DNA Extraction by Cross Pairing PCR

(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


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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


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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


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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


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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 αγ

2) PCR (γ, β) => dsDNA γβ

3) XPCR (α, β’) => dsDNA αβ (correct strand)


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PCR (PCR (αα, , γγ’) => dsDNA ’) => dsDNA αγαγ


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PCR (PCR (γγ, , ββ) => dsDNA ) => dsDNA γβγβ


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XPCR (XPCR (αα, , ββ’) => dsDNA ’) => dsDNA αβαβ


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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)


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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


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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

DNA Extraction by Cross Pairing PCR

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