1) Introduction To Biomolecular Computing 2) Hamilton
1) Introduction To Biomolecular Computing 2) Hamilton
1) Introduction To Biomolecular Computing 2) Hamilton
5) APPLICATION 17
6) EFFICIENCY___________________________________________________ 21
7) ADVANTAGES-DISADVANTAGES 22
8) FUTURE 24
9) CONCLUSION___________________________________________________ 29
FIGURES INDEX
2.2 Connecting
Block___________________________________7
2.3 Double
Helics_____________________________________ 7
2.4 Long
Chain________________________________________7
2.5 Different
Colour___________________________________ 7
4.1 Synthetic
DNA_____________________________________11
4.5 Complmentary
Coupling_______________________________13
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4.6 Double Helix
Structure_______________________________13
4.7 Complementary
Strands______________________________14
4.9 Complementary
Strands______________________________15
5.1 DNA
MicroArray__________________________________20
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1. INTRODUCTION TO BIO-MOLECULAR COMPUTING
Computer chip manufactures are furiously racing to make the next
microprocessor that will topple speed records. Sooner or later, though, this
competition is bound to hit a wall. Microprocessor made of silicon will
eventually reach their limits of speed and miniaturization. Chip makers need a
new material to produce faster computing speeds.
You won’t believe where scientists have found the new material they
need to build the next generation of microprocessors. Millions of natural
supercomputers exist inside living organisms, including your living body. They
are nothing else but Bio-Molecules itself. Especially DNA. DNA
(deoxyribonucleic acid) molecules, the material our genes are made of, have the
potential to perform calculations many faster than the world’s most powerful
human-built computers. The other Bio-Molecules like Nucleotides,
Nuclesoides, Saccharides, Lignin, Lipids, Amino acids…
DNA computer can’t be still found at your local electronics store yet. The
technology is still in their development, and didn’t exist as concept before a
decade. In 1994, LEONARD ADELMAN introduced the idea of using DNA to
solve complex mathematical problems. Adelman, computer scientist at the
university of Southern California, came to the conclusion that DNA had
computational potential after reading the book “MOLECULAR BIOLOGY
OF THE GENE” written by JAMES WASTON, who co-discovered the
structure of DNA in 1953.In fact, DNA is more similar to computer. DNA is
very similar to a computer hard drive in how it stores permanent information
about your genes.
Figure 2.1
Figure showing the possible flight routes between the seven cities.
The key to solving the problem was using DNA to perform the five steps in
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solving the above algorithm.
Figure 2.2
DNA likes to form long double helices:
Figure 2.3
Figure 2.4
Figure 2.5
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Figure 3.1
Here the red block represents the city a, while the orange block represents
the city B. the half-red half-orange block connecting the two other blocks
represents the path from A to B.
In a test tube, all different pieces of DNA will randomly link with each
other, forming paths through the graph.
STEP 3: Going by weight, the DNA sequences which were 7 "cities" long
were separated from the rest. A "sieve" was used which would allow
smaller pieces of DNA to pass quickly, while larger segments are slowed
down. the procedure used actually allows you to isolate the pieces which are
precisely 7 cities long from any shorter or longer paths.
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Figure 3.2
STEP 5: all that was left to sequences the DNA, revealing the path from
A to B to C to D to E to F to G.
4. WORKING OF DNA
Figure 4.1
The only fundamental difference between conventional computers and
DNA computers is the capacity of memory units: electronic computers have two
positions (on or off), whereas DNA has four (C, G, A or T). The study of
bacteria has shown that restriction enzymes can be employed to cut DNA at a
specific word(W). Many restriction enzymes cut the two strands of double-
stranded DNA at different positions leaving overhangs of single-stranded DNA.
Two pieces of DNA may be rejoined if their terminal overhangs are
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complementary. Complements are referred to as 'sticky ends'. Using these
operations, fragments of DNA may be inserted or deleted from the DNA.
Figure 4.2
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other.
Figure 4.3
This ability of the nucleotides to bind side by side allows them to form
long chains without it mattering which type of nucleotide is binding to which
other type (see figure 3.2).
