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Advances in DNA Computing: Design and Operation of Surface-Bound DNA Words

This study presents innovative strategies in DNA computing by utilizing fixed-length DNA words (16mers) to store and process information. It discusses the principles of designing these DNA words to create large combinatorial sets through T4 DNA ligase. Key aspects include a balanced GC content, careful arrangement to prevent structural issues, and specific sequence design for operations like marking and destroying. The authors detail the scalability of the DNA computing process, allowing for immense variations in DNA sequences, showcasing the potential for future applications in molecular computing.

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Advances in DNA Computing: Design and Operation of Surface-Bound DNA Words

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  1. Multiple Word DNA Computing on Surfaces L. Wang, Q. Liu, R.M. Corn, A.E. Condon, and L.M. Smith Journal of the American Chemical Society, vol. 122, no. 31, pp. 7435-7440, August 2000 Cho, Dong-Yeon

  2. Previous Study Complement sequence E. coli exonuclease I

  3. DNA Word Strategy • Store information in “DNA words” of fixed length (16mers) • Link DNA Words together to form large combinational sets of molecules (T4 DNA ligase)

  4. 16mer Word Design • Word Structure • DNA Word Label Format • Have a 50% GC content • Arranged ABCD…DCBA to avoid hairpins and slide matches • Complete mismatches with the other word labels

  5. Sequence Design • Surface-bound Oligonucleotides • Two-Word DNA Sequences

  6. MARK and DESTROY Operations

  7. Example

  8. Discussion • Scale-up of the DNA Computing Process • 108 different word sequence for each 6 words • 1086 = 1.6  1012 (240 = 1.1  1012) • Oligonucleotide length: (16  6) + 16 + 4 + 5 = 121 • 6 words: 16  6 = 96 • 1 primer site: 16 • 1 Restriction site: 4 • 1 Adjacent spacer: 5

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