RECOMB-BEDr. Laurie J. Heyer July 20, 2011

Designing and Buildinga Bacterial Computer

laheyer@davidson.edu

Synthetic Biology

Application of engineering principles and mathematical modeling to the design and construction of biological parts, devices, and systems with applications in energy, medicine, environment, and technology.

Hamiltonian Path Problem

Is there a path that:– Starts at node 1– Ends at node 7– Visits each node

exactly once 1

23

4

5

6

7

YES

NO

Hamiltonian Path Problem

Is there a path that:– Starts at node 1– Ends at node 7– Visits each node

exactly once 1

23

4

5

6

7

YES

NO

✔

A Biological Computer

Node = gene

Edge = 2 half-genes

1 2 3 4 5 6 7

GFP BLa CAT Cre cFP T7 TT

1

4

A Biological Computer

Use hin/hix to rearrange edges:

Hin recombinase fromSalmonella typhimurium

A Biological Computer

Use hin/hix to rearrange edges:

Hin recombinase fromSalmonella typhimurium

Hin Recombinase

Identify Solutions

1 4 5 2 3 6 Terminate

GFP BLa CATCre cFP T7 TT

# True Positives = (e - v + 1)! * 2(e - v + 1)

# False Positives = ?

RBS

Promoter

ReporterDetectable Phenotype

Splitting a Gene

✔

hixCRBS

Promoter

Repo- rterDetectable Phenotype? ✔

hixCRBS

Promoter

Repo- rterDetectable Phenotype? ✖

GFP displaying hixC insertion point

Minimize Structural Disruption

Gene-Splitting Strategy

http://gcat.davidson.edu/iGEM07/genesplitter.html

GFP-1 GFP-2

Gene Splitting Tool

Note: Oligos are optimized for melting

temperatures.

Gene Splitter Output

Embed hixC With Silent Mutations

hixC = ttatcaaaaaccatggtttttgataa

L S K T M V F D X

Y Q K P W F L I X

I K N H G F * *

Find genes with the “best” match to one of:L S K…… V F D a a t Y Q K…… F L I a

^ ^ ^ ^ ^ ^ ^ ^

t Y Q K … F L I a

L S K … V F D a a

Conclusion

• Synthetic biology is an emerging bioinformatics playground

• Biology is more efficient with automation• Existing tools are insufficient

– Learn programming (Perl, Python, etc.)– Learn algorithms and data structures– Think and work across disciplinary boundaries

Acknowledgements

Malcolm Campbell (Biology, Davidson College)Todd Eckdahl, Jeff Poet (Missouri Western State Univ.)iGEM ’06 team: Lance Harden, Karmella Haynes, Sabriya Rosemond, Samantha Simpson, Erin ZwackiGEM ’07 team: Oyinade Adefuye, Will DeLoache, Jim Dickson, Andrew Martens, Amber Shoecraft, and Mike Waters Karen Acker ’07 Phillip Compeau ’08 Funding from HHMI, Davidson College, Missouri Western State University, NSF UBM DMS-0733952 and -0733955