DNA COMPUTING

SAYAN BHOWAL PALLAB KUNDU SWARUP GANGULY ABHIK MISRA SAIKAT DAS

DNA Computing-A Leap Into The Future ComputingBasics Of DNA:



DNA (deoxyribonucleic acid) is a double stranded sequence of four nucleotides The four nucleotides are 1. Adenine (A) 2. Guanine (G) 3. Cytosine (C) 4. Thymine (T)

DNA Computer -The Basics:

1. A collection of specially selected DNA strands whose combinations will result in the solution to some problem,depending on the problem at hand. 2. Promises Massive parallelism. 3. With a given setup and enough DNA, one can potentially solve huge problems by parallel search. 4. Can be much faster than a conventional computer. 5. Class of algorithms available for implementation on DNA Computers. 6. Algorithms based on dynamic programming.

DNA Computing Contd

Uniqueness Of DNA Computing: Transistor based computers typically handle operations in a sequential manner. manner. All modern CPUs are basically Von Neumann machines. machines. Fetches an instruction and the appropriate data from main memory, and executes the instruction repeatedly. repeatedly. DNA computers, however, are non Von-Neumann,stochastic machines Von Possible to approach computation in a di erent way from ordinary computers for the purpose of solving a di erent class of problems. problems. The power comes from the memory capacity and parallel processing. processing. If forced to behave sequentially, DNA loses its appeal. appeal. Example: Example: In bacteria, DNA can be replicated at a rate about 500 base pairs per second. second. But this is equivalent to only 1000bits/sec,much slower than any hard 1000bits/sec,much drive. drive.However after each replication is finished the no. of strands increases no. exponentially, with each new strand the data rate increases by 1000 bits/sec. bits/sec. This amounts to 1000Gbps after 30 iterations. 1000Gbps iterations.

Why DNA: Huge Information density-1 bit/nm3 Vs 1 bit/1012 nm3 in standard storage devices. Massively Parallel Operations Each operation is carried out on all strands in parallel.

DNA Computing-How It All Began ComputingHistory:

DNA computing began in 1994. The Famous Adlemans Experiment Leonard Adleman,a professor at the University of Southern California first showed computing can be done using DNA also. His findings were published in his paper Molecular Computation of Solutions of Combinatorial Problems. Massive parallelism of a trillion DNA strands. Even the toughest combinatorial problems, such as the governments supposedly uncrackable Data Encryption Standard can be cracked.

DNA Operations
Synthesis: Synthesis:
A desired strand of DNA upto a certain length can be synthesized in the Lab by using a synthesizer that is supplied with the four nucleotide bases in a solution, it combines these according to a sequence entered by the user. user.

Denaturing,annealing and ligation: ligation:



DoubleDouble-stranded DNA may be dissolved into single strands (or denatured) by heating the solution to a temperature determined by the composition of the strand. strand. Annealing is the reverse of melting, whereby a solution of single strands is cooled, and allowing complementary strands to bind together. together. If one of the strands contains discontinuity it can be repaired by the enzyme ligase. ligase.

DNA Operations-Contd.. OperationsPolymerase Chain Reaction(PCR):



 

PCR is a process that quickly amplies the amount of a specic molecule of DNA in a given solution using primer extension by polymerase. Each cycle of the reaction doubles the quantity of this molecule, giving an exponential growth in the number of strands. A common problem in DNA computation is how to read-out the readnal solution to a problem encoded as a DNA strand. The laboratory steps carried out may result in a very dilute solution. PCR solves this problem. If a sought after molecule is present in the solution, then it will be hugely (exponentially) multiplied so that the volume of the solution will visibly grow.

DNA Operations-Contd.. OperationsGel-Electrophoresis: 1. 2. 3. Electrophoresis is the movement of charged molecules. An important technique for sorting DNA strand size. Since DNA molecules carry negative charge, when placed in an electrical field they tend to migrate towards the positive pole. The rate of migration of a molecule in an aqueous solution depends on its shape and electrical charge. Smaller molecules therefore migrate faster through the gel, thus sorting them according to the size.

4.

5.

DNA Operations-Contd.. OperationsHybridization:



Separation by Hybridization involves the extraction from a test tube of any single strand containing a specic short sequence (e.g., extract all strands containing the sequence TAGACT). It is an operation often used in DNA computation.

Extraction:


Given a test tube T1 and a strand S, it is possible to extract all the strands in T1 that contain S as a subsequence and to separate them from those that do not contain it.

Union:


Given two or more test tubes, say T1; T2; .. ; Then, it is possible to put in a new test tube the union of all the strands contained in T1; T2;; Tn.

Detection:


Conrm presence/ absence of DNA in a given test tube.

Adlemans Experiment

Non deterministic polynomial time problem Hamiltonian path problem (HPP) Description of the problem

Adleman solution to HPP using DNA computing

CITY KANPUR MUMBAI DELHI KHARAGPUR DNA_NAME ATCGTCGA GTACACTA TCAGACGA CGATCGAT DNA_COMPLEMENT TAGCAGCT CATGTGAT AGTCTGCT GCTAGCTA

FLIGHT KANPUR-MUMBAI

DNA_FLIGHT_NUMBER TCGAGTAC

Algorithm to solve
Step1 :Generate a set of random paths through the graph Step2 :Elimination of unnecessary paths(a,b,c) Step3 :if set is non-empty then a HP exist, otherwise not

Implementation of Algorithm
Step 1: Generation of large number of DNA chain and Amplification of path by PCR Step 2: Elimination by Gel-Electrophoresis Step 3: Watson-Crick Affinity-Separation

How to Define DNA Nanotechnology

A subfield of Nanotechnology incorporates molecular recognition property to create a controllable structure out of DNA It involves the idea of using DNA as a structural material rather than simply a genetic information carrier Out of 3 different structures of DNA only bDNA is much of our interest as far as DNA computing is concerned

