200 likes | 207 Views
Cascading Whiplash PCR with a Nicking Enzyme. Daisuke Matsuda and Masayuki Yamamura. MEC Seminar 2002. 9. 27 Park, Ji-Yoon. Introduction. Previous history - Proposed by Hagiya et al. - Wood et al - Yamamura et al - State copy on aqueous computing with PNA
E N D
Cascading Whiplash PCR with a Nicking Enzyme Daisuke Matsuda and Masayuki Yamamura MEC Seminar 2002. 9. 27Park, Ji-Yoon
Introduction • Previous history - Proposed by Hagiya et al. - Wood et al - Yamamura et al - State copy on aqueous computing with PNA • Disadvantage - Back annealing - Rose et al; scheme to inhibit back annealing with bis-PNA • In this paper… - Scheme to cascade results of WPCR from molecules to molecules
Scheme to Cascade WPCR • Nicking enzyme - cleave only one DNA strand & introduce a nick into the DNA - N.BstNBI(nonpalindromic sequence 5’-GAGTCNNNN^N-3’)
Preliminary Experiments Table 1. DNA sequences used in this paper Nick site Fig 2. The structure of Trans3
The Products of the Transitions Fig 3. The products of the transitionState 1: 1st transition State 2: 2nd transition State 3: 3rd transition
State 3 of WPCR State 2 of WPCR No transition Fig 4. Gel electrophoresis of the transition products Denaturing PAGE
The Output Reaction from WPCR Fig 6. The results of output reaction from WPCR Lane M2: Marker output product Lane 1: separated output product Lane 2: thermal output product Lane 3: Isothermal output product
Fig 7. Ideas to realize [IF A AND B THEN C] and [IF ~A AND B THEN C]
Discussion & Conclusion • Discussion about preliminary experiments * Equilibrium between divorced output fragments & back-annealed output fragments→ The concentration of the output products tends to converge * Isothermal output reaction(64°C) * Polymerase, ds DNA target • Further Issues- Plan to implement an expert system for medical diagnosis - Scheme to cascade WPCR - Reliability study to produce output fragments by a nicking enzyme
Output reaction from WPCR • Three successive transitions(64°C for 1min/ 80°C for 1min / 80°C for 5min); 8 cycles * Component:Trans3(7 pmol), dNTP(60 μmol each), Bst DNA polymerase(4 Units), Bst DNA pol buffer/ N.BstNBI buffer * WPCR : 64°C for 90min with N.BstNBI & template s4-s5 * Separated output reaction: control reaction - two partical reaction(WPCR & output reaction) are performed separately* N.BstNBI & template s4-s5 poured into the reaction mixture before WPCR - isothermal & thermal reaction
Whiplash PCR B x b a C x B A x
Whiplash PCR B C x B A x
Whiplash PCR a x x B A x C B
Whiplash PCR a c b x x B A x C B