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Joining and Rotating Data with Molecules

Joining and Rotating Data with Molecules. Masanori Arita, Masami Hagiya and Akira Suyama Summarized by Sung-Kyu Kim. Introduction. Molecular operation is so unreliable to perform sophisticated computations

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Joining and Rotating Data with Molecules

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  1. Joining and Rotating Data with Molecules Masanori Arita, Masami Hagiya and Akira Suyama Summarized by Sung-Kyu Kim

  2. Introduction • Molecular operation is so unreliable to perform sophisticated computations • Feasible way of implementing significant operations such as Cartesian product or selection in database theory • Data encoded in the following form • (tag data tag)+ • DNA manipulation using PCR

  3. Computer Database • Tuples • Operations • Selection, Projection, Union, Difference, Catesian product (or join) tuples

  4. Performed Experiments • Simple polymerization • PCR from single-stranded templates • Circularization in diluted solution • Using biotin for circularization • Streptavidin-coated magnetic beads • Experiment output is analyzed by capillary electrophoresis system with LIFluor daDNA1000Kit and System Gold • Output graph with RFU (relative fluorescence unit) • measures the amount of dsDNA

  5. Sequence Design conditions • Both 5bp ends of each data (or tag) do not appear in the ends of other data • The GC content of each data (or tag) is not greatly biased • A tag sequence does not form a stable structure by itself • ssDNA for generating each tuple anneals at the expected sites

  6. Data Representation (1/3) • Each tuple was made from ssDNA of 60 or 45 bp • Primer sequence can be either 15 or 30 bp • DNA sequences for the experiments

  7. Data Representation (2/3) • Data: striped block • Tag: shaded block • indicates what kind of data is stored after or before it • Can be used as target sites for PCR primers

  8. Data Representation (3/3) • Concatenated sequence of seq1, seq2 and seq3 • 1-2-3 • ssDNA has a header (fwd or rev) before a sequence of numbers • Fwd: 5’ →3’ • Rev: 3’ →5’ • e.g) fwd 1-2-3-4, rev 4-5-6 • dsDNA has no header

  9. Simple polymerization • Using overlapping region which anneals at low temperature • Not a good result • RFU value was less than 20 • Time consuming

  10. PCR from single-stranded templates • Direct amplification of dsDNA from the ssDNA templates

  11. Concatenation of overlapping sequences • Concatenation of three templates • tupleA(B) + seq7 • seq6 + tupleC(D) + seq13 • seq12 + tupleE • With primers fwd1, rev18 • Output: A-C-E or A-D-E or B-C-E or …

  12. Concatenation with bridges • Using bridge primers

  13. Rotation

  14. Rotation in diluted solution • DNA favors circularization rather than polymerization in diluted solution • inverse PCR on circular DNA produces rotated data unexpected ligation

  15. Rotation with biotin • Use biotin to avoid unