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Prospects and Present Hurdles of DNA Computing

Parmeshwar Tukaram Panchal*
Neha Kode**
*State Bank of India
Parmeshwar.panchal@sbi.co.in
**S.N.D.T Women's University
P.G.D. of Computer Science, Mumbai
kodeneha@yahoo.com

Abstract
It is found that silicon in microprocessors will reach to its limits as it is physical material.
Demanding more mentality and requirements as well will enforce to seek a new material to
replace Si. New material-DNA is ready to replace. This paper discuss about the theory of DNA
Computing, studies,possibilities,drawbacks and threats.

Introduction
DNA computing, or, more generally, molecular computing, is an exciting fast developing
Interdisciplinary area. Research in this area concerns theory, experiments, and applications of
DNA computing. In this paper, we demonstrate the theoretical developments by discussing a
number of selected topics. We also give an introduction to the basic structure of DNA and the
basic DNA processing tools.

Why DNA Computation?

 Miniature

Comparatively very small in size

Hold more data

E.g. 1 trillion DNA molecules fit in 1 cm3.

 Using DNA logic gates PCs can be more powerful than super computers.

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 This approach decreases the size and increases the speed of processors.

 It can be thought as rigorous alternative to solve the existing critical problems.

 It can be used as a tool to overcome current economic (cheaper than silicon) and
environmental problems (does not have harmful contents to environment).

DNA Structure

 The DNA is a double stranded molecule.

 Each strand is based on 4 bases:

 Adenine (A)

 Thymine (T)

 Cytosine (C)

 Guanine (G)

 Those bases are linked through a sugar (desoxyribose)

 IMPORTANT:

 The linkage between bases has a direction.

 There are complementarities between bases (Watson-Crick).

(A)ßà (T)

(C)ßà(G)

 Annealing is promoted by cooling, and reversed by heating

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History
Since the presentation of Feynman’s vision there has been an steady growth of interest in
performing computations at a molecular level. In 1982,Charles Bennett (3) proposed the concept
of a “Brownian computer” based around the principle of reactant molecules touching, reacting,
and effecting state transitions due to their random Brownian motion. Bennett developed this idea
by suggesting that a Brownian Turing Machine could be built from a macromolecule such as
RNA. “Hypothetical enzymes”, one for each transition rule, catalyze reactions between the RNA
and chemicals in its environment, transforming the RNA into its logical successor.Adleman had
successfully solved "travelling salesman problem”. It inspired many.

The first DNA computation

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This is the first ever successful computation performed using strands of DNA. The instance of
the HPP that Aldeman solved is shown in above figure with dashed lines .His approach was
simple:

1.Generate strands encoding random paths such that the Hamiltonian Path (HP) is
represented with high probability .The quantities of DNA used far exceeded those necessary for
the small graph under consideration ,so it is likely that many strands encoding the HP were
present.

2. Remove all strands that do not encode a solution to the HPP.

3. Check that the remaining strands encode a solution to the HPP.

Basic operational change

Computers today all use binary codes - 1's and 0's or on's and off's. These codes are the basis for
all possible calculations a computer is able to perform. Because the DNA molecule is also a
code, Adleman saw the possibility of employing DNA as a molecular computer. However, rather
than relying in the position of electronic switches in a microchip, Adleman relied on the much
faster reactions of DNA nucleotides binding with their complements, a brute force method that
would indeed work (1). Some DNA-based computations apply a sequence of biological
operations to a set of strand.

Usually these operations are performed by using synthesizer .Thus any problem can be encoded
in DNA strand.

Modern advances in genetic s have provided a powerful range of tools for manipulating DNA
like PCR,Gel electrophoresis, Magnetic bead separation ,Bacterial cloning.

DNA computation consists of manipulations, the result of which is encoded in the resulting DNA
sample

Research work in progress

Currently, at the University of Wisconsin, a research team is looking into DNA computing. The
university team created a crude molecular computer "chip" made of a small glass plate covered
with a thin layer of gold (2). Strands of DNA were coded to represent solutions to a

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computational problem with 16 possible answers. Then, enzymes were applied to the gold slide
to strip out the entire DNA with the incorrect answers and, and thus, solving the calculation. "It
opens up the possibility of ultrahigh-capacity storage and massively parallel searches," explains
Robert Corn, a professor of chemistry and a member of the research team. A DNA computer the
size of a penny, for example, could hold up to 10 terabytes of data, far exceeding the capacity of
any computer storage medium available today(2).

The research on DNA computers is ongoing still. All over the country, research teams like the
one at the University of Wisconsin are concentrating their efforts in order to put this new
nanotechnology to good use. And even though Adleman's DNA computer would have a hard
time computing two 100-digit integers - an easy task for a supercomputer - its ability to solve
complex problems is unmatched. As this new nanotechnology continues to evolve, we might yet
be surprised again. The DNA based system of computing has had millions of years to evolve,
while the man-made systems have only been around for a small fraction of that time (1). The
future of DNA computing has yet to be decided. Anne Condon, a computer scientist on the
Wisconsin team, likens compares current DNA computing to that of ENIAC computers. Built in
1946, ENIAC computers used punch cards and closets full of vacuum tubes to solve simple
arithmetical problems (2).

Working?
DNA computation is based on the fact that technology allows us to 'sequence' (design) single
DNA strands which can be used as representations of bits of binary data. Technology also allows
us to massively 'amplify' (reproduce) individual strands until there are sufficient numbers to
solve complex computational problems.

Structure discovered by Watson and Crick consists of two strands of DNA wound around each
other. Each strand has a long polymer backbone built from repeating sugar molecules and
phosphate groups. Each sugar group is attached to one of four "bases". These four bases -
guanine (G), cytosine (C), adenine (A) and thymine (T) - form the genetic alphabet of the DNA,
and their order or "sequence" along the molecule constitutes the genetic code.

In the cell, DNA is modified biochemical by a variety of enzymes, which are tiny protein
machines that read and process DNA according to nature's design. Just like a CPU has a basic
suite of operations like addition, bit- shifting, logical operators (AND, OR, NOT NOR), etc. that

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allow it to perform even the most complex calculations; DNA has cutting, copying, pasting,
repairing, and many others. Many copies of the enzyme can work on many DNA molecules
simultaneously. This is the power of DNA computing, that it can work in a massively parallel
fashion. Pairs of molecules on a strand of DNA represent data and two naturally occurring
enzymes act as the hardware to read copy and manipulate the code.

Limitations
However, there are certain shortcomings to the development of the DNA computers:

1. A factor that places limits on his method is the error rate for each operation. Since these
operations are not deterministic but stochastically driven, each step contains statistical errors,
limiting the number of iterations one can do successively before the probability of producing an
error becomes greater than producing the correct result.

2. Algorithms proposed so far use relatively slow molecular-biological operations. Each

primitive operation takes hours when you run them with a small test tube of DNA. Some
concrete algorithms are just for solving some concrete problems. Every Generating solution sets,
even for some relatively simple problems, may require impractically large amounts of memory.
Also, with each DNA molecule acting as a separate processor, there are problems with
transmitting information from one molecule to another that have yet to be solved.

Advantages
1. Perform millions of operations simultaneously. The massively parallel processing
capabilities of DNA computers may give them the potential to find tractable solutions to
otherwise intractable problems, as well as potentially speeding up large, but otherwise
solvable, polynomial time problems requiring relatively few operations.

2. Another advantage of the DNA approach is that it works in "parallel," processing all
possible answers simultaneously. Therefore it enables to conduct large parallel searches
and generate a complete set of potential solutions.

3. DNA can hold more information in a cubic centimeter than a trillion CDs, thereby
enabling it to efficiently handle massive amounts of working memory.

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4. The DNA computer also has very low energy consumption, so if it is put inside the cell it
would not require much energy to work and its energy-efficiency is more than a million
times that of a PC.

Challenges to Implementation:
1. Practical protocols for input and output of data into the memory.

2. A Representation of data in DNA sequences.

3. An Understand the information capacity of the hybridization interactions in

large collections of many different DNA sequences.

4. Appropriate physical models to guide design and experimentation

Conclusion

1. This is the environment-friendly approach decreasing the size and increasing the speed of
processors.

2. It can be thought as rigorous alternative to solve the existing critical problems.

3. As molecular computation is to be sustainable, we should search for efficient DNA

algorithm.

4. Though, theoretically it is reliable alternative in many dimensions, still substantial

practical difficulties in implementing in lab.

5. Much more work has to be done in the field of biological implementation

References
1) http://www.englib.cornell.edu/scitech/w96/DNA.html , the server home page

2) Research article , on the University of Wisconsin web site

3) C.H. Bennett. The thermodynamics of computation – a review. Interna-

tional Journal of Theoretical Physics, 21:905–940, 1982.