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2014 ; 47
(6
): 1845-52
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Exercises in molecular computing
#MMPMID24873234
Stojanovic MN
; Stefanovic D
; Rudchenko S
Acc Chem Res
2014[Jun]; 47
(6
): 1845-52
PMID24873234
show ga
CONSPECTUS: The successes of electronic digital logic have transformed every
aspect of human life over the last half-century. The word "computer" now
signifies a ubiquitous electronic device, rather than a human occupation. Yet
evidently humans, large assemblies of molecules, can compute, and it has been a
thrilling challenge to develop smaller, simpler, synthetic assemblies of
molecules that can do useful computation. When we say that molecules compute,
what we usually mean is that such molecules respond to certain inputs, for
example, the presence or absence of other molecules, in a precisely defined but
potentially complex fashion. The simplest way for a chemist to think about
computing molecules is as sensors that can integrate the presence or absence of
multiple analytes into a change in a single reporting property. Here we review
several forms of molecular computing developed in our laboratories. When we began
our work, combinatorial approaches to using DNA for computing were used to search
for solutions to constraint satisfaction problems. We chose to work instead on
logic circuits, building bottom-up from units based on catalytic nucleic acids,
focusing on DNA secondary structures in the design of individual circuit
elements, and reserving the combinatorial opportunities of DNA for the
representation of multiple signals propagating in a large circuit. Such circuit
design directly corresponds to the intuition about sensors transforming the
detection of analytes into reporting properties. While this approach was unusual
at the time, it has been adopted since by other groups working on biomolecular
computing with different nucleic acid chemistries. We created logic gates by
modularly combining deoxyribozymes (DNA-based enzymes cleaving or combining other
oligonucleotides), in the role of reporting elements, with stem-loops as input
detection elements. For instance, a deoxyribozyme that normally exhibits an
oligonucleotide substrate recognition region is modified such that a stem-loop
closes onto the substrate recognition region, making it unavailable for the
substrate and thus rendering the deoxyribozyme inactive. But a conformational
change can then be induced by an input oligonucleotide, complementary to the
loop, to open the stem, allow the substrate to bind, and allow its cleavage to
proceed, which is eventually reported via fluorescence. In this Account, several
designs of this form are reviewed, along with their application in the
construction of large circuits that exhibited complex logical and temporal
relationships between the inputs and the outputs. Intelligent (in the sense of
being capable of nontrivial information processing) theranostic (therapy +
diagnostic) applications have always been the ultimate motivation for developing
computing (i.e., decision-making) circuits, and we review our experiments with
logic-gate elements bound to cell surfaces that evaluate the proximal presence of
multiple markers on lymphocytes.
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