Hello, and welcome to Crystalline Entity’s design studio, where the name of the game is crystallization. Like a mosaic tile, crystals begin with a single building block that grows into a patterned masterpiece. Patterned crystals of biomolecules, like protein and DNA, can be analyzed by X-ray crystallography. Here, a beam of X-rays shoots a crystal to reveal the structure of the building block in the diffraction pattern. However, growing a single crystal for X-ray diffraction can be time consuming and expensive. So, we need an improved crystallization method.
Our goal is to provide a host crystal! This crystal should be porous enough to host guest molecules, like the one shown in magenta. To accomplish this, we use co-crystals made of DNA and protein. This single co-crystal unit is the building block of our host crystal. The co-crystals shown are unique, as the DNA stacks up end-to end, acting like pillars in the crystal. At the same time, the protein insulates the structure, holding the crystal together. With these principles in mind, let us show you how to play the new crystallization game. To play DNA Tile, you must design, make, and host.
First, design the co-crystal. To simplify things, we will use a cartoon representation of our tile. We have made our DNA pillars into a network of four blocks, also known as DNA tiles. Here is our DNA Tile design strategy:
To start, we want the four blocks to easily assemble into two DNA tile halves. These tile halves are brought together with a unique phosphate linker. Once the full tile is formed, we ensure that the insulating proteins are still able to bind with the DNA tile. Using NUPACK, a nucleic acid design tool, we make predictions about our proposed tile designs and decide the optimal DNA sequence for the tile. You can imagine, there are a lot of possible tile designs.
Once you choose a design, the next step is to make co-crystals in the lab!Due to the relatively low cost of DNA synthesis, DNA sequences can be ordered online. Then, the sequence specific strands are annealed together to form the completed tile. In the Snow Lab, we synthesize and purify the desired protein. With both building blocks in hand, we can co-crystallize!
Once we have a porous co-crystal, we can host guest molecules. The porous crystal is a channel for other molecules to come join the free DNA, shown here in magenta. Any guests that can bind to DNA can join the host crystal structure pattern for X-ray diffraction.
So, with these guidelines, are you ready to play the crystallization game? The high score to beat is our 8-strand tile, that anneals easily and successfully with the protein to crystallize!