Towards Molecular Computation:
or Genetically-modified Computers
David A. Hodgson
Dept. Biological Sciences
University of Warwick
The Warwick - Exeter- London Connection
Warwick
•Dr David A. Hodgson
•Dr Gerald Owenson (now left)
King’s College London
•Professor Alan Gibbons
Exeter
•Dr Martyn Amos
Towards Molecular Computing - David A. Hodgson
Presentation plan
•Feynman’s proposal for a molecular computer
•Schrödinger’s paradox
•The cell as a molecular computer, information transfer in the cell
•DNA as a computing matrix
•The Map Three Colour Problem
- Our solution
•Boolean circuits
- Our solution
•Sporulation induction
- An illustration of a simple integrative switch
Towards Molecular Computing - David A. Hodgson
Feynman’s Paper “There’s Plenty of Room at the Bottom”
Towards Molecular Computing - David A. Hodgson
Schrödinger’s paradox
Towards Molecular Computing - David A. Hodgson
The cell as a molecular computer, information transfer in the cell
THE CENTRAL DOGMA
Replication
Transcription
DNA
Translation
RNA
PROTEIN
Information
Transfer
Effector
Molecule
Reverse
Transcription
Information
Storage
Towards Molecular Computing - David A. Hodgson
Central Dogma – WHAT IS DNA?
3’ hydroxyl
5’ phosphate
Space-filling model of
DNA. Note major and
minor grooves
Stick and ball
representation of DNA
showing anti-parallel
chains 3’ hydroxyl
5’ phosphate
Expanded view of
a chromosome,
ignoring the proteins
Towards Molecular Computing - David A. Hodgson
CENTRAL DOGMA - WHAT IS A GENE?
Start of translation
- Ribosome Binding Site
including the start codon
Operators - binding sites
for regulatory proteins
- Repressors and Activators
End of translation
- Stop codons
Start of transcription
- Promoter
Towards Molecular Computing - David A. Hodgson
End of transcription
- Terminator
CENTRAL DOGMA - PROTEINS AS EFFECTORS
•Enzymes and gene regulators are proteins (usually)
•Protein function is dependent on its shape
•Protein shape is dependent on protein sequence
•Protein sequence is dependent on gene sequence
Towards Molecular Computing - David A. Hodgson
CENTRAL DOGMA - SHAPE DETERMINES FUNCTION
C released
C
A
Enzyme binds
substrate A
B
A & B react
to form C
C
A
Enzyme binds
substrate B
A
B
B
Towards Molecular Computing - David A. Hodgson
CENTRAL DOGMA – ALLOSTERY
D
A
B
D
Binding inhibitor D changes
active site so substrates
cannot bind
A
B
D
Binding activator D changes
active site so substrates can bind
A
A
B
D
B
Towards Molecular Computing - David A. Hodgson
The Map Colouring or Three Vertex Colouring Problem
5
4
4
5
6
1
1
3
3
2
4
5
2
Soluble
4
5
1
1
3
2
3
2
Insoluble
Towards Molecular Computing - David A. Hodgson
6
Our solution to the three colour map problem - 1
vertex 1
sequence representing vertex 1
contains sequence representing
one of three colours
Assemble vertex sequences in a colour independent manner
vertex 1
vertex 2
vertex 3
vertex 4
vertex 5
vertex 6
Colour sequences
"red" "blue" or
"green"
Towards Molecular Computing - David A. Hodgson
vertex 7
vertex 8
Our solution to the three colour map problem - 2
vertex 1
vertex 2
vertex 3
vertex 4
Destroy all chains with
red or green at vertex1
vertex 5
vertex 6
vertex 7
Destroy all chains with
red or blue at vertex1
vertex 1 vertex 2
vertex 3
vertex 4
vertex 5 vertex 6
vertex 8
Destroy all chains with
green or blue at vertex1
vertex 7
blue
Destroy all chains with blue
vertices that contact vertex 1
directly or indirectly
Towards Molecular Computing - David A. Hodgson
vertex 8
Our solution to the three colour map problem - 3
After destroying with red vertex 1 chains with restricted red vertices
and green vertex 1 chains with restricted green vertices,
pool red blue and green vertex 1 chains.
Destroy all chains with
red or green at vertex2
Destroy all chains with blue
vertices that contact vertex 2
directly or indirectly
Destroy all chains with
red or blue at vertex2
Destroy all chains with green
vertices that contact vertex 2
directly or indirectly
Destroy all chains with
green or blue at vertex2
Destroy all chains with red
vertices that contact vertex 2
directly or indirectly
Pool and continue cycle of restriction until all vertices dealt with.
Towards Molecular Computing - David A. Hodgson
Our solution to the three colour map problem - 4
1. No chains left at end = insoluble problem
2. Chains left at end can be cloned and
sequenced to reveal solutions
Towards Molecular Computing - David A. Hodgson
Molecular v. Silicon Computing
Computation
Desktop PC
Supercomputer
Theoretical biocomputer
6
10 operations s-1
1012 operations s -1
20
10 operations s -1
Limitation
Linear computational time BUT exponential DNA mass.
e.g. 200 vertex HPP needs an amount of DNA greater
than the mass of the Earth
Towards Molecular Computing - David A. Hodgson
Boolean Circuits - Gates
AND gate
1
0
0
OR gate
1
0
1
NAND gate
1
0
1
0 0=0
1 0=0
0 1=0
1 1=1
Inclusive
0 0=0
1 0=1
0 1=1
1 1=1
0
1
0
1
Exclusive
0 0=0
1 0=1
0 1=1
1 1=0
0=1
0=1
1=1
1=0
Towards Molecular Computing - David A. Hodgson
Boolean Circuits - NAND Circuits
1
0
1
1
G1
G3
G2
Towards Molecular Computing - David A. Hodgson
? =1
Gene regulation 1 - Definitions
Activator
- Protein that binds to promoter and switches it on.
