Unravel four hairpins!
DNA machines consisting of consecutive hairpins, which we have previously described, have various potential applications in DNA computation. In the present study, a 288-base DNA machine containing four consecutive hairpins was successfully constructed by ligation and PCR. PAGE and fluorescence spectroscopy experiments verified that all four hairpins were successfully opened by four opener oligomers, and that hairpin opening was dependent on the proper openers added in the correct order. Quantitative analysis of the final results by fluorescence spectroscopy indicated that all four hairpins were open in about 1/4 to 1/3 of the DNA machines.
KeywordsDNA computing DNA nanotechnology Molecular computing Molecular memory Molecular machine
The work presented in this paper was partially supported by Grand-in-Aid for Scientific Research on Priority Area No. 14085202, Ministry of Education, Culture, Sports, Science and Technology, Japan.
- Hagiya M, Yaegashi S, Takahashi K (2005) Computing with Hairpins and Secondary Structures of DNA. In: Nanotechnology: science and computation, Natural computing series. Springer, pp 293–308Google Scholar
- Seelig G, Yurke B, Winfree E (2005) DNA Hybridization catalysts and catalyst circuits. In: DNA computing, 10th international workshop on DNA computing. Lecture Notes in Computer Science, vol 3384, pp 329–343Google Scholar
- Takahashi K, Yaegashi S, Kameda A, Hagiya M (2006) Chain reaction systems based on loop dissociation of DNA. In: DNA computing: 11th international workshop on DNA computing, DNA11. Lecture Notes in Computer Science, vol 3892, pp 347–358Google Scholar
- Takahashi N, Kameda A, Yamamoto M, Ohuchi A (2005) Aqueous computing with DNA hairpin-based RAM. In: DNA computing, 10th international workshop on DNA computing. Lecture Notes in Computer Science, vol 3384, pp 355–364Google Scholar
- Uejima H, Hagiya M (2004) Secondary structure design of multi-state DNA machines based on sequential structure transitions. In: DNA computing, 9th international workshop on DNA-based computers. Lecture Notes in Computer Science. Springer, vol 2943, pp 74–85Google Scholar
- Yan H (2005) An inexpensive LED-based fluorometer used to study a hairpin-based DNA nanomachine. In: DNA computing, 10th international workshop on DNA computing. Lecture Notes in Computer Science, vol 3384, pp 399–409Google Scholar