Biomedical Engineering Reference
In-Depth Information
a
b
c
A in
A T,in
A in
A T,in
A in
+
A c
A T,in
A T
A
A
A T
+
A
A T
A c
A c
Fig. 7.2 Strand displacement mechanism: ( a ) A double-stranded molecule with a toehold and the
input strand. ( b ) The input complementary strand binds to the toehold A T and displaces shorter
hybridized sequences. ( c ) The resulting molecules
binds to a toehold A T , which is a single-stranded overhang, and then invades and
displace shorter hybridized sequences by a mechanism known as three-way branch
migration. The sequence of processes involved in strand displacement is illustrated
in Fig. 7.2 .
The 0 and 1 logic values are represented, respectively, by high and low
concentrations of each ssDNA molecules. The output strand of a gate (Ac) is
complementary to and hybridizes with a ssDNA molecule .A C A T / immobilized
on a substrate by T, such that different logic gates are immobilized on different
supports. Successfully cascading logic operations implies that the toehold region
of a certain gate can bind only to the output strand of the preceding gate, which
is released only when the latter gate is executed by a suitable combination of its
inputs. This gate executed operations such as AND, OR, and AND-NOT, the final
output being reported by a REPORT gate, which emitted a fluorescent signal for an
appropriate input, by releasing/displacing a fluorescent molecule into solution. This
molecule fluoresce only in solution since on support is preventing of doing so by the
action of an immobilized quencher. An AND gate is implemented such that either
one of the XX T or YY T input sequences displaces a single duplex region (X or Y)
of an anchored molecule, the resulting XYZZ T strand remaining anchored, while
both inputs release the output strand XYZZ T into solution. In an OR gate, the inputs
XX T or YY T displace the respective strands XZZ T or YZZ T , whereas both inputs
double the effective output ZZ T . Other logic circuits or combinations of them are
implemented in a similar way ( Frezza et al. 2007 ). Rewiring implies a modification
of the output sequences of logic gates. Successful cascading requires taking into
account that differences in gate output levels amplifies in a multilevel circuit so that
corrections are needed.
An example of a sequence-addressable DNA logic device is presented in
Voelcker et al. ( 2008 ). It can implement in solution simple logic gates (AND, OR,
XOR) and can combine then in a half-adder, which consists of an AND gate and
a XOR gate that implement, respectively, the carry and the sum bit. The working
principle of the device is based on the fact that ssDNA molecules can invade and
displace shorter sections of a matching double-stranded DNA (dsDNA). These
ssDNA attach first to short single-stranded toehold regions and then replace the
base pairing in a smaller duplex, the thermodynamic driving force for the displace-
ment being the longer duplex that the input DNA forms in the toehold region.
Search WWH ::




Custom Search