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DNA Extraction by Cross Pairing PCR

DNA Extraction by Cross Pairing PCR. Giuditta Franco, Cinzia Giagulli, Carlo Laudanna, Vincenzo Manca Summarized by Tak Min Ho. Abstract. 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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DNA Extraction by Cross Pairing PCR

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  1. DNA Extraction by Cross Pairing PCR Giuditta Franco, Cinzia Giagulli, Carlo Laudanna, Vincenzo Manca Summarized by Tak Min Ho (C) 2004, SNU Biointelligence Lab, http://bi.snu.ac.kr/

  2. Abstract • 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/

  3. 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 (C) 2004, SNU Biointelligence Lab, http://bi.snu.ac.kr/

  4. Cross 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/

  5. Cross Pairing PCR (C) 2004, SNU Biointelligence Lab, http://bi.snu.ac.kr/

  6. Cross Pairing PCR (C) 2004, SNU Biointelligence Lab, http://bi.snu.ac.kr/

  7. Extraction 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 • PCR (α, γ’) => dsDNA αγ • PCR (γ, β) => dsDNA γβ • XPCR (α, β’) => dsDNA αβ (correct strand) (C) 2004, SNU Biointelligence Lab, http://bi.snu.ac.kr/

  8. PCR (α, γ’) => dsDNA αγ (C) 2004, SNU Biointelligence Lab, http://bi.snu.ac.kr/

  9. PCR (γ, β) => dsDNA γβ (C) 2004, SNU Biointelligence Lab, http://bi.snu.ac.kr/

  10. XPCR (α, β’) => dsDNA αβ (C) 2004, SNU Biointelligence Lab, http://bi.snu.ac.kr/

  11. Electrophoresis result (test of the 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/

  12. 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/

  13. Conclusion • 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 (C) 2004, SNU Biointelligence Lab, http://bi.snu.ac.kr/

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