Little Data: NextGen Info Storage in DNA
3:55-4:50 PM CBA 7-Mar-2013 12:12-12:21 PM
Thanks to:
.gov
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NIGMS
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.edu
ArmRev.org
.org
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.com
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Oppenheimer
Foundation
NHGRI
Azco
LSRF
Gen9
Read = = = = = = = = I/O = = = = = = = Write

Next-generation Digital Information Storage in DNA
1. Read/write DNA 10-fold/yr: Next = FISSeq
2. E.coli & human genome engineering
3. DNA data archiving
4. Brain Activity Map I/O: Polymerase
Biologically Inspired Engineering

‘Optimistic’ exponential extrapolation
1E+13
1E+12
DNA sequencing
1E+11
& Moore's law
1E+10
1E+9
1.5x/yr for electronics
6 decades
1E+8
1E+7
1E+6
1E+5
1E+4
1E+3
1965 1970 1975 1980 1985 1990 1995 2000 2005 2010 2015 2020 2025 2030 2035 2040
3

1E+13
1E+12
1E+11
1E+10
1E+9
1E+8
1E+7
1E+6
1E+5
1E+4
Early arrival
DNA sequencing
& Moore's law
1.5x/yr for electronics
1E+3
1965 1970 1975 1980 1985 1990 1995 2000 2005 2010 2015 2020 2025 2030 2035 2040
4

Fluorescent in situ Sequencing (FISSEQ)
60 cycles x 4 colors
Single base differences
Lee, Yang, Terry, Nilsson, Church et al.
5

Next-generation Digital Information Storage in DNA
1. Read/write DNA 10-fold/yr: Next = FISSeq
2. E.coli & human genome engineering
3. DNA data archiving
4. Brain Activity Map I/O: Polymerase
Biologically Inspired Engineering

Smaller.
Higher speed & accuracy requires a few extra genes
( E.coli
20 min. doubling)
Reconstituted ribosomes:
Jewett & Church
Pure translation:
Forster & Church
MSB ’ 05
GenomeRes.
’ 06
Shimizu, Ueda ’ 01
113 kbp DNA 151 genes
7

First Genomically Recoded Organism (GRO)
3 New Biological Functions
4.7 Mbp
Metabolic dependence
Safety
New Amino Acids
Lajoie MJ, Rovner AJ, Goodman DB, Aerni HR, Haimovich AD,
Mercer JA, Wang HH, Carr PA, Mosberg JA, Rohland N, Schultz PG,
Jacobson JM, Rinehart J, Church GM, Isaacs FI
Virus resistance
Safety

M ultiplex A ssembly G enome E ngineering (MAGE)
#1: ss-90mer x ds-Circle
Costantino &Court PNAS ’ 03
Wang et al., Nature '09
#2: ss-Mb x ds-Circle conjugation
Isaacs et al., Science
‘
11
CAGE
MAGE
200 kbp BAC
#3: CRISPR #4: 10 Mbp Microcell-Mediated
Chromosome Transfer ( MMCT)
9

ZnF nuclease CCR5 double null in T-cells Sangamo
Phase 2 clinical trial (AIDS treatment)
2007 Leukemia & AIDS:
Timothy Ray Brown
Next: CRISPR RNA guided Nucleases

Next-generation Digital Information Storage in DNA
1. Read/write DNA 10-fold/yr: Next = FISSeq
2. E.coli & human genome engineering
3. DNA data archiving
4. Brain Activity Map I/O: Polymerase
Biologically Inspired Engineering

1977: 3- & 4-way DNA. 2009: caDNAno.org
2012: Douglas, Bachelet, Church. Science
Nanorobot: Sensors, Logic, Actuators
D N A +mAb

12K CustomArray Electrolytic
55K Agilent Ink-jet
80K LCSci/Mycroarray Photo-Acid
6.3M Roche Photo 5’ protection
($0.2K-$13K / chip)
Amplify pools with flanking universal primers
Paths to error correction
1.Hyb-Select: Tian et al. 2004 Nature
2. MutS: Carr & Jacobson 2004 NAR
3. MutHLS: Smith & Modrich 1997 PNAS
4. Endo/Exonuclease : Bang Nat Meth. 2008
5. Errase
6. Sequencing
13

Images  Camera  Computer  Inkjet  DNA  Polymerase
Text printer copying
Images

RNA Polymerase
DMD + Nitrobenzyl

2012 Church, et al
2013 Goldman et al.
1986 Davis, et al.
Digital Inkjet 2012
DNA-video 2013
Kosuri
15

Next-generation Digital Information Storage in DNA
1. Read/write DNA 8-fold/yr
2. Fluorescent In Situ Sequencing (FISSeq)
3. Nanorobots & DNA data archiving
4. Brain Activity Map I/O: Polymerase
Biologically Inspired Engineering

