demonstration of a universal surface dna computer
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Demonstration of a universal surface DNA computer. Nucleic Acids Research , 2004, Vol. 32, 3115-3123 Xingping Su and Lloyd M. Smith Presented by Je-Keun Rhee. Introduction. - PowerPoint PPT PresentationTRANSCRIPT
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-contiguous
The two input words are non-contiguousThe two input words arenext 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 gate
TRUE 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