DNA Optimisation Algorithms for Improved Gene Expression in the Field of Synthetic Biology

Oxford Genetics is a new biotechnology company that aims to become the UK’s pre-eminent
producer of genes and DNA plasmids. The company has been trading for just under one year,
and has already established a worldwide market for our DNA products.
Genes encode proteins, and in this project we will develop a technology that can ensure the
genes customers buy from us work efficiently. A gene is normally represented in biology
using a string of letters, A, T, G and C to represent the DNA sequence. The order of these
letters contains the information that allows the gene to encode a particular protein. However,
the genetic code is highly redundant, and the same protein can be encoded using many
different sequences (strings of A, T, G or C) that ‘work’ with different efficiencies. This
influences the overall efficiency of gene expression and protein production, making it very
difficult to know which particular DNA sequence will be optimal for biological investigation.
In this project we will deconvolute this complexity by designing DNA sequences that can be
tested side-by-side to enable us to determine which particular DNA base sequences work best
in mammalian and bacterial cells. This is a tricky question, as the order of the DNA bases
used can have complex effects that may interfere with the efficiency of protein production.
We have therefore designed a series of experiments that will enable us to generate a unique
algorithm that can applied to all of the genes that we provide to our customers for expression
in a particular organism. This provision to our customers will position us a leading DNA
provider and instil confidence to customers using our sequences.