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(C) 2004, SNU Biointelligence Lab, Introduction DNA algorithm for solving an instance of a combinatorial problem All of the encoded DNA strand for pool DNA Select(extract) the exact solution So many problems were in this stage XPCR method can extract the accurate solution that we are needed
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(C) 2004, SNU Biointelligence Lab, http://bi.snu.ac.kr/
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DNA Extraction by Cross DNA Extraction by Cross Pairing PCRPairing PCR
Giuditta Franco, Cinzia Giagulli, Carlo Laudanna, Vincenzo Manca
Summarized by Tak Min Ho
(C) 2004, SNU Biointelligence Lab, http://bi.snu.ac.kr/
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AbstractAbstract
A special type of PCR can extract specific DNA strand from the pool of DNA
It is called Cross Pairing PCR (XPCR) was tested in several conditions
(C) 2004, SNU Biointelligence Lab, http://bi.snu.ac.kr/
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IntroductionIntroduction
DNA algorithm for solving an instance of a combinatorial problem All of the encoded DNA strand for pool DNA Select(extract) the exact solution
So many problems were in this stage XPCR method can extract the accurate solution that we are
needed
(C) 2004, SNU Biointelligence Lab, http://bi.snu.ac.kr/
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Cross Pairing PCRCross Pairing PCR
Specific sequence ‘γ’ of bases Input pool ‘P’ of different dsDNA molecules with
a same length ‘n’ and sharing a common prefix and suffix
Ouput pool P’ which include the given sequence γ are represented
(C) 2004, SNU Biointelligence Lab, http://bi.snu.ac.kr/
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Cross Pairing PCRCross Pairing PCR
(C) 2004, SNU Biointelligence Lab, http://bi.snu.ac.kr/
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Cross Pairing PCRCross Pairing PCR
(C) 2004, SNU Biointelligence Lab, http://bi.snu.ac.kr/
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Extraction AlgorithmExtraction Algorithm
Given a string γ, let us assume that P is γ-invariant, that is, either γ does not occur at the
same position in different strands of P If it is not the case, then ατ1γτ2β, ατ3γτ4β € P
implies that ατ1γτ4β, ατ3γτ2β € P 1) PCR (α, γ’) => dsDNA αγ2) PCR (γ, β) => dsDNA γβ3) XPCR (α, β’) => dsDNA αβ (correct strand)
(C) 2004, SNU Biointelligence Lab, http://bi.snu.ac.kr/
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PCR (PCR (αα, , γγ’) => dsDNA ’) => dsDNA αγαγ
(C) 2004, SNU Biointelligence Lab, http://bi.snu.ac.kr/
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PCR (PCR (γγ, , ββ) => dsDNA ) => dsDNA γβγβ
(C) 2004, SNU Biointelligence Lab, http://bi.snu.ac.kr/
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XPCR (XPCR (αα, , ββ’) => dsDNA ’) => dsDNA αβαβ
(C) 2004, SNU Biointelligence Lab, http://bi.snu.ac.kr/
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Electrophoresis result (test of the Electrophoresis result (test of the validity of XPCR)validity of XPCR) Lane 1 : Marker (100b) Lane 2 : ατγτ-strands of
human RhoA (582bp) Lane 3 : γτβ-strands
(253bp) Lane 4 : XPCR, product is
ατγτβ-strands (606bp)
(C) 2004, SNU Biointelligence Lab, http://bi.snu.ac.kr/
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Electrophoresis result Electrophoresis result Lane 1 : Marker (25bp) Lane 2 : αγ-strands (120bp) Lane 3 : γβ-strands (45bp) Lane 4 : ατγτβ XPCR (150bp) Lane 5 : positive control by
PCR(γ,β’) Lane 6 : negative control by
PCR(γ’β’) Lane 7,8 : positive controls by
PCR(γ1,β’) and PCR(γ2β’) respectively, with γ1 at position 125 and γ2 at position 75
(C) 2004, SNU Biointelligence Lab, http://bi.snu.ac.kr/
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ConclusionConclusion
αΑφγψβ, αδγηβ → αφγηβ, αδγψβ like ατ1γτ2β, ατ3γτ4β € P implies that ατ1γτ4β, ατ3γτ2β € P
XPCR method is good for the extracting a correct answer from the DNA pool
But problems could arise if the encoding is not robust enough for avoiding unexpected annealing