AAWSAP DIRD, Quantum Computing and Utilizing Organic Molecules in Automation Technology, December 2010

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Engineering DNA-Based Logic Gates
This branch of nanotechnology employs DNA enzymology to induce molecular behavior in
solution that responds to an appropriate nucleic acid input. The goal is to make reliable DNA
based logic gates that can be used to assemble complicated logic circuits, which, in turn, can
be used to control complex molecular devices (115). Strictly speaking the silicomimetic
solution-phase approaches are not connected to traditional DNA nanotechnology, or
Adleman's model of DNA computing (116). However, there is some overlap of concepts, and
all these approaches can be integrated in order to achieve complex functional behaviors.
There are two primary requirements that a DNA-based logical device has to fulfill: first, the
device should have the ability to integrate the presence or absence of several inputs into a
single output. Second, a device has to be designed in such a way that a limited number of
simple devices can be combined into a variety of complex circuitries. This usually means that
one device can communicate with other components through some kind of information
transfer. Furthermore, devices that could communicate with sensors, and produce outputs
for autonomous therapeutic and diagnostic devices are of our interest, because they may one
day function as silicon-free expert systems. DNA-based logic gates are intended to perform
as traditional binary logic gates, which turn 1's and O's of input into 1's and O's of output,
which form the central processing units in digital computers. Recently, Seeman and
colleagues at New York University have found a clever new way to tease DNA strands into
mimicking exclusive OR (XOR) logic gates ( 117). In the case of an XOR gate, the rule is
simple: when the same two digits enter the gate, a 0 comes out; two different entering digits
return a 1. In this latest case of DNA computing, inputs are replaced by single-stranded
molecules, and how they bind with each other--base pair to base pair--dictates the
operations. In essence, the collection of input molecules that are used set up the problem;
once that's done, the answer self-assembles in a single step. The near term goal is to build
DNA-based computing modules and to develop nanoscopic machines that could exist in living
organisms, sensing conditions and making decisions based on what they sense, then
responding with actions such as releasing medicine or killing specific cells.
Logic Operation by Deoxyribozymes
This biocomputing approach is based on two libraries of nucleic acids, one consisting of an
allosterically modified deoxyribozyme (nucleic acid catalysts made of DNA) and the second,
its substrates. A DNAzyme is associated with gene replication only, and they exist only in the
laboratory. Nevertheless, they are very powerful tools for building DNA-based nanosystems.
The functions of these molecular units are essential for molecular logic gates and the
seamless integration into DNA-based computing devices. These constructs are capable of
carrying out simple arithmetic operations ( 118) and have the capability to arrange several
gates around a common substrate. (119)
These devices have oligonucleotides (short ssDNA) as both inputs and outputs.
Phosphodieseterase deoxyribozymes cleave other oligonucleotides, producing shorter strands
as outputs. For example, operation of the simplest sensors is illustrated in Figure 20. The
stem-loop of YESx molecule inhibits the catalytic module through the overlap of the stem
with the substrate recognition region. Hybridization of ix to the complementary loop opens
the stem to allow substrate binding to proceed. The YESx gate behaves as a two-state switch,
with the active state in the presence of input. The combination of these sensors for input to
gate logic is illustrated in Figure 21. Generalized approaches have three-input gates
(including NOT, AND, ANDNOT, ANDANDNOT gates) based on the deoxyribozyme logic. (121)
These gates are generic and modular, in the sense that other deoxyribozymes could be
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