I believe things like DNA computing will

eventually lead the way to a “molecular

revolution,” which ultimately will have a
very dramatic effect on the world.
L. Adleman

DNA Computing
COMP308
 Presentation Outline
• Basic concepts of DNA
• Origin of DNA Computing
• Solution for NP-Complete Problems
• Advantages of DNA Computing
• Problems with Adleman’s Experiment
• DNA Computers
 What is DNA?
• All organisms on this planet are made of the same type of
genetic blueprint.
• Within the cells of any organism is a substance called DNA
which is a double-stranded helix of nucleotides.
• DNA carries the genetic information of a cell.
• This information is the code used within cells to form proteins
and is the building block upon which life is formed.
• Strands of DNA are long polymers of millions of linked
nucleotides.
Graphical Representation of inherent bonding properties of
DNA
 Double Helix shape of DNA
The two strands of a DNA molecule are anti
parallel where each strand runs in an opposite
direction.

GC base pair and AT base pair

 Basics And Origin of DNA Computing

• DNA computing is utilizing the property of DNA for massively

parallel computation.

• With an appropriate setup and enough DNA, one can

potentially solve huge problems by parallel search.

• Utilizing DNA for this type of computation can be much faster

than utilizing a conventional computer

• Leonard Adleman proposed that the makeup of DNA and its

multitude of possible combining nucleotides could have
application in computational research techniques.
 Travelling Salesman Problem
• In early 1994, Adleman put his theory of DNA computing to
the test on a problem called the Traveling Salesman Problem.
 Travelling Salesman Problem
• Adleman, created randomly sequenced DNA strands 20 bases
long to chemically represent each city and a complementary
20 base strand that overlaps each city’s strand halfway to
represent each street
 Travelling Salesman Problem

• By placing a few grams of every DNA city and street in a test

tube and allowing the natural bonding tendencies of the DNA
building blocks to occur, the DNA bonding created over 109
answers in few hours.

• Adleman only needed to keep those paths that exhibited the

following properties:
– The path must start at city A and end at city G.
– Of those paths, the correct paths must pass through all 7
cities at least once.
– The final path must contain each city in turn.
 Travelling Salesman Problem
The HPP solving algorithm
Input: oriented graph G with n vertices, the initial node
Vin (0) and the final node Vout (0) are denoted in the graph.
• Step 1: generate random paths in the graph (large quantity).
• Step 2: remove all the paths that do not start in the vertex Vin and do not end in
the vertex Vout.
• Step 3: remove all the paths that do not involve exactly n vertices.
• Step 4: for each of the n vertices v, remove all the paths that do not involve
vertex v.
Output: if the set of remaining paths is empty, the result of HPP states No, the
Hamiltonian path does not exist, otherwise Yes, the Hamiltonian paths does
exist and the resulting set contains the solution of HPP
• L. Adleman carried out individual steps of described algorithm with the aid of
DNA molecules and of operations with them.
• The initial calculation took approximately four hours but Adleman’s
extrapolation was performed over a period of a week.
 Advantages of DNA Computing
• Perform millions of operations simultaneously

• Generate a complete set of potential solutions

• Conduct large parallel searches

• Efficiently handle massive amounts of working memory

• cheap, clean, readily available materials

• amazing ability to store information

 Princeton Research
• There have been other researchers since Adlemans work that
have demonstrated similar possibilities of DNA computing.

• In Feb 2000, a group of researchers at Princeton in early 2000

demonstrated a RNA computer similar to Adleman’s which
had the ability to solve a chess problem involving how many
ways there are to place knights on a chess board so that none
can take the others.
 Princeton Research
• "Molecules can store more information than silicon chips, and
this was the largest problem ever solved by a molecular
computer-using either DNA or RNA." said professor Laura
Landweber, the leading Princeton researcher on the project.

• The group demonstrated that using RNA could inherently

scale up to real-world-size problems by virtue of the universal
enzyme
 Problems with Adleman’s Experiment
• The researchers performed Adleman’s Experiment and the
results obtained were inconclusive.

• The researchers state that “At this time we have carried out
every step of Adleman’s Experiment but have not gotten an
unambiguous final result.”

• The problem is because of the underlying assumption that the

biological operations are error-free.
 Problem Instance
• There are 2 problems with extraction:
– The removal of strands containing the sequence in not 100% efficient.
– May at times inadvertently remove strands that do not contain the
specified sequence.

• Adleman’s did not encounter problems with extraction

because only a few operations were required.

• However, for a large problem instance , the number of

extractions required may run into hundreds or even
thousands.
 Problem Instance
• For example, a particular DNA based algorithm may rely upon
repeated “sifting” of a “soup” containing many strands.

• At each stage we may wish to extract only those strands which

satisfy certain criteria.

• Only strands that satisfy the criteria at one stage go through

to the next.
 Problem Instance
• At the end of the sifting process we are left only with strands
that encode legal solutions.

• Assuming 95% efficiency of the extraction process, repetitive

extraction will not guarantee 100% efficiency.

• Furthermore, as the length of the DNA strands being used

increases, so does the probability of the errors.
 Problems Contd.

• Time- Adleman talked of a week of work in lab, but tuning

such an experiment could take one month work

• Contradictory results- We do not know a lot of experiments

like Adleman’s, nor Adleman’s trials of repeating the
experiment.
 Advantages of a DNA Computer
• Parallel Computing- DNA computers are massively parallel.

• Incredibly light weight- With only 1 LB of DNA you have more

computing power than all the computers ever made.

• Low power- The only power needed is to keep DNA from

denaturing.

• Solves Complex Problems quickly- A DNA computer can solve

hardest of problems in a matter of weeks
 Disadvantages of DNA Computer
• High cost is time.

• Occasionally slower-Simple problems are solved much faster

on electronic computers.

• It can take longer to sort out the answer to a problem than it

took to solve the problem.

• Reliability- There is sometime errors in the pairing of DNA

strands