Repressor
- Protein that binds to promoter and switches it off.
Co-activator
- Small molecule that activates an activator or
inactivates a repressor.
Co-repressor
- Small molecule that activates a repressor or
inactivates an activator.
Towards Molecular Computing - David A. Hodgson
Gene regulation 2 - Lactose operon
Activator
- Cyclic Amp (cAMP) binding protein - CBP.
Repressor
- Lactose repressor - LacI.
Co-activator
- cAMP - activates CBP. cAMP level dependent on
glucose concentration. High glucose - low cAMP.
Co-activator
- Lactose - inactivates LacI.
Towards Molecular Computing - David A. Hodgson
Gene regulation 3 - Lactose operon
ALLOSTERY AND GENE REGULATION
Binding inhibitor changes
protein so DNA cannot bind
Binding activator changes
protein so DNA can bind
Towards Molecular Computing - David A. Hodgson
Gene regulation 4 - Lactose operon
LacI
Gene off
Promoter
CBP
Lactose
LacI
Gene off
Promoter
Towards Molecular Computing - David A. Hodgson
Gene regulation 5 - Lactose operon
Glucose high - cAMP low
CBP
LacI
Gene off
Glucose low - cAMP high
LacI
cAMP
CBP
Promoter
Towards Molecular Computing - David A. Hodgson
Gene on
Boolean Circuits. Our Solution - 1
Arabinose
Lactose
G1
HSL
G3
Rhamnose
Maltose
G2
Light
LuxR
HSL = homoserine lactone - co-activator of the LuxR activator
Towards Molecular Computing - David A. Hodgson
Boolean Circuits. Our Solution - 2
Arabinose
Lactose
HSL
G1
HSL
Arabinose
Lactose
AraC
CI
LacI
araC
Promoter 1
AraC
Promoter 2
CI inactivates
promoter 3
λcI
LuxI
luxI
Promoter 3
The CI repressor is made only if both arabinose and lactose are present. Therefore
LuxI, and hence HSL, will be made unless both arabinose and lactose are present.
Towards Molecular Computing - David A. Hodgson
Boolean Circuits. Our Solution - 3
Rhamnose
Maltose
LuxR
G2
Rhamnose
Maltose
RhaC
MalT
Promoter 4
rhaC
MuC
RhaC
Promoter 5
MuC inactivates
promoter 6
Muc
LuxR
luxR
Promoter 6
The MuC repressor is made only if both maltose and rhamnose are present. Therefore
LuxR will be made unless both maltose and rhamnose are present.
Towards Molecular Computing - David A. Hodgson
Boolean Circuits. Our Solution - 4
HSL
LuxR
G3
Light
Light
HSL
P1C
LuxR
Promoter 7
P1C inactivates
promoter 8
LuxA LuxB
luxAB
P1c
Promoter 8
The P1C repressor is made only if both HSL and LuxR are present. Therefore
LuxAB, and hence light, will be made unless both HSL and LuxR are present.
Towards Molecular Computing - David A. Hodgson
Boolean Circuits. Our Solution - 5
Arabinose
Lactose
G1
HSL
G3
Rhamnose
Maltose
G2
Light
LuxR
HSL = homoserine lactone - co-activator of the LuxR activator
Towards Molecular Computing - David A. Hodgson
Exploiting the integrative
function of living systems - 1
Spore Resistance
• Heat
• Solvents
• UV Light
Cues for Sporulation
Internal
Cell cycle
Cell physiology
Stress - Heat
- Alcohol
- pH
External
Nutrient levels
Population
Towards Molecular Computing - David A. Hodgson
Exploiting the integrative
function of living systems - 2
Phosphorylated
0A (0A~P) is the
master sporulation
gene regulator.
The closer the
operator to the
consensus
sequence (0A~P
Box) the lower the
concentration of
0A~P needed
0A~P Box
5’TGNCGAA3’
Towards Molecular Computing - David A. Hodgson
Exploiting the integrative
function of living systems - 3
KinA
0F
0F~P
0B~P
0B
0A
0A~P
Towards Molecular Computing - David A. Hodgson
Exploiting the integrative
function of living systems - 4
MEMBRANE
KinB KapB
KinC
KinA
0F
0F
0F~P
0B~P
0B
0A
0A~P
0B
0B
0A
0A
0F~P
0F~P
0B~P
0B~P
0F
0A~P
0A~P
KinD
KinE
Towards Molecular Computing - David A. Hodgson
KinC?
Exploiting the integrative
function of living systems - 5
ARNQT
MEMBRANE
KinA
ARNQT
SRNVT
0F~P
0F
RapA
RapB
RapE
Towards Molecular Computing - David A. Hodgson
SRNVT
Exploiting the integrative
function of living systems - 6
KinA
STRESS
Heat
Alcohol
Oxygen
0F
0F~P
0B~P
0B
0A
0A~P
PROTEASES
0E
Towards Molecular Computing - David A. Hodgson
Exploiting the integrative
function of living systems - 7
Chromosome
Partition
Complex
Cell Cycle
Signals
KinA
0J
0F
0F~P
0B~P
0B
0A
0A~P
Soj
Towards Molecular Computing - David A. Hodgson
0bg
Exploiting the integrative
function of living systems - 8
Nutrient Status
Population Density
Cell Physiology
Cell Cycle
Environmental Stress
Chromosome Partition
Sporulation
Towards Molecular Computing - David A. Hodgson