Download Error-Corrected DNA Synthesis

Why synthsize genes and genomes?
-minimal life
-genome rewrite
-genetic circuits
-metabolic pathways
DNA length
(base pairs)
103
-individual genes
-assembly scaffolds
104
105
-vaccines
-gene therapy
106
Error Correction with Flawed Components
A circuit containing N (error-free) gates can be simulated with
probability of error at most e, using N log(N/e) faulty gates, which
fail with probability p, so long as p<pth.
von Neumann (1956)
A C G G
T C T G
A C T A
DNA “consensus vote”
Winograd and Cowan (1967) “Reliable
Computation in the Presence of Noise”
A C T G
Complete error correction when no strand
is error-free
Repair Operation
N
M
x
N
M
x
N
M
x
Mismatch
Recognition
+
Nuclease
Activity
Complete error correction when no strand
is error-free
Repair Operation
Exchange
Repair
Copies 1
and 2
N
M
x
Complete error correction when no strand
is error-free
Repair Operation
Exchange
Repair
Copies 1
and 2
N
M
x
Complete error correction when no strand
is error-free
Repair Operation
Exchange
Repair
Copies 2
and 3
Complete error correction when no strand
is error-free
Repair Operation
Exchange
Repair
Copies 2
and 3
Current milestone: 1 error per 20,000 bp
Next milestone: 1 error per 100,000 bp
Why Synthetic Genomes?
Genome Engineering
Nonnatural amino acids
Cellular Chassis
Virus-resistant strains
• Drug biosynthesis of new proteins
– Nonnatural Amino Acids
• Optimal codons
• Genome stability  Safer Bio-isolation
E. coli
rE.coli
Recoding E.coli: rE.coli
1. UAG stop > UAA stop
E. Coli
MG1655
4.6 MB
Remove RF1
- one codon available for unnatural amino acids
- Viral resistance?
2. AGR (R) > CGR (R)
Remove tRNAs, tRNA synthetases
- three codons “free”
- Viral resistance?
3. AGY (S) > UCX (S)
tRNAs: AGY (S) > AGY (L)
3. UUR/CUX (L) > AGY (S)
tRNAs: UUR (L) > UUR (S)
1.
2.
3.
4.
5.
Codons: AGY Ser > UCX Ser
tRNAs: AGY Ser > AGY Leu
Codons: UUR/CUX Leu > AGY Ser
tRNAs: UUR Leu > UUR Ser
Codons: UCX Ser > UUR Ser
(Leu & Ser now switched)