Deoxyribozyme-Based Molecular Computation - DNA Nanotechnology: From Structure to Function - page 344

Fig. 17.1 ( a ) YES gate is established by attaching a stem loop to the substrate-recognition region
of deoxyribozyme E6. Upon the addition of an input i1 which is complementary to the loop, the
gate is turned into its active form, allowing the catalytic reaction to proceed to cleave the substrate.
The reaction is monitored in fluorescence change. ( b ) NOT gate is constructed by adding a stem
loop to the catalytic core of E6. Opening of the stem loop will distort the catalytic core and
inhibit the catalytic reaction. ( c ) AND gate is constructed when two stem loops are added to the
two opposite ends of the substrate-recognition region of deoxyribozyme. This gate requires the
presence of both inputs for enzyme activity. ( d ) ANDNOT gate is constructed by combining a
YES gate with a NOT gate; this gate is active in the presence of one input as long as a second
input is not present. ( e ) ANDANDNOT gate is established by adding a NOT gate to an AND gate.
This gate is active in the presence of two inputs while being deactivated in the presence of the third
input. ( f ) ANDAND gate is established by pre-complexing the third input with an ANDANDNOT
gate. An input complementary to this pre-complexing oligonucleotide has to be added to close the
stem and activates the gate
pre-complexing the third input with ANDANDNOT gate. The pre-complexation of
stem loop with a complementary oligonucleotide leads to open the stem, distorting
the catalytic core. An input complementary to this complementary oligonucleotide
has to be added to close the stem and activates the gate [ 42 ]. By parallel arrangement
of these logic gates, the simple circuits for basic arithmetical operations, including
a half and a full adder, have been constructed [ 41 , 42 ].
An important aspect of these deoxyribozyme-based logic gates is that they are
highly modular. This allows the use of arbitrary oligonucleotides as inputs, within
some limitations. For example, some inputs have strong secondary structures and