Biomedical Engineering Reference
In-Depth Information
An example of the implementation of the AND gate utilizes as inputs two 24-nt
sequences designed to bind to one 10-nt toehold end of a stationary 55-nt sequence
immobilized on functionalized silica beads. As a result of this binding, the three-way
branch migration mechanism induces a displacement of 14 bp of the 28-nt output
strand which is duplexed to the center of the stationary strand. The output strand,
labeled with a fluorescent molecule, is bounded to the immobilized stationary strand
as long as no input or only one input is present, in the second case the binding
becoming weaker. The result of computation is followed monitoring the release of
the fluorescent molecule into the supernatant. This release occurs only in the pres-
ence of both inputs. A similar OR gate can be implemented if the 14-nt output strand
is bound to the 30-nt immobilized stationary strand, both strands having ssDNA
overhang regions. Either one of the 24-nt inputs can displace the output strand by
binding to output strand itself or to the toehold region of the stationary strand first.
In both case, the fluorescent molecule is released in the supernatant. Several logic
gates can be cascaded if the output of a gate acts as input for the subsequent gate
and if the sequence of reactions is implemented such that cross contamination is
avoided.
A digital biomolecular circuit with a modular construction, which implements
logic gates, as well as signal amplification and restoration, feedback, and cascaded
operation, is described in
Seelig et al.
(
2006
). This enzyme-free circuit uses short
oligonucleotides as input and output, the logic values 0 and 1 being assigned,
respectively, to low and high concentrations. The gates operate based on Watson-
Crick interactions/base pairing and breaking, which is used also for cascading
several gates. A gate is composed of one or more gate strands, A and B in
Fig.
7.3
, which contain recognition regions complementary to the input and one
output strand, O, which can either act as input for the next gate or can be labeled
by a fluorescent molecule. As shown in Fig.
7.3
, for an AND gate, computation
begins when input strands are added in the solution containing the gate. The
input strands A
in
binds to the toehold region (gray) of the double-stranded gate,
displacing the first gate strand by the mechanism of three-way branch migration
and releasing a double-stranded waste. The toehold is thus ready for the next
input, B
in
, which induces similar processes. The output strand is released in the
solution only in the presence of both inputs, and the result of computation is read
by fluorescence experiments. In a similar manner, OR and NOT circuits can be
implemented.
a
b
c
Ain
Bin
O
A
O
B
A
O
B
B
Fig. 7.3
Implementation of an AND gate: (
a
) gate and output strands, (
b
) displacement of the A
strands, and (
c
) displacement of the B strand
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