Sep 2011: Kavli, Gatsby, Allen: Chun
Imaging: Greenspan, Yuste, Zhaung, Reid
Optical fibers: Roukes, Boyden, Scherer
Nano: Alivisatos, Park, Weiss, McEuen
Stimulation: Donoghue, Deisseroth
Computation: Kording, Sejnowski
Polymerase: Zamft, Marblestone, Schmidt, Tyo,
Martín-Alarcón, Marcus
17

Quiroga et al. 2005 Nature. Invariant visual representation by single neurons in the human brain (left posterior hippocampus)

Konrad Kording

Polymerase
7e25 Op/kWh
economist.com/node/2153
1350
20

DNA
Pol

Dpo4 Pol
Zamft, Marblestone et al. PLoS One 2012
DNA
Pol

.

.

Brain Activity Map I/O
Why?
Blindness, deafness, stroke, traumatic brain injuries, spinal cord injuries, Parkinson ’ s, chronic pain, depression, locked-in syndrome, dystonia, essential tremor, epilepsy, neurodegenerative diseases.
Alivisatos, Chun, Church, Donoghue, Greenspan, Roukes,
Yuste; The Brain Activity Map Project and the Challenge of Functional Connectomics. Neuron 2012
25

Ju Lu, Harvard University Miesenböck Science 2009

Wireless molecular I/O. 100M Neural cells

Next-generation Digital Information Storage in DNA
1. Read/write DNA 8-fold/yr
2. Fluorescent In Situ Sequencing (FISSeq)
3. Nanorobots & DNA data archiving
4. Brain Activity Map I/O: Polymerase
Biologically Inspired Engineering

Zorzos et al 2012 Optics Letters
.

42nm spacing fluorescent barcodes . Nature Chem 2012
Lin, Jungmann, Leifer, Li, Levner, Church, Shih, Yin

RNA & DNA
Jay Lee
Evan Daugharthy
Reza Kalhor
Jonathan Scheiman
Michael Sismour
Joyce Yang
John Aach
Kun Zhang
Yoav Mayshar
Polonator & Advanced
Technology Team:
Nicholas Conway
Daniel Levner
Chao Li
Richard Terry
Brian Turczyk
Frederick Vigneault

•
Exercise
•
Drink your milk
•
Eat your grains
•
& beans
•
& iron
•
& meat
•
Get more rest

•
Exercise HCM (cardiac arrest)
•
Drink your milk MCM6 (gastric distress)
•
Eat your grains HLA-DQ2 (diarrhoea)
•
& beans
•
& iron
•
& meat
•
Get more rest
G6PD (red cell lysis)
HFE (Liver damage)
LDLR (clogged arteries)
HLA-DR2 (excessive sleep)

Most new Sequencing = single-molecule imaging
1. Danaher MA
2. Roche-454 CT
3. AB-SOLiD MA
4. Illumina UK,CA
5. CGI/BGI CA
6. Helicos MA
7. Pacific Bio CA
8. IBS/Qiagen MA
9. Ion Torrent CT
17. LightSpeed CA
10. Genapsys CA
11. Electronic Biosci CA
12. Nabsys RI
13. OxfordNanopore UK
14. Genia CA
15. IBM-Roche NY
16. NobleGen MA
18. GnuBio MA
19. Bionanomatrix PA
20. Halcyon CA
21. ZS Genetics NH
22. Electron Optica CA
23. Genizon BioSci QC
24. LaserGen TX
25. GE Global NY
26. Stratos Genomics WA
27. Reveo NY
28. Firebird FL
29. Zeiss MA
30. Lucigen WI
31. Adv. Liquid Logic NC
32. Caerus Molec Diag CA
33. Nanophotonics Biosci CA
34. Network Biosystems MA
35. SeiraD NM
36. Affymetrix CA
37. Population Gen Tech UK
38. AQI Sciences AZ
39. Base4innovation UK
40. Li-Cor NE
41. U.S. Genomics MA
42. Mobious Genomics UK
43. Visigen TX
44. Starlight CA
34 http://arep.med.harvard.edu/gmc/nexgen.html

Nanopore : Polymer vs Monomer vs NanoTag
1988-1995 :
Church,
Deamer,
Branton,
Baldarelli,
Kasianowicz.
2012: Oxford & Genia
GG
TTT CCC
AAA
2009 Clarke, Bayley, et al
2010 Derrington, Gundlach, et al
2012 Cherf, Akeson, et al
5′ GCAACAGAGCCAGC CCC
35
GCAACAGAGCCAGC AAA GCAACAGAGCCAGC CCC
GCAACAGAGCCAGC TTT GCAACAGAGCCAGC GG
A A15 3′.

Nanopore: Polymer vs Monomer vs NanoTag
A
C
“accuracy better than
1 in 5x10 8 events”
G T
Oxford, Genia
PEG-Labeled PP: Ju, Kasianowicz, et al.
Scientific Reports 2012