DNA Computing

Zhe Wang

• Molecular computation of solutions to combinatorialproblems. Adleman. Science 266, 1021-1024. 1994.

• Computing with DNA. Parker. EMBO reports 4, 7-10. 2003.

• DNA provides a compact means of data storage. Each gram of DNA can contain more than 1021 bits of information.

• Recombinant DNA techniques for detection, amplification, and editing of DNA can be used for massively parallel molecular computation. Routine experiments can involve between 1015 and 1017 strands of DNA in a small test tube.

• The first DAN based computer was built by Adleman In 1994.

• It solved the Traveling Salesman problem (TSP) with seven cities.

TSP is a Hamiltonian path problem and NP-complete problem.

There is a unique Hamiltonian path (01, 12, 23, 34, 45, 56)that begins with city 0 and ends with city 6.

Using 20mer oligos to present each vertex and edge.

Lane 1: Product of the ligation reaction.Lane2-5: PCR amplification of the product of the ligation reaction.Lane6: Molecular weight marker.

Printing out the results by Graduated PCR.(Bands of 40, 60, 80, 100, 120, 140 bp in successive lanes representa Hamiltonian path.)

Purifying PCR products before printing out the results by Graduated PCR.(Bands of 40, 60, 80, 100, 120, 140 bp in successive lanes representa Hamiltonian path.)

DNA computing - Advantages

• Computing with DNA has massive advantages over silicon-based machine.

• Adleman’s DNA computer did 1,014 operations per second, a rate of 100 Trilion floating point operations per second (100 Teraflops). The world’s fastest supercomputer, Earth Simulator, runs at just 35.8 Teraflops.

• Another advantage is the potential of information storage .

DNA computing - Disadvantages

• Printing out the result is a tedious work.

• It requires an exponential amount of DNA to solve the TSP problem with high number of cities.

• The most important problem is the accuracy of DNA strand synthesis.

• “The general consensus now is that DNA computing will never be able to compete directly with silicon-based technology.”

• “The rich potential of DNA computing is to demonstrate control at the molecular level.”