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.
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.
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.
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.