DNA Crossover Molecules

Nanotech makes use of branched DNA structures to create DNA complexes Different junctions can also be made Most important is the DoubleCrossover molecule or DX

Tile Based Array

Double crossover molecule can be equipped to form a 2D lattice More than one type of DX can be used which can be made to arrange in rows or any tessellated pattern

DNA Nanotubes
In addition to flat sheets, DX arrays have been made to form hollow tubes of 4-20 nm diameter Somewhat similar by the nature of carbon nanotubes

DNA Polyhedra
No. of 3D molecules can also be made which resembles the structure of a polyhedra DNA duplexes trace the edges of a polyhedron with a junction at each vertex It involves multiple ligations and solid phase synthesis

DNA origami
An alternative to the tile-based approach, two-dimensional DNA structures can be made from a single, long DNA strand of arbitrary sequence which is folded into the desired shape This allows the creation of two-dimensional shapes at the nanoscale using DNA

DNA Nanomechanical Devices

DNA complexes change their conformation upon some stimulus. So these are intended to have applications in nanorobotics Firstly used as Molecular Twizzers changes from open to closed state based upon the presence of control strands One of the earlier DNA machines makes use of transition between b-DNA to z-DNA form to respond to a change in buffer condition

DNA structures can provide framework for next generation nanosystems

Special structures Engineered proteins Structural DNA

DNA Based Encryption

What is It?
Concept of using DNA Computing in the fields of cryptography in order to increase the security of encryption algorithms. First Introduced by Asish Gehani,Thomas LaBean and John Reif in DNABased Cryptography. DIMACS DNA Based Computers, V, American Mathematical Society, 2000. Proposed use of principle idea of the central dogma of molecular biology.

Design Rationale:
High throughput due to the promise of massive parallelism and huge storage DNA holds. Abundance of nucleotide sequences to represent characters or pixels.

DNA Based Encryption Contd..

Procedure:
Plain Text Or Image DNA Based Encryption System File Of Random Pointers of DNA Nucleotides

Binary form of information of the plain-text message on sender s end is transformed in to DNA form using the following convention 1. Adenine for 00 2. Cytosine for 01 3. Guanine for 10 4. Thymine for 11 This results in a single DNA strand which represents the message Each four DNA nucleotides sequence represents a binary octet that in turn represents a plain-text characters of the message. The capital plain-text character H is represented by the sequence CAGA C-01 A-00 G-10 A-00 which translates to 01001000 binary representation of the number 72,ASCII value for H .

Procedure Contd..
Canis Familiaris chromosome: (gi|73948581|ref|NW_876270.1|Cfa1_WGA2_2 Canis familiaris chromosome 1 genomic contig) is delivered from the sender to the receiver of the encrypted message through a secured channel. The sender will match all the quadruple DNA nucleotides sequence representing all the plain-text characters against the single strand DNA representing the Canis Familiaris genome in order to locate all of its occurrences and positions or in other words its pointers. Subsequently, the sender randomly retrieves from the single Canis DNA strand one location coordinate for each quadruple DNA nucleotides sequence representing a plain-text character for all characters in the message. This process will generate a file that contains random location pointers for all plain-text characters called the ciphertext. Upon receiving this file, the receiver uses the ciphered text to recover the sequences of quadruple DNA nucleotides sequence from the Canis DNA strand. In the reverse order, the recovered DNA form of information will be used to retrieve the binary form of information, which will be then translated into plain text.

Security Analysis of the Algorithm

The entire novel Uncle Tom s Cabin was downloaded from project Gutenberg [http://www.gutenberg.org/] and used for encryption. Table 1, illustrates a portion of the 82 characters occurring in the novel, and their total frequency in the Canis familiaris chromosome.Canis Familiaris with its 53,004,966 bp DNA sequence in chromosome 1 has the ability to encode all the novel s plaintext characters within its strand sequence due to the abundance of nucleotides combination. However, for higher levels of security one can always resort to larger genome sequence.

Progress So Far
Encryption process tested on images to show how random is the selection of DNA octet s locations on the encrypting sequence. A 350x258 TIF image used for the test. Dog chromosome was used for reference.

Gehani A,LaBean T H and Reif J H achieved a one time pad based on DNA. Clelland C T,Risca V,Bancroft C successfully hid the famous June 6 invation:Normandy in DNA microdots.

DNA Based Encryption Contd

Special Features:
Based on symmetric DNA cipher consisting of recording pointers to the randomly selected locations for each plain text character. Even in a relatively simple DNA strand the patterns found can range from tens of thousand times to hundred of thousands,Consequently reducing the vulnerability to frequency attacks. High throughput ranging from 0.3 to 1.2 microseconds per nucleotide.

The Long Road Ahead.

Main Problems:
Lack of related theoratical basis. Difficult to realize and expensive to apply.

Focus Of Current Research:

1. The advantages inherent in DNA (such as developing nanoscopic storage based on tiny volume of DNA)needs to be fully explored in order for DNA encryption to become viable. 2. The main task is to establish the theory foundations and accumulate the practical experience. 3. Standardization of security requirements and focus on feasability.

References:
Gehani A, LaBean T H, Reif J H. DNA-based cryptography. Dimacs Series In Discrete Mathematics & Theoretical Computer Science, 2000. Celland C T, Risca V, Bancroft C. Hiding messages in DNA microdots. Nature, 1999.

DNA Computing Applications

Potential technological Applications and Combinatorial Optimization problems

Programmable Nanofabrication

Summary and Prospects

Silicon vs. DNA Microprocessors

Scope and Recent Updates

Pros and Cons

Advantages

Disadvantages

Conclusion