Demonstration of a universal Demonstration of a universal surface DNA computersurface DNA computer

Nucleic Acids Research, 2004, Vol. 32, 3115-3123

Xingping Su and Lloyd M. Smith

Presented by Je-Keun Rhee

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Introduction

A fundamental concept in computer science is that of the universal Turing machine, which is an abstract definition of a general purpose computer.

A general purpose (universal) computer is defined as one which can compute anything that is computable.

It has been shown that any computer which is able to simulate Boolean logic circuits of any complexity is such a general purpose computer.

In this study, it is shown that a NOR gate can be built based on the surface computing model.

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Computational complexity classes

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A circuit consisting of a NOR gate andan OR gate

For simplicity, this circuit had only two inputs to each gateand had three initial input variables.

Truth table and an equivalent circuit to the one in (a)

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Sequences (5’->3’) of the DNA encoding the inputs Three 16nt words encoded three bits of information: X1, X2, and X3. Each word was made up of an 8 nt encoding region, v8, and a 4 nt word fix

ed label, F4, at either end. These DNA oligonucleotides were attached to the surface through the thiol

group at their 3’end.

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Sequences of the words and word complements

Sequences of the words (5’->3’)

Sequences of the words complements (5’->3’)

The design tool at the Proligo website (http://www.proligo.com) were used.

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Computation of a simple circuit consisting of a NOR gate and an OR gate.

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Computation of a simple circuit consisting of a NOR gate and an OR gate.

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A circuit when the two input words are non-contiguous

Contiguous Non-contiguousThe two input words are non-contiguousThe two input words are

next to each other

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LNA (locked nucleic acids)

In non-contiguous case, LNA/DNA chimeras were hybridized. Such LNA/DNA chimeras were used to block the polymerase

extension reaction.

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Computation when the two inputs to a gate are non-contiguous

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Results from the circuit computations

After NOR gate After OR gateTRUE FALSE TRUE FALSE

The program NIH Image (http://rsb.info.nih.gov/nih-image/) was used to processthese fluorescence images for presentation

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Results from the circuit computations

The truth-table for the circuitin both the contiguous andnon-contiguous cases

DNA oligonucleotides A-H wereattached to the gold slide surfacesin an ‘addressed’ fashion

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The overall computational efficiency

Background-corrected fluorescence intensitiesof the complements to the third word and thecorrectly appended fourth and fifth words.

Efficiencies of the NOR gate, OR gate andthe overall computation