DNA BASED EMPLOYEE RECOGNITION

BY, Rahul.R, Adith.N.S, Ashwin Deepu, Priyanka .E.Nair S8 CS, MBCET

Introduction to DNA:

The lifes molecule:

Introduction:

What is DNA computing ?

Around 1950 first idea (precursor Feynman) First important experiment 1994: Leonard Adleman

Molecular level (just greater than 10-9 meter) Massive parallelism.

In a liter of water, with only 5 grams of DNA we get around 1021 bases ! Each DNA strand represents a processor !

What is DNA?

DNA stands for Deoxyribonucleic Acid DNA represents the genetic blueprint of living creatures DNA contains instructions for assembling cells Every cell in human body has a complete set of DNA DNA is unique for each individual

A bit of biology

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) (T) (C)(G)

Double Helix

Sides Sugar-phosphate backbones ladders complementary base pairs Adenine & Thymine Guanine & Cytosine Two strands are held together by weak hydrogen bonds between the complementary base pairs

Source: Human Physiology: From Cells to System 4th Ed., L. Sherwood, Brooks/Cole, 2001, C-3

Instructions in DNA
Sequence to indicate the start of an instruction

Instruction that triggers Hormone injection

Instruction for hair cells

Instructions are coded in a sequence of the DNA bases A segment of DNA is exposed, transcribed and translated to carry out instructions

DNA/CPU COMPARISON

CPU
Sequential Operations addition, bit-shifting, logical operations (AND, OR, NOT, NOR)

DNA
Parallel Operations Cut, Copy, Paste, Repair

Can DNA Compute?

DNA itself does not carry out any computation. It rather acts as a massive memory. BUT, the way complementary bases react with each other can be used to compute things. Proposed by Adelman in 1994

DNA manipulations:

If we want to use DNA as an information bulk, we must be able to manipulate it . However we are talking of handling molecules ENZYMES = Natural CATALYSERS. So instead of using physical processes, we would have to use natural ones, more effective:

for lengthening: polymerases for cutting: nucleases (exo/endo-nucleases) for linking: ligases
Thank this reaction we get millions of identical strands, and we are allowed to think of massive parallel computing.

Serialization: 1985: Kary Mullis PCR

Ligases

Bind molecules together Concatenates DNA strands

Polymerase

Copies DNA Primers (Start, Complement of End) PCR

Gel Electrophoresis

Sort molecules by length Molecules have a charge Magnets used

And what now ?

Situation:
Molecular level. Lots of agents. (strands) Tools provided by nature. (enzymes)

How can we use all this? If there is a utility

Leonard M. Adleman

Background in Mathematics & Computer Science HIV Research DNA/Turing Machine similar Proof of Concept

Coding the information:

1994: THE Adlemans experiment. Given a directed graph can we find an hamiltonian path (more complex than the TSP). In this experiment there are 2 keywords: massive parallelism (all possibilities are generated) complementarity (to encode the information)

This experiment proved that DNA computing wasnt just a theoretical study but could be applied to real problems like cryptanalysis (breaking DES ).

Adlemans Experiment

Hamilton Path Problem

(also known as the travelling salesperson problem)
Darwin

Perth

Alice Spring

Brisbane

Sydney Melbourne Is there any Hamiltonian path from Darwin to Alice Spring?

Adlemans Experiment (Contd)

Solution by inspection is:

Darwin Brisbane Sydney Melbourne Perth Alice Spring

BUT, there is no deterministic solution to this problem, i.e. we must check all possible combinations. Darwin
Perth Brisbane Alice Spring Sydney Melbourne

Adlemans Experiment (Contd)

1.

Encode each city with complementary base vertex molecules

Sydney - TTAAGG Perth - AAAGGG Melbourne - GATACT Brisbane - CGGTGC Alice Spring CGTCCA Darwin - CCGATG

Adlemans Experiment (Contd)

2.

Encode all possible paths using the complementary base edge molecules
Sydney Melbourne AGGGAT Melbourne Sydney ACTTTA Melbourne Perth ACTGGG etc

Recipe

In a test tube add

10^14 molecules of each city 10^14 molecules of each flight Water, ligase, salt

Answer generated in about one second 100 trillion molecules representing wrong answers also generated

Adlemans Experiment (Contd)

3.

Marge vertex molecules and edge molecules.

All complementary base will adhere to each other to form a long chains of DNA molecules
Solution with vertex DNA molecules Marge & Anneal

Solution with edge DNA molecules

Long chains of DNA molecules (All possible paths exist in the graph)

Adlemans Experiment (Contd)

Darwin

The solution is a double helix molecule:

Brisbane Sydney

Melbourne

Perth

Alice Spring

CCGATG CGGTGC TTAAGG GATACT AAAGGG CGTCCA TACGCC ACGAAT TCCCTA TGATTT CCCGCA
Darwin Brisbane Brisbane Sydney Sydney Melbourne Melbourne Perth Alice Spring Perth

Operations

Melting
breaking the weak hydrogen bonds in a double helix to form two DNA strands which are complement to each other

Annealing
reconnecting the hydrogen bonds between complementary DNA strands

Operations (Contd)

Merging
mixing two test tubes with many DNA molecules

Amplification
DNA replication to make many copies of the original DNA molecules

Selection
elimination of errors (e.g. mutations) and selection of correct DNA molecules

Pros and Cons

+

Massively parallel processor DNA computers are very good to solve Nondeterministic Polynomial problems such as DNA analysis and code cracking. Small in size and power consumption

Pros and Cons (Contd)

-

Requires constant supply of proteins and enzymes which are expensive Errors occur frequently a complex selection mechanism is required and errors increase the amount of DNA solutions needed to compute Application specific Manual intervention by human is required

Why dont we see DNA computers everywhere?

DNA computing has wonderful possibilities:

Reducing the time of computations* (parallelism) Dynamic programming !

However one important issue is to find the killer application. Great hurdles to overcome

Some hurdles:
Operations

done manually in the

lab. Natural tools are what they are

Formation

of a library (statistic way) Operations problems

Conclusion

Many issues to be overcome to produce a useful DNA computer. It will not replace the current computers because it is application specific, but has a potential to replace the high-end research oriented computers in future. Nanotechnology?

Bibliography:

DNA Computing, New Computing Paradigms. Gheorghe Paun,Grzegorz Rozenberg,

Arto Salomaa

DIMACS: DNA based computers Reducing Errors in DNA Computing by Appropriate Word Design.

wdesign.pdf