1. PNA-mediated Whiplash PCR
J. A. Rose et al.
DNA7 poster
Summarized by Shin, Soo-Yong

2. (C) 2001, SNU Biointelligence Lab, http://bi.snu.ac.kr/
Abstract
Whiplash PCR (WPCR)
Recursive, self-directed polymerase extension of a mixture of DNA hairpins.
Problems : backhybridization
In this paper, WPCR is modeled by a statistical thermodynamic model & Markov chain.
To prevent backhybridization, PNA2/DNA triplex formation (P-WPCR) will be proposed.
(C) 2001, SNU Biointelligence Lab, 

3. (C) 2001, SNU Biointelligence Lab, http://bi.snu.ac.kr/
WPCR
Computational steps are implemented by the template-directed, recursive polymerase extension of a mixture of DNA hairpins.
(C) 2001, SNU Biointelligence Lab, 

4. (C) 2001, SNU Biointelligence Lab, http://bi.snu.ac.kr/
WPCR
In the original protocol, computation begins with a reduction in reaction temperature.
A computational transition occurs by the polymerase extension of hybridization head.
Stop sequence is implemented by a length 3 poly0A sequence (absence of free dTTP)
After polymerization, hairpins are thermally denatured.
(C) 2001, SNU Biointelligence Lab, 

5. (C) 2001, SNU Biointelligence Lab, http://bi.snu.ac.kr/
Drawbacks of WPCR
A tendency for extended molecules to participate in backhybridication
More stable
Less stable
(C) 2001, SNU Biointelligence Lab, 

6. (C) 2001, SNU Biointelligence Lab, http://bi.snu.ac.kr/
Statistical model
Assume encounters/strand
More study is needed.
(C) 2001, SNU Biointelligence Lab, 

7. (C) 2001, SNU Biointelligence Lab, http://bi.snu.ac.kr/
PNA mediated WPCR
WPCR architecture may be redesigned to enable the specific inhibition of backhybridized structures by targeted PNA2/DNA triple formation.
Polyamine nucleic acid (PNA) bind to complementary ssDNA with extremely high affinity
Under appropriate reaction condition, rapid, irreversible formation of the triplex structure occurs even if the target DNA single strand is involved in hybridization. (strand invasion)
Triplex formation : P-loop
(C) 2001, SNU Biointelligence Lab, 

8. (C) 2001, SNU Biointelligence Lab, http://bi.snu.ac.kr/
PNA mediated WPCR
The sequence TTTTCTTCTT
ssDNA target sequence of the highly efficient cationic bis-PNA molecules.
(C) 2001, SNU Biointelligence Lab, 

9. (C) 2001, SNU Biointelligence Lab, http://bi.snu.ac.kr/
PNA mediated WPCR
(C) 2001, SNU Biointelligence Lab,