DNA COMPUTING

ASSIGNMENT 3
DNA LOGIC GATES

Submitted to: Sir’ Muhammad Qasim

Submitted by: Aleena Amjad
Reg id: 180389
BCE VIII-A
Logic gates:
A logic gate is a device that acts as a building block for digital circuits. They perform
basic logical functions that are fundamental to digital circuits. Most electronic devices
we use today will have some form of logic gates in them. For example, logic gates can
be used in technologies such as smartphones, tablets or within memory devices. There
are seven basic logic gates: AND, OR, XOR, NOT, NAND, NOR, and XNOR.

DNA logic gates:

Recent researchers designed new set of devices based on nanotechnology for
switching DNAzymes on and off by either integrating the substrate recognition
domains in to the stem of a molecular beacon or deactivating the DNAzymes central
catalytic region by binding it to a complementary oligonucleotide. In this way the
logic gates are designed.
DNAzymes:
Unlike the restriction enzymes which are basically proteins, DNAzymes are made of
DNA. DNAzymes consists of central catalytic region flanged by two substrate
recognition domains. Their basic operation binds the recognition domains to a specific
substrate, comprising a ribonucleotide flanged by two regions that are complementary
to the substrate recognition domains. as illustrated in the image below, when the
substrate binds to the recognition domain, its catalytic action cleaves the substrate at
the ribonucleotide position.

Molecular beacon:
Molecular beacons are hairpin-shaped molecules with an internally quenched
fluorophore whose fluorescence is restored when they bind to a target nucleic acid
sequence.
AND gate
In this device both recognition domains of DNAzymes are integrated in molecular
beacons. The recognition domains will only be free to operate in the presence of two
different input signals, each one complementary to the respective molecular beacon
loop. It will give a positive output in the presence of two expected input signals and
negative otherwise.
Input 1 Input 2 Output
0 0 0
0 1 0
1 0 0
1 1 1

YES
This device will give a positive in the presence of an input signal and negative in the
absence of the input signals. This gate is opposite to the NOT gate.
Input 1 Output
0 0
1 1
NOT
This device is sort of an inverter, it will give a positive response in the absence of an
input signal and negative response in the presence of an input signal.
Input 1 Output
0 1
1 0

Related work and innovation:

This set of logic gates was applied to the implementation of molecular automation that
encoded a 3x3 version of game tic tac toe. The automation was able to compete
interactively with the human opponent. Another work presented more recently has
implemented a similar game called tit for tat.

Main Drawback:
One of the main drawbacks of these gates lies in the different input and output
formats, preventing the implementation of cascades where the output of the gate is
provided as input for another gate.