DNA as Puzzle Design

Example of dna strand segment represented by letters

The Secret of Chimera Labs features a puzzle about manipulating a strand of Deoxyribonucleic Acid, DNA. The puzzle consists of a two redundant mono-alphabetic substation cipher, a pattern-match, item assembly and player action. The ciphers are redundant not because they are the same, because only one needs to be utilized in order to solve the puzzle.

A representation of the molecular structure of a DNA strand.
A representation of the molecular structure of a DNA strand.

Deoxyribonucleic acid (DNA) is a molecule that encodes and carries genetic instructions used in the growth, development, functioning and reproduction of all known living organisms and many viruses. Hydrogen, Carbon, Nitrogen, Oxygen and Phosphorus are the elements which are found in DNA. The structure of DNA consists of two classes of molecule: bases and backbone.

Elements present in DNA
Elements present in DNA

The four nucleobases (Guanine, Cytosine, Adenine, Thymine) are divided into two groups purines and pyrimidines. These base pairs are abbreviated as G C A T. An example strand using letter-glyph symbols to represent a nucleobases is shown at the top of this article. The enciphering of ‘molecular structure’ to ‘symbols’ is one of the mono-alphabetic substitution ciphers at the core of the puzzle.

DNA bases: Guanine, Adenine, Cytosine, Thymine
DNA bases: Guanine, Adenine, Cytosine, Thymine

The purine Guanine is paired with pyrimidine Cytosine and will only connect with eachother in a closed strand of DNA. The purine Adenine is paired with the pyrimidine counterpart Thymine. Thus it is possible to determine both side of pair when only one molecule is known. Hydrogen bonds, electrostatic attractions between polarized groups of molecules or atoms, bond the bases to together.

DNA base-pair hydrogen bonding
DNA base-pair hydrogen bonding

The backbone of DNA is based on a repeated pattern of a sugar group and a phosphate group. The sugar present, deoxyribose, gives DNA its “D.”

DNA Backbone
DNA Backbone

The second enciphering was the encoding of the base-pairs, both structure and letter-glyph symbol to a color. These colors were purely fictitious. Their purpose is to ease user-experience by providing a more easily recognized attribute with which to trace back the substitutions to the puzzle solution.

Color for mono alphabetic substitution
Color for mono alphabetic substitution

With these pieces (structure, symbol, color) it is possible to quite readily create a pattern match puzzle as shown below. In this particular puzzle design, the symbol encoding (GACTA for example) serves as the key and is made available elsewhere in the game.

Puzzle from The Secret of Chimera Labs
Puzzle from The Secret of Chimera Labs

To play the puzzle in action and try to solve it your self, download The Secret of Chimera Labs on to your mobile device of choice.

Learn more about DNA.
Learn more about substitution ciphers.

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