Download Challenging traditional approaches to

Challenging Traditional Approaches to Computation:
A Biomolecular Transducer Employing Ternary Language
and Rendering a Biological Output
Paul Lazarescu and Mark Chaskes
Mentor: Tamar Ratner
The Schulich Faculty of Chemistry, Technion-Israel Institute of Technology
Design and Development
Abstract
Biomolecular computing is a new
field of research, merging several
sciences. Previous works were
based on finite state automata
and have had limited computing
capabilities. In this project, a
transducer model was used in
order to design a biomolecular
machine with greater computing
potential. In this research, two
automata were designed as
software for the transducer: one
able to divide a ternary input by
three and the other by two. By
making use of a plasmid this
transducer could perform multiple
computations consecutively.
Figure
r1p0
S0
S0 r2p1 S0
S0 r1p0 S1
S1 r1p2 S0
S1 r0p1 S1
S1 r2p2 S1
S1
S0
r1p2
r2p2
r0p0
Figure 3
r2p0
A.
r0p0
B.
S1
S0
S2
r0p1
r2p2
S1 r0p1 S0 S2 r0p2 S0
S1 r1p1 S1 S2 r1p2 S1
S1 r2p1 S2 S2 r2p2 S2
r1p2
S0 to S0, read 0, print 0
AGTCTT...8 base...CTCCTCGCAGC...2 base
AATCAGAA...pairs ...GAGGAGCGTCG...pairs...TCAG
0
BseRI BbvI
S0 to S1, read 1, print 0
AGTCTT...8 base...CTCCTCGCAGC...1 base
AATCAGAA...pairs ...GAGGAGCGTCG...pairs...CCAT
AGTCTT...8 base...CTCCTCGCAGC
AATCAGAA...pairs ...GAGGAGCGTCGGAGC
S1 to S0, read 0, print 1
GGTATT...8 base...CTCCTCGCAGC...3 base
AACCATAA...pairs ...GAGGAGCGTCG...pairs...CAGA
S1 to S1, read 1, print 1
Figure 4
r0p2
Figure 4: The divide-by-three transducer used in this project. A. A schematic
diagram of the transducer. ‘r’ represents the ‘read’ symbol and ‘p’ represents the
‘printed’ symbol. B. Transition rules of this transducer.
0
B.
Sequences decided upon AGTCTT
for each symbol
TCAGAA
Sticky ends left by
AGTCTT
sequences cleaved in S0
AA
1
2
GGTATT
CCATAA
CTCGTT
GAGCAA
GGTATT
AA
Figure 5: A. The state of
the transducer depends
Sticky ends left by
GTCTT
GTATT
on the way the symbol
sequences cleaved in S1
A
A
was cleaved. B. The
symbols
cleaved
in
Sticky ends left by
TCTT
TATT
different states leaving sequences cleaved in S2
unique sticky ends
Figure 5
Terminator
TGCTGA
ACGACT
CTCGTT
AA
TGCTGA
CT
TCGTT
A
GCTGA
T
CGTT
CTGA
Results
1[1]
GGTATT...8 base...CTCCTCGCAGC...2 base
AACCATAA...pairs ...GAGGAGCGTCG...pairs...CATA
S1 to S2, read 2, print 1
GGTATT...8 base...CTCCTCGCAGC...1 base
AACCATAA...pairs ...GAGGAGCGTCG...pairs...AGCA
S2 to S0, read 0, print 2
CTCGTT...8 base...CTCCTCGCAGC...4 base
AAGAGCAA...pairs ...GAGGAGCGTCG...pairs...AGAA
Terminator
AATTCGGCCGTT..8 base..CTCCTCGCAGC..8 base..CTCGTTAGTCTTAGTCTTTGCTGAAATT
TTAAGCCGGCAA..pairs ..GAGGAGCGTCG..pairs ..GAGCAATCAGAATCAGAAACGACTTTAA
BseRI Recognition Site
+
A
(18 in base ten)
2
0
0
BbvI Recognition Site
Spacers
BbvI
BseRI
Plasmid
First cut by restriction enzymes
AATTCGGCCGTT
TTAAGCCGGC
B
CTCGTTAGTCTTAGTCTTTGCTGAAATT
AATCAGAATCAGAAACGACTTTAA
(S0,2)
+ All TM
First Ligation
addition of transition molecule S0 to S2 (read 2, print 0)
C
AATTCGGCCGTTAGTCTT..8 base..CTCCTCGCAGCCTCGTTAGTCTTAGTCTTTGCTGAAATT
TTAAGCCGGCAATCAGAA..pairs ..GAGGAGCGTCGGAGCAATCAGAATCAGAAACGACTTTAA
Figure 2[2]
DNA Based Transducer: a more
complex version of an automaton,
that can both ‘read’ and ‘print’
information using double-stranded
DNA (dsDNA).
+
BbvI
BseRI
Restriction Enzyme Type II (Fig.
2A): cleaves dsDNA at a certain
distance from a recognition site.
Final Cut
AATTCGGCCGTTAGTCTTCTCGTTAGTCTT
TTAAGCCGGCAATCAGAAGAGCAATCAG
(S0,T)
+ All DM
Soreni, S. Yogev, E. Kossoy, Y. Shoham, E. Keinan, Parallel
Biomolecular Computation on Surfaces with Advanced Finite
Automata. J. AM. CHEM. SOC. 127, 3935-3943 (2005).
TGCTGAAATT
CTTTAA
Final Ligation
bonding of detection molecule to sticky ends of terminator
AATTCGGCCGTTAGTCTTCTCGTTAGTCTTTGCTGA...Reporter...TGCTGAAATT
TTAAGCCGGCAATCAGAAGAGCAATCAGAAACGACT....Gene 0....ACGACTTTAA
0
Plasmid: a circular vector found in
bacteria, in which a foreign DNA
sequence is easily inserted.
from the National Human Genome Project
TCTTAGTCTTTGCTGAAATT
TCAGAAACGACTTTAA
Repeat cycle of restriction, hybridization, and ligation until the terminator is cleaved
DNA Ligase (Fig. 2A): covalently
bonds different fragments of
dsDNA to each other.
Sticky End (Fig. 2C): unpaired
single
strand
DNA
(ssDNA)
overhangs. These sequences
bond to other DNA sticky ends
with complementary base pair
sequences.
Second Cut
AATTCGGCCGTTAGTCTT
TTAAGCCGGCAATCAG
2
0
Terminator
CTCGTT...8 base...CTCCTCGCAGC...3 base
AAGAGCAA...pairs ...GAGGAGCGTCG...pairs...ATAA
S2 to S2, read 2, print 2
CTCGTT...8 base...CTCCTCGCAGC...2 base
AAGAGCAA...pairs ...GAGGAGCGTCG...pairs...GCAA
Figure 8: The TM for the divide-by-three
transducer. For every transition rule of the
transducer, one transition molecule had to be
designed. Another six transition molecules
were created for the divide-by-two transducer.
Detection Molecule (DM)
Input (divide-by-three transducer)
EagI Recognition Site
D
[2] M.
S0 r0p0 S0
S0 r1p0 S1
S0 r2p0 S2
r1p1
A.
Transition Molecules (TM)
S0 to S2, read 2, print 0
r2p1
r1p0
DNA Based Automaton (Fig. 2):
a model that can ‘read’ DNA
symbols and change it’s state
according to the read data.
[1] Adapted
Figure 3: The divide-by-two transducer used
in this project. The transduer begins in state
0 (S0). A. A schematic diagram of the
transducer. 'r' represents the 'read' symbol
and 'p' represents the 'printed‘ symbol. B.
Transition rules of this transducer. For each
transition rule there is a transition molecule.
r 0 p 1 B. S0 r0p0
S2 to S1, read 1, print 2
Introduction Terms
DNA (Fig. 1): double
strand molecule. Made
of base pairs: cytosine
(C) only bonds to
guanine
(G),
and
adenine (A) only bonds
to thymine (T).
A. r 2 p 1
Molecules Design
Terminator
Reporter Gene 0 inserted and can be expressed by
bacteria, or, a second computation can occur.
Figure 6
Figure 6: An example of a computation process on an input string of ‘200’ (equivalent
to 1810), using the DNA based transducer that divides by three.
Figure 9: The DM TGCTGA...Reporter...
AAACGACT....Gene 0....ACGA
bonds
with
the
cleaved
terminator. TGCTGA...Reporter...
These
molecules AAACGACT....Gene 1....CGAC
instigate a biological
function (releasing a TGCTGA...Reporter...
drug, giving a bacterial AAACGACT....Gene 2....GACT
Figure 9
phenotype output, etc.) and print
the terminator symbol to continue
the computation.
Discussion
Two software for a DNA based
transducer were created. A
variety of molecules were also
designed as the components of
the transducers. The models and
the molecules were simulated
and checked using a computer
program. The molecules were
processed and functioned as
expected, and the design worked
properly. Creating a biomolecular
transducer has not yet been
accomplished
experimentally.
However, this science can have
many applications.
Conclusions
In
the
future
biomolecular
computers will hopefully integrate
into biological systems. Because
these machines are capable of a
biological output, this project is
literally cutting-edge science.
These devices are unlikely to
replace the common computer.
Instead, due to their capability for
direct interface, the importance of
biomolecular
computing
lies
within the integration of biological
systems, in fields ranging from
medicine to agriculture.
Acknowledgements: We would like to sincerely thank our mentor Tamar Ratner for her dedication, as well as Professor Ehud Keinan for allowing us to use his
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laboratory. We also would like to thank Mr. Russell N. Stern and the Louis Herman Israel Experience Fund for their generosity and donation.
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