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

2. (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

3. (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

4. (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

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

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

7. (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 1)PCR (α, γ’) => dsDNA αγ 2)PCR (γ, β) => dsDNA γβ 3)XPCR (α, β’) => dsDNA αβ (correct strand)

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

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

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

11. (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)

12. (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

13. (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