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Introduction.
Biochemistry basics.
Adleman’s Hamiltonian path problem.
Danger of errors.
Limitations.
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Introduction
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Dense Information Storage
This image shows 1 gram of
DNA on a CD. The CD can
hold 800 MB of data.
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How enormous is the parallelism?
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How extraordinary is the energy efficiency?
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A Little More………
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Biochemistry Basics
Extraction
given a test tube T and a strand s, it is possible to extract all the strands in T that contain
s as a subsequence, and to separate them from those that do not contain it.
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Why not brute force algorithm?
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Adleman’s Experiment
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Algorithm(non-deterministic)
Assumptions
Random single stranded DNA sequences with 20 nucleotides
are available.
Generation of astronomical number of copies of short DNA
strands is easy to do.
Vertex representation
Each vertex v in the graph is associated with a random 20-
mer sequence of DNA denoted by Sv..
For each such sequence obtain its complement Sv.
Generate many copies of each Sv sequence in test tube T1.
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For example, the sequences chosen to represent vertices 2,4 and 5 are
the following:
S2 = GTCACACTTCGGACTGACCT
S4 = TGTGCTATGGGAACTCAGCG
S5 = CACGTAAGACGGAGGAAAAA
5’ 20 mer 3’
The reverse complement of these sequences are:
S2 = AGGTCAGTCCGAAGTGTGAC
S4 = CGCTGAGTTCCCATAGCACA
S5 = TTTTTCCTCCGTCTTACGTG
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Step1. Random Path Generation.
Edge representation
For each edge uv in the graph, the oligonucleotide Suv is
created that is 3’ 10-mer of Su followed by 5’ 10-mer of Sv
If u=s then it is all of Su or if v=t then it is all of Sv.(i.e.each edge
denoted by 20-mer while the edge that involves either s or t is a
30-mer.)
With this construction, Suv = Svu. (Preservation of Edge
Orientation.)
Generate many copies of each Suv sequence in test tube T2
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5’ S2 3’ 5’ S4 3’
Edge(2,4)
5’ S4 3’ 5’ S5 3’
Edge(4,5)
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S2 = GTCACACTTCGGACTGACCT
S4 = TGTGCTATGGGAACTCAGCG
S5 = CACGTAAGACGGAGGAAAAA
S2 = AGGTCAGTCCGAAGTGTGAC
S4 = CGCTGAGTTCCCATAGCACA
S5 = TTTTTCCTCCGTCTTACGTG
So,we build edges (2,4) and (4,5) from the above sequences obtaining
them in the following manner:
(2,4) = GGACTGACCTTGTGCTATGG
(4,5) = GAACTCAGCGCACGTAAGAC
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Step1.Random Path Generation
Path Construction
Pour T1 and T2 into T3.
In T3 many ligase reactions will take place.
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Step1.Random Path Generation
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Examples of random paths formed
S2 S4 S6 S2 s S3
E24 E46 E62 E2s Es3
S6 S3 S5 t
E63 E35 E5t
s S2
Es2
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Formation of Paths from Edges
and compliments of vertices
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Finally the path (2,4,5) will be encoded by the following double strand.
5’ (2,4)
GTCACACTTCGGACTGACCTTGTGCTATGG……………
CAGTGTGAAGCCTGACTGGAACACGATACCCTTGAGTCGC
S2 S4
(4,5) 3’
………..GAACTCAGCGCACGTAAGACGGAGGAAAAA
…..GTGCATTCTGCCTCCTTTTT
S5
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Step 2
“keep only those that start at s and end at t.”
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Step 3
“keep only those that visit exactly n vertices”
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Step 3
“keep only those that visit exactly n vertices”
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Step 4
“keep only those that visit each vertex at least once”
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Step 5:Obtaining the Answer
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B. Graduated PCR of the product
A. Product of the ligation from step 3( 1 thru 6)
reaction (lane 1),
the molecular weight marker is in
PCR amplification of the lane 7.
product of the ligation
reaction ( 2 thru 5)
molecular weight marker
in base pairs (lane 6).
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Recap of HDPP
Deepthi Bollu 36
ADVANTAGES
Parallelism
Gigantic Memory Capacity
information density =1 bit per cubic
nanometer
data density = 18 Megabits per inch
Low Power Dissipation
Clean, Cheap and Available
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LIMITATIONS
DNA Vs Electronic computers
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Size restrictions
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Error Restrictions
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Hidden factors affecting complexity
There may be hidden factors that affect the time and
space complexity of DNA algorithms with
underestimating complexity by as much as a
polynomial factor because:
they allow arbitrary number of test tubes to be poured
together in a single operation.
Unrealistic assessment of how reactant concentrations
scale with problem size.
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Some more……….
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THE FUTURE!
Algorithm used by Adleman for the traveling salesman problem was simple. As
technology becomes more refined, more efficient algorithms may be discovered.
DNA Manipulation technology has rapidly improved in recent years, and future
advances may make DNA computers more efficient.
DNA computers are unlikely to feature word processing, emailing and solitaire
programs.
Instead, their powerful computing power will be used for areas of encryption,
genetic programming, language systems, and algorithms or by airlines wanting to
map more efficient routes. Hence better applicable in only some promising areas.
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THANK YOU!
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References
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