The Basics

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 […]

Applications

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 […]

Future Work

To simulate guest molecule binding to a DNA strut insert in an expanded ICC. To use gaussian probability to create more realistic simulations involving molecular interactions. To reengineer protein-protein interfaces in an ICC.

Results

Goal 1: To overexpress and purify two candidate proteins. In order to express the protein of choice, the first step is Cloning. There are two parts to make a plasmid: a vector and the gene of interest. The plasmid with the gene of interest is transformed into E. coli with the molecular machinery to make the protein. We […]

Results

  Goal 1: To acquire an initial list of candidate ICC structures from the Protein Data Bank.   In order to decide which candidates to expand, all available PDB files were fed into a series of Python scripts to isolate feasible units. Feasibility criterion included proper number of alpha carbons, correct number of oxygen prime atoms, […]

Goals

  Goal 1: To acquire an initial list of candidate ICC structures from the Protein Data Bank. Goal 2: To establish DNA insert sizes for creating output model files of priority candidates in Pymol. These priority candidates will be used in  GROMACs simulations. Goal 3: To successfully use GROMACs software to  run molecular dynamic (MD) simulations […]