DNA in which single strands stick out like tails from the DNA’s
double helix. The single-stranded DNA molecules act as input and output signals
that interact with the partially double-stranded ones.
“The
molecules are just floating around in solution, bumping into each other from
time to time,” Winfree explains. “Occasionally, an incoming strand
with the right DNA sequence will zip itself up to one strand while
simultaneously unzipping another, releasing it into solution and allowing it to
react with yet another strand.” Because the researchers can encode
whatever DNA sequence they want, they have full control over this process.
“You have this programmable interaction,” he says.
Qian and Winfree
made several circuits with their approach, but the largest—containing 74
different DNA molecules—can compute the square root of any number up to 15 and
round down the answer to the nearest integer. The researchers then monitor the
concentrations of output molecules during the calculations to determine the
answer. The calculation takes about 10 hours, so it won’t replace your laptop
anytime soon. But the purpose of these circuits isn’t to compete with
electronics; it’s to give scientists logical control over biochemical
processes.
Their circuits
have several novel features, Qian says. Because reactions are never perfect—the
molecules don’t always bind properly, for instance—there’s inherent noise in
the system. This means the molecular signals are never entirely on or off, as
would be the case for ideal binary logic. But the new logic gates are able to
handle this noise by suppressing and amplifying signals—for example, boosting a
signal that’s at 80%, or inhibiting one that’s at 10%, resulting in signals
that are either close to 100% present or nonexistent.
All the logic
gates have identical structures with different sequences. As a result, they can
be standardized, so that the same types of components can be wired together to
make any circuit you want. What’s more, Qian says, you don’t have to know
anything about the molecular machinery behind the circuit to make one. If you
want a circuit that, say, automatically diagnoses a disease, you just submit an
abstract representation of the logic functions in your design to a compiler
that the researchers provide online, which will then translate the design into
the DNA components needed to build the circuit. In the future, an outside
manufacturer can then make those parts and give you the circuit, ready to go.
The circuit
components are also tunable. By adjusting the concentrations of the types of
DNA, the researchers can change the functions of the logic gates. The circuits
are versatile, featuring plug-and-play components that can be easily
reconfigured to rewire the circuit. The simplicity of the logic gates also
allows for more efficient techniques that synthesize them in parallel.
“Like Moore’s Law for silicon
electronics, which says that computers are growing exponentially smaller and
more powerful every year, molecular systems developed with DNA nanotechnology
have been doubling in size roughly every three years,” Winfree says. Qian adds,
“The dream is that synthetic biochemical circuits will one day achieve
complexities comparable to life itself.”
