Methods and systems for engineering a nanostructure are provided. An exemplary method includes creating at least one cytosine-cytosine and/or thymine-thymine mismatch in at least one oligonucleotide sequence, placing a metal ion into the mismatch of the oligonucleotide sequence to form an electronically functionalized nanostructure, and inducing self-assembly of the oligonucleotide sequence into a defined structure.

An optical logic gate includes: a DNA based nanostructure including DNA and metal nanoparticles coupled to the DNA, the DNA based nanostructure being configured to rotate a polarization plane of an incident light; a polarizer to which light passing through the DNA based nanostructure is incident, the polarizer being configured to extract a component in a direction of a predetermined reference axis from light whose polarization plane is rotated by the DNA based nanostructure; and a detection unit to which light passing through the polarizer is incident, the detection unit being configured to generate a logic signal based on a result obtained by comparing the intensity of the component in the reference axis direction extracted by the polarizer with a predetermined threshold value.