Cells roles for molecular electronic circuits

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Cells roles for molecular electronic circuits

• Lin Zhong
• ELE580B

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Outline

• Background
• Biomolecule assisted fabrication
• DNA and collagen
• Cells possible role
• Size matters
• Cell fabricating
• DNA complex, Collagen/polypeptides
• Get products out

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DNA assisted

• Tagging ssDNA with molecules is not difficult in
  vitro
• DNA annealing is also simple

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DNA assisted

• Challenges
• Annealing neighboring molecules
• Beyond our scope
• Only one dimensional circuit templates

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Beyond one dimensional template

• Seemans work
• No exposed ssDNA!!!
• No active base for annealing or even tagging
• Tag ssDNA before they form the complex
• Form molecular device connections at the same
  time as ssDNA form the complex

Much more complicated than the one-dimensional
case
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Collagen

• Triple helix of polypeptides
• Very stable
• Must have the residues as -Gly-X-Y-
• X and Y are well exposed and active
• Very sticky ends
• Form extracellular matrix
• Collagen synthesis
• Important for many medical purposes
• Recombination collagen

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Circuit assembly
Not difficult once you know what bricks you need
Most challenging!!!
Straightforward
We have to see what roles cells can play
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Outline

• Background
• Cells possible role
• Size matters
• Cell fabricating

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Size matters

• Limit of lithography 10nm
• Atom 0.1-0.4nm
• C-C bond 0.154nm
• Benzene
• hexagon edge0.28nm
• dsDNA width
• 2nm
• Cell membrane
• 7-10 nm thick
• Gate length
• Current CMOS 130nm
• 2007 45nm
• Bacterial cell 3000-5000nm

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Cells possible roles
200 transistors current 0.13um CMOS

• Cell is too big
• They can not be used as templates or movers at
  least for fine granularity .
• Cells are not the best choices for making devices
  directly
• Cells do not scale
• We need a fabrication paradigm to fit cells in

1,500 transistors 2007 0.045um CMOS
30,000 transistors for 1012/cm2 transistor
density expected for molecular electronics
Intels first processor 4004 has only 2,600
transistors. Famous 8086 has about 29,000
transistors.
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Assembly using templates
Cells provide the scaffold. Not itself, but the
building blocks for the scaffold
Facilitate the most challenging task
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The paradigm with biomolecule assistance
Cell fab biomolecule tiles
Reif et al (DNA)
Tile library
Computing during assembly
With or without cell patterning
Tiles assemble into patterned template
Seeman et al (DNA)
Tagging tile with molecular electronic devices
Forming molecular circuit on the template
Well established
???
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Outline

• Background
• Cells possible role
• Cell fabricating
• DNA complex, Collagen/polypeptides
• Get products out

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Cell fabricating

• Are cells better molecule synthesizer?
• DNA crossover
• Holliday junction/DX/TX
• Collagen/polypeptide
• Get the products out

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Cells vs. molecule synthesizers

• Pros.
• May automate the synthesis process
• Productive and versatile
• High product concentration if cross-membrane
  transport possible
• Cons.
• Low product concentration if product
  cross-membrane transport not possible

ABI 3900 High-Throughput DNA Synthesizer
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Get products out
http//www.leeds.ac.uk/arc/e_coli.jpg

• Cell lyse
• Obviously easy
• Low product concentration
• Cross membrane transport
• DNA
• Collagen/polypeptide

http//www.colorado.edu/epob/epob1220lynch/image/S
hHP40205.jpg
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DNA crossover

• Background
• Base for Seemans DNA complex synthesis
• In vivo fabrication
• Cross membrane transport

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Background

• DX/TX tile assembly based computing
• Holliday junction/DX/TX assembly for circuit
  template

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In vivo fabrication

• Homologous recombination
• Plasmid DNA recombination
• Single strand assimilation

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Homologous recombination
http//www.accessexcellence.org/AB/GG/comeiosis.ht
ml
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Plasmid DNA recombination

• E. coli contains 20 copies of pMB9 per cell
• Expose cells to chloramphenicol
• of plasmid molecules increase to 1000 per cell
• Chance of recombination increase
• Digest plasmid preparations with EcoRI
• 0.5 to 3 of the molecules were X shaped.
• http//www.mun.ca/biochem/courses/3107/Lectures/To
  pics/Recombination_holliday.html

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Single strand assimilation (skip)

• Generating single strand DNA
• RecBCD
• Chi site
• Single strand with free 3 end
• Single strand invasion
• RecA promoted
• ATP needed
• RecA mediated exchange
• Partially duplex and entirely duplex DNA
• An intermediate with crossover

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DNA cross membrane transport

• Transport into cells
• Gene delivery for gene therapy
• Cyrus Safinya, UCSB
• Steven Regen, Lehigh
• Transport out of cells
• Bacterial conjugation
• Bacterial budding
• Exocytosis

Errington et al, 2001
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DNA cross membrane transport

• Fool the donor cell
• Lyse the bud
• Exocytosis
• may not work for DNA

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Lyse the bud

• For each manufacturing cell, mark it with a token
  gene or plasmid
• During DNA replication, prohibit replicating the
  token
• After budding, only one of the resulting two
  cells has the token
• Lyse the one without token to get the DNA product
  out

Rons solution
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Collagen fabrication

• Polypeptides
• Intracellular modification
• Form triple helix procollagen
• Procollagen secretion
• Not well understood
• Exocytosis pathway
• Extracellular modification
• Remove protective ends
• Form fibers or other extracellular structures

http//www.fibrogen.com/q/fibers.gif
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DNA vs. Collagen

• Stability
• Both are very stable
• Flexibility
• DNA are more flexible
• DNA bases more active than amino acid residues
• Manufacturability
• DNA synthesis is more mature
• Recombination
• DNA is much better than collagen
• Annealing
• DNA anneal readily if the strands match
• Cross-membrane transport
• Hard for DNA
• Easy for collagen in the form of procollagen
  (secretory pathway exists)
• Potential to form complex super molecules
• DNA demonstrated
• Collagen not yet.

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Conclusions

• Cells are too big for circuit manipulate and
  fabrication at fine granularity
• We need new fabrication paradigms for cells to
  assume more roles
• Not very optimistic
• The current roles for cell
• Not basic unit supplier
• Not assembler
• Not mover
• Just scaffold unit supplier
• Cross-membrane transport important for cells to
  be more productive
• Important even for applications beside molecular
  electronics