Biology Reference
In-Depth Information
7
CHAPTER
Computer-Aided Design
of Synthetic Biological
Constructs with the
Synthetic Biology Software
Suite
Katherine Volzing, Konstantinos Biliouris, Patrick Smadbeck
and Yiannis Kaznessis
University of Minnesota, Minneapolis, MN, USA
123
INTRODUCTION
Robustly controlled biomolecular interactions are the key to maintaining optimal cellular
function. DNA
protein interactions are instrumental in
governing the underlying intracellular behaviors that define living organisms.
1,2
Over the
last 60 years, molecular resolution studies have revealed the inner workings of biomolecular
interactions. Specific protein domains and amino acid sequences that drive protein
DNA, DNA
protein, and protein
DNA
binding and protein multimerization are now well known for many molecules. In addition,
the particular DNA base pairs that are required for transcription factor binding,
transcription, and translation initiation and termination have also been identified for
numerous operons.
3
8
This increasingly comprehensive understanding of natural cell function at the molecular
level is propelling engineering efforts to utilize the control mechanisms and their
downstream targets as molecular biology tools. To date numerous nonnatural, or synthetic,
systems have been designed and built experimentally, employing this knowledge of
molecular interaction mechanisms. Many of these systems couple an extracellular signal (or
input) to a unique intracellular target (or output), as is the case of synthetic receptor
kinases.
9
14
Other significant efforts have focused on building systems to study or address
previously unmet needs in gene expression regulation. Gene expression can be controlled at
the level of transcription,
15,16
mRNA stability,
17
translation,
18
or protein stability.
19,20
While
all four of these approaches are very powerful, the following discussion will focus on the
development of synthetic systems that regulate gene transcription.
Two pioneering systems constructed to achieve novel gene expression control are the
bistable switch and the repressillator.
21,22
Both systems are based on synthetic promoter
