Electrical and Computer Engineering Graduate Program
Center for Nanotechnology
Faculty Advisor: Franco Cerrina
Our research group’s work is cross-disciplinary in nature, combining engineering, chemistry, and biology to develop a potentially revolutionary method of gene assembly. Venter has demonstrated the assembly of a 5 kilobase gene from synthetic oligonucleotide segments; from start to finish the process took a large research team a number of weeks and many thousands of dollars. Our group (led by Profs. Cerrina, Sussman, and Belshaw) is working to allow the production of even larger genes in a shorter amount of time (hours vs. weeks), and at a fraction of the cost (hundreds vs. thousands of dollars). To be successful, a significant amount of automation and process control is necessary, and my work has focused on this aspect of the project.
At present, I am working on developing “one-step” assembly of genes from microarray oligos. Currently, to assemble these oligos, we are cleaving them from the chip surface, drying the sample down, resuspending the oligos, PCR amplifying, stripping the PCR primers with restriction enzymes, PCR assembling the oligos, and then perhaps further amplifying sthe product and doing some error filtering or sequence verification. To be sure, this is time-consuming and labor-intensive. I would like to use a combination of microfluidics, “macro”fluidics, and some unique biology to remove the human element from the process. My first step was to develop a PCR protocol that would directly make copies of the chip-bound oligos: this has removed the need to cleave, dry down, and resuspend the oligos. My next step is to take advantage of the PCR already being done on-chip, and apply it to the assembly of the copied oligos.
Aside from gene assembly, I have been involved in the design and construction of custom DNA synthesis machines and have just begun work on applying pyrosequencing techniques to the analysis of microarray oligo quality.