Synthetic BiologySynthetic Biology

A Biohacker’s Perspective

[Modified from Sprinzak and Elowitz, 2005]

[Modified from Gardner et al., 2000]

A B Positive feedback loopNegative feedback loop

[Modified from Benner and Sismour, 2005]

[Modified from Purnick and Weiss, 2009]

[Mukherji and van Oudenaarden, 2009]

[Modified from Rothemund, 2006]

[Modified from Andersen et al., 2009] [Modified from Hung et al., 2009]

[Modified from Qian and Winfree, 2011]

Engineered 

Natural 

[Modified from Benner and Sismour, 2005]

[syntheticgenomics.com]

[Gibson et al., 2010]

MOTIVATIONS OF A BIOHACKER“What I cannot build, I cannot understand.” – Richard Feynman

MOTIVATIONS OF A BIOHACKER

[http://2010.igem.org/Image:TU_Delft_ethics_arabidopsis.jpg][http://www.newscientist.com/gallery/microbe‐art/7] [http://www.wired.com/wiredscience/2008/11/amid‐doom‐synth/]

[http://adambluestein.com/2009/11/visible‐results‐2009‐igem‐roundup/][http://adambluestein.com/2009/11/visible results 2009 igem roundup/]

http://www.nytimes.com/imagepages/2010/12/19/JP‐AMATEUR2.html

http://www.nytimes.com/2010/12/19/fashion/19amateur.html?_r=1&ref=fashion

[http://xeobits.com/wp‐content/uploads/2010/12/steve‐jobs‐Steve‐wozniak.jpg]

[http://rt.com/news/biohacking‐harmless‐hobby‐or‐global‐threat/]

[http://magazine.ucla.edu/features/outlaw_biology/]

[http://diybio.org/safety/biosafety‐resources]

[http://www.fas.org/blog/bio/tag/synthetic‐biology/] [http://oba.od.nih.gov/biosecurity/pdf/NSABB%20SynBio%20DRAFT%20Report‐FINAL%20(2)_6‐7‐10.pdf]

[http://www.bioethics.gov/documents/synthetic‐biology/PCSBI‐Synthetic‐Biology‐Report‐12.16.10.pdf]

HOW TO ENGINEER BIOLOGYHOW TO ENGINEER BIOLOGY

LAYER DEFINITION

System Multiple devices connected together to realize a goalSystem Multiple devices connected together to realize a goal

Device Multiple parts with a higher level function

Part A finite sequence of nucleotides with a specific function

[http://ocw.mit.edu/courses/biological‐engineering/20‐020‐introduction‐to‐biological‐engineering‐design‐spring‐2009/lecture‐and‐studio‐notes/wk07/]

DNA Sequence of nucleotides

[http://partsregistry.org/Main_Page]

[http://www.neb.com/nebecomm/products/productE0546.asp]

[http://ginkgobioworks.com/works.html]

[Modified from Martin et al., 2009]

Input Output

[Canton et al., 2008]

[http://ginkgobioworks.com/works.html]

P

GeneR R P

Promoter

Repressor Protein R P

Absent Present

Present Absent

0 1

1 0

Inverter

[Canton et al., 2008]

Plasmid  DNA

Bacterial Cells Mammalian Cells

Yeast Cells

[Purnick and Weiss, 2009]

THE IGEM COMPETITIONTHE IGEM COMPETITION

The challenge: Use (or create) standard biological parts to construct a novel biological t bl f l i l ld isystem capable of resolving a real‐world issue

The rules:1) Undergraduate or high school team members only2) All progress must be meticulously documented in an online wiki lab notebook3) All work must be correctly attributed to the original researcher(s)4) All parts must be constructed to Registry standards and all part DNA must be sent to 

the Registry (after being sequence verified)the Registry (after being sequence‐verified)5) All participants must adhere to the safety guidelines in order to minimize any 

potential risks from newly constructed parts (e.g. adenovirus gene transfer vectors)

[http://2011.igem.org/Requirements]

[Modified from http://parts.mit.edu/wiki/index.php/Schools_Participating_in_iGEM_2006]

[http://ung.igem.org/Results?year=2010]

[http://2011.igem.org/Safety]