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The priming of DNA synthesis by digested literal strings probably produced the "recombinant" strings of the full length, which cannot be distinguished from the undigested DNA. By the definition of literal strings, this unusual priming of DNA synthesis does not generate such literal strings that contain any erroneous literal that is absent in the corresponding clauses of the formula. The profile of the band ladder (the band intensity drastically decreased with the DNA length) indicated that the extent of this contamination was negligible for the size of the present instance. However, rigorous estimation may be necessary for larger instances, and molecular biology techniques could cope with this issue; for example, dideoxyribonucleotides can be added to the 3′ end of the digested strings so that they cannot prime DNA synthesis. Recombination between the "solution-candidate" molecules during PCR amplification has been reported (8). This is another possible cause of the band ladder, although PCR amplification of pool 0 by itself did not produce any band ladder (Fig. 3B, lane 1).
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To avoid the loss of DNA, we amplified the product once after 10 cycles of ePCR by the normal PCR protocol. This amplified DNA was then applied to another 10 cycles of ePCR and was finally recovered by PCR with the primers pbs1 and pbs2c that have additional bases of the Eco RI and Hind III sites, respectively, at the 5′ end. The shift of the bands to the origin of the electrophoresis was due to the use of these longer PCR primers. The band Ladder produced after ePCR was caused probably because the purification of the full-length products after the enzymatic digestion was incomplete, and the contamination of the shorter molecules was amplified during ePCR and the succeeding PCR. The recovered full-length DNA was purified and then digested with the restriction enzymes for cloning in an appropriate vector.
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note
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These additional data came from the 64 sequenced clones picked up from pools 1 through 3 and 9 clones from other prototype computations. These 73 clones include 71 different literal strings.
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32
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0342335810
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note
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We thank A. Nishikawa for designing the DNA sequences used in the experiments, E. Winfree for the critical reading of the manuscript, and Y. Husimi for valuable discussions on the physicochemical nature of hairpins. This work was supported in part by the Japan Society for the Promotion of Science under the Research for the Future program (JSPS-RFTF 96100101).
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