Figure 4.4
DNA can form digital strings of information because the four nucleotides
cannot be linked to each other in any order
A long string of these four bases can thus contain a massive amount of
information. The nucleotides also have another pair of complementary
coupling sites which, from a hardware point of view, give DNA other very
important characteristics. They allow each nucleotide to link up to a third
nucleotide. These extra binding sites are not universal coupling points like the
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chain building coupling sites, these binding sites allow only specific pairs of
nucleotides to bond - A will bind with T and T with A; C will bind with G and
G with C. These specific coupling pairs are illustrated in figure 3.3.
Figure 4.5
This extra bonding site allows the formation of double strand, with one
strand being the complement of other. This forms the famous "double helix"
structure which carries genetic code.
Figure 4.6
The complementary coupling sites allow strings of DNA to form into double
strands with one strand being the complement of the other. The two
strands form into a double helix
The first advantage of the double strand structure is the increased stability
it provides. Although nucleotide bonding is quite secure there is so much
jostling in the environment of a cell that individual nucleotides can get
displaced.
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A double stranded structure of complementary strands allows
damaged sections of the strand to be repaired by referring to the
complement nucleotides
Figure 4.7
Enzymes can split a double stranded DNA into a two chain of nucleotides
Figure 4.8
The splitting process forms two separate chains with one the complement of
the other
Figure 4.9
The two halves of a DNA section which has been split down the middle
can each rapidly build an additional complementary strand. These results in the
splitting operation producing two copies of the original (see figure 3.8).
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Figure 4.10
The splitting of strands and then regrowing the complementary
strands results in the original strand being copied and is exactly analogous
to the way in which binary data is copied within a computer program.
Most of the possible answers are incorrect, but one or a few may be
correct, and the computer's task is to check each of them and remove the
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incorrect ones using restrictive enzymes. The DNA computer does that by
subjecting all of the strands simultaneously to a series of chemical reactions that
mimic the mathematical computations an electronic computer would perform on
each possible answer. When the chemical reactions are complete, researchers
analyze the strands to find the answer -- for instance, by locating the longest or
the shortest strand and decoding it to determine what answer it represents.
Computers based on molecules like DNA will not have a vonNeumann
architecture, but instead function best in parallel processing applications. They
are considered promising for problems that can have multiple computations
going on at the same time. Say for instance, all branches of a search tree could
be searched at once in a molecular system while vonNeumann systems must
explore each possible path in some sequence.
Information is stored in DNA as CG or AT base pairs with maximum
information density of 2bits per DNA base location. Information on a solid
surface is
stored in a NON-ADDRESSED array of DNA words(W) of a fixed length (16
mers). DNA Words are linked together to form large combinatorial sets of
molecules.
DNA computers are massively parallel, while electronic computers would
require additional hardware, DNA computers just need more DNA. This could
make the DNA computer more efficient, as well as more easily programmable.
5.APPLICATIONS
DNA2DNA Applications
Another area of DNA computation exists where conventional computers
clearly have no current capacity to compete is the concept of DNA2DNA
computations as suggested and identified as a potential killer app. DNA2DNA
computations involve the use of DNA computers to perform operations on
unknown pieces of DNA without having to sequence them first. This is
achieved by re-coding and amplifying unknown strands into a redundant form
so that they can be operated on according to techniques similar to those used in
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the sticker model of DNA computation. Many of the errors inherent in other
models of DNA computing can hopefully be ignored in DNA2DNA computing
because there will be such a high number of original strands available for
operations.
There are other models of DNA computation that suggest that DNA
might be used to detect and evaluate other chemical and biochemical
substances. It is suggested that nucleic acid structures, could play an important
role in molecular computation. Various shapes of folded nucleic acid can be
used to detect the presence of drugs, proteins, or other molecules.
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Implications to Biology, Chemistry, and Medicine
A particular area within the natural and applied sciences that may benefit
from advances in - DNA computation is combinatorial chemistry.
Combinatorial chemistry involves the construction of enzymes, sequences of
RNA, and other molecules, for use in biomolecular engineering or medicine.
The combinatorial chemistry involves generating large sets of random RNA
sequences and searches for molecules with the desired properties. Advances in
either area could easily benefit the other field or even pave a way to combining
the two fields, producing both products and related computational results in
parallel.
Several papers also extend the use of biomolecular computing into
applications in the emerging science of nanotechnology, specifically nano-
fabrication, making use of both the small scale computational abilities of DNA
and the manufacturing abilities of RNA. Since both fields are still very
embryonic, the practical or even experimental implementation of this use is still
highly speculative but promising.
Applying the techniques of DNA2DNA computing could result in
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improved laboratory interfaces capable of performing computations prior to
input into conventional computers and may lead to improved methods of
sequencing DNA by motivating the use of magnetic beads, optical scanners, and
other emerging techniques that may allow DNA to be read directly into an
electronic interface.
DNA MICROARRAY
Figure 5.1
DNA microarray, or DNA chips are fabricated by high-speed robotics,
generally on glass but sometimes on nylon substrates, for which probes* with
known identity are used to determine complementary binding, thus allowing
massively parallel gene expression and gene discovery studies. An experiment
with a single DNA chip can provide researchers information on thousands of
genes simultaneously - a dramatic increase in throughout.
There are two major application forms for the DNA microarray
technology: 1) Identification of sequence (gene / gene mutation); and 2)
Determination of expression level (abundance) of genes.
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6.Efficiency :
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time to reduce false positives. Some molecular proposals, such as using DNA
with a peptide back bone for stability, have also been recommended.
DNA might also be used to mirror, and even improve upon, the
associative capabilities of the human brain. A content addressable memory
occurs when a data entry can be directly retrieved from storage by entering an
input that most closely resembles it over other entries in memory. This input
may be very incomplete, with a number of wildcards, and in an associative
memory might even contain bits that do not actually occur within the closest
match. This contrasts with a conventional computer memory, where the
specific address of a word must be known to retrieve it. The use of this
technique would replicate what is thought by many to be a key factor in
human intelligence.
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Baum has further speculated that a memory could be constructed where
only portions of the data are content addressable and associative, with other
information on an object compactly stored in addresses relative to the
associative portion of the entry. To save on operating costs and reduce error
frequency, this portion of the memory could be kept in double stranded form.
DISADVANTAGES
8. FUTURE
DNA computing is -few years old (November 11, 1994), and for this
reason, it is too early for either great optimism of great pessimism. Early
computers such as ENIAC filled entire rooms, and had to be programmed by
punch cards. Since that time, computers have since become much smaller and
easier to use. DNA computers will become more common for solving very
complex problems; Just as DNA cloning and sequencing were once manual
tasks, DNA computers will also become automated.
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In addition to the direct benefits of using DNA computers for performing
complex computations, some of the operations of DNA computers already have,
and perceivably more will be used in molecular and biochemical research.
Future Outlook
With so many different methods and models emerging from the current
research, DNA computing can be more accurately described as a collection of
new computing paradigms rather than a single focus. Each of these different
paradigms within biomolecular computing can be associated with different
potential applications that may prove to place them at an advantage over
conventional methods. Many of these models share certain features that lend
them to categorization by these potential advantages. However, there exist
enough similarities and congruencies that hybrid models will be possible, and
that advances made in both "classic" and "natural" areas of DNA computing
will be mutually beneficial to both areas of research. Advancements in DNA
computing may also serve to enhance understanding of both the natural and
computer sciences. For these reasons, and due to the many areas dependent on
each of computer science, mathematics, natural science, and engineering,
continued interdisciplinary collaboration is very important to any future
progress in all areas of this new field.
A "killer app" is yet to be found for DNA computation, but might exist
outside the bulk of current research, in the domain of DNA2DNA applications
and other more natural models and applications of manipulated DNA. This
direction is particularly interesting because it is an area in which DNA based
solutions are not only an improvement over existing techniques, but may prove
to be the only feasible way of directly solving such problems that involve the
direct interaction with biological matter.
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On the "classical" front, problem specific computers may prove to be the
first practical use of DNA computation for several reasons. First, a problem
specific computer will be easier to design and implement, with less need for
functional complexity and flexibility. Secondly, DNA computing may prove to
be entirely inefficient for a wide range of problems, and directing efforts on
universal models may be diverting energy away from its true calling. Thirdly,
the types of hard computational problems that DNA based computers may be
able to effectively solve are of sufficient economic importance that a dedicated
processor would be financially reasonable. As well, these problems will be
likely to require extensive time they would preclude the need for a more
versatile and interactive system that may be able to be implemented with a
universal computing machine.
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9.CONCLUSION:
DNA computers will become more common for solving very
complex problems; Just as DNA cloning and sequencing were once manual
tasks, DNA computers will also become automatedes. Studying DNA
computers may also lead us to a better future enhancement.
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