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). Credit: 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—complex networks of reactions and pathways that
enable organisms to function. 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 the June 3 issue of
the journal 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 (technically speaking, any four-bit binary
number) 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 percent, or inhibiting one that’s at 10 percent, resulting in
signals that are either close to 100 percent 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.”
The
research described in the Science paper, “Scaling up digital circuit
computation with DNA strand displacement cascades,” is supported by a
National Science Foundation grant to the Molecular Programming Project
and by the Human Frontier Science Program.