Protein-DNA Complex In order to achieve a crystalline structure, we must combine the protein and matching DNA to form a Protein-DNA Complex. This process involves finding the best ratio of protein to DNA to add together and incubating the mix. Screening With the DNA bound by the protein, we can now set up crystallization… Continue reading Crystallization
Purification For crystallography, we need DNA that is ultra-pure. When DNA is ordered from a synthesis company, there is a certain level of purity obtained. We can order the DNA very pure but the price sky rockets. Instead, our experimental team collaborated with Dr. Shing Ho, a DNA crystallography lab at CSU, to purify the… Continue reading DNA
Cloning A very common method of cloning uses restriction enzymes. Restriction enzymes were first discovered by Ronald W. Davis from Stanford. The basic mechanism is shown in the image below. We use a version of sequence and ligation independent cloning (SLIC). We call this LICKI...(for you Pokemon fans, this is named after… Continue reading Protein
The Video Script The starting point of our project is to reengineer DNA-protein complexes. What you’re looking at here is an atomic detail model of one of our designable co-crystals: it contains a short double stranded DNA duplex with two monomers of the protein. To prevent confusion, we will use a simplified representation. Now,… Continue reading Design
Here, we will introduce key definitions to help you understand our design. Scientists have observed that short pieces of double stranded DNA spontaneously order end-to-end (Nakata et. al Science 2007).We can use this interaction to build a biomolecular scaffold. The starting materials for this project are co-crystals, made of two or more distinct components. We are specifically using co-crystals… Continue reading The Basics
The versatility of the DNA inserts will provide a rapidly evolvable material for multiple applications. Current structure determination technology is labor intensive and haphazard. Guest capture is one key use for ICC bioscaffolds. Any guest molecule that binds the designed crystals tightly and specifically may join the periodic lattice that is visible in the electron… Continue reading Applications
Co-crystallize with the DNA inserts. Use specific sequence on the DNA inserts for guest capture. Strengthen the co-crystals with chemical cross linking via covalent bonds.