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Connecting Minimal Synthetic Biology with Millibiology. 16-Oct-2008 DARPA Cambridge, MA. Classification of replication/reproduction How close to atomic inputs ? (e.g. autotrophs use CO2, N2, etc.) Non-translational, non-universal construction replication: - PowerPoint PPT Presentation
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16-Oct-2008 DARPA Cambridge, MA
Connecting Minimal Synthetic Biology with Millibiology
Classification of replication/reproduction
How close to atomic inputs ?(e.g. autotrophs use CO2, N2, etc.)
Non-translational, non-universal construction replication:•Schulman & Winfree. ECAL 2005. Self-Replication and Evolution of DNA crystals•Sievers D, von Kiedrowski G. Nature. 1994 Self-replication of complementary nucleotide-based oligomers.
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1E-4
1E-2
1E+0
1E+2
1E+4
1E+6
1E+8
1E+10
1E+12
1E+14
1840 1860 1880 1900 1920 1940 1960 1980 2000 2020
Daltons synth
Bits/sec
Seq bp/$
3 Exponential technologies“law of accelerating returns”
Shendure et al. 2004 Nature Reviews of Genetics. Kurzweil 2002; Moore 1965 (24 month doubling til 2020)
urea B12
tRNA
telegraph
Computation &Communication
Analytic
tRNA
Synthetic chemistry
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NextGen Synthesis: off chip
8K Xeotron Photo-Generated Acid
12K Combimatrix Electrolytic
120K Roche, Febit Photolabile 5'protection
244K Agilent Ink-jet standard reagents
Tian et al. 2004 Nature Elledge, Hannon, et al.
$500 per 15Mbp
Application to shRNA & exon capture libraries
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Not minimal genomesHigh speed & accuracy
Mycoplasma 500 RNA & protein genesMitochondria 1500 genesMike Jewett E.coli in vitro 151 genes
• Ease of synthesis• More radical designs • Existing applications -Roche Rapid Translation System (RTS) -Ambion ActivePro In Vitro Translation Kit -Novagen, Promega, Invitrogen, Qiagen Stratagene, Paragon, Amersham
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113 kbp DNA 151 genes
Pure translation:Forster & Church
MSB ’05 GenomeRes.’06
Shimizu, Ueda ’01
Not minimal:High speed &
accuracy requires a few extra genes(E.coli 20 min.
doubling)
Reconstituted ribosomes:
Jewett & Church
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CharalelChurchIsaacsSun
Wang
CarrJacobson
Kong Sterling
New genetic code: viral-resistance, novel amino acidsno functional GMO DNA exchange
TTT
F
30362 TCT
S
11495 TAT
Y
21999 TGT
C
7048
TTC 22516 TCC 11720 TAC 16601 TGC 8816
TTA
L
18932 TCA 9783 TAASTOP
STOP
2703 TGA STOP 1256
TTG 18602 TCG 12166 TAG 314 TGG W 20683
CTT
L
15002 CCT
P
9559 CAT
H
17613 CGT
R
28382
CTC 15077 CCC 7485 CAC 13227 CGC 29898
CTA 5314 CCA 11471 CAA
Q
20888 CGA 4859
CTG 71553 CCG 31515 CAG 39188 CGG 7399
ATT
I
41309 ACT
T
12198 AAT
N
24159 AGT
S
11970
ATC 34178 ACC 31796 AAC 29385 AGC 21862
ATA 5967 ACA 9670 AAA
K
45687 AGA
R
2896
ATG M 37915 ACG 19624 AAG 14029 AGG 1692
GTT
V
24858 GCT
A
20762 GAT
D
43719 GGT
G
33622
GTC 20753 GCC 34695 GAC 25918 GGC 40285
GTA 14822 GCA 27418 GAA
E
53641 GGA 10893
GTG 35918 GCG 45741 GAG 24254 GGG 15090
PEG-pAcPhe-hGH (Ambrx) high serum stability314 TAG to TAA changes
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