Biology Reference
In-Depth Information
optimized the dynamic range within a specified context, allowing extension of utility of
RNAi as regulatory tools and a valuable component for building complex biological
systems.
18
Orthogonal ribosome and mRNA pairs are duplicated molecules in an organism that are
capable of processing information in parallel with their progenitors without any
crosstalk, which have been developed to create a regulatory network controlled by
Boolean logic operators.
19
The development of orthogonal pairs of ribosomes and
mRNA requires an extensive and exhaustive screening of ribosomes that are capable of
specifically translating the orthogonal mRNA with a high efficiency. The ribosomes and
mRNA are then evolved through a duplication strategy developed to evolve highly
specific and active orthogonal pairs using positive and negative selection. With
orthogonal ribosomal and mRNA pairs, Boolean AND and OR gates were constructed.
19
In addition to engineering orthogonal ribosomes, the design of synthetic ribosome
binding sites (RBSs) has been investigated.
19
The major goal of designing synthetic RBSs
is to alter and optimize protein expression levels within the cell where orthogonal
ribosomes are not used to synthesize proteins. The design of RBSs was performed using
a predictive method that interconverts between the DNA sequence of the RBSs and their
function inside a genetic system, allowing for the optimization of the system at a
genetic level. Combination of a biophysical model of translation initiation with an
optimization algorithm allows predictions of the sequence of a synthetic RBS sequence
that provides target translation initiation rate on a proportional scale. This design
method provides prediction of reusing identical RBS sequences in different genetic
contexts that can result in different protein expression levels.
COMPUTATIONAL PREDICTION TOOLS FOR SYNTHETIC BIOLOGY
COMPONENTS
Biomolecular Design
Biomolecular design is a significant aspect of synthetic biology, as demonstrated by the
highlights and development of new tools in biomolecular design applied towards protein
engineering to create proteins with modified or novel functions, engineering of controllable
ribosome binding sites with a specific translation initiation rate, and the design of synthetic
promoter sequences with specific transcription rates.
19,21,24,25
Rosetta is one molecular
modeling tool widely used in protein engineering.
25
Some features of Rosetta include
structure prediction of proteins through ab initio calculation (RosettaAbInitio),
protein
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protein (RosettaDock) and protein
small molecule (RosettaLigand) docking
protein interaction evaluation (RosettaDNA).
25
simulations, and DNA
RBS Designer and RBS Calculator are two tools used to design synthetic RBSs to optimize
the translation of natural or synthetic gene constructs. These tools incorporate
thermodynamic characteristics of the RBS binding to specific coding sequences (CDS)
and the molecular interaction between the ribosomes and mRNA (
Table 8.1
).
19,21
DNA Assembly
In a large genetic combinatorial space, construction of a defined set of DNA sequences is
a powerful method for synthetic biology. However, the process of assembling more than a
few small DNA sequences can be time-consuming, costly, and error-prone. To reduce the
time and cost, as well as improve the efficiency of DNA assembly, a number of standardized
and automatable DNA assembly methods or algorithms have been developed for synthetic
biology.
26
30
Gene Designer is an easy and fast tool for building artificial DNA segments by
a graphic user interface (GUI) that provides facile manipulation of genetic elements. Using
this tool, synthetic new genes can be visually assembled by combining DNA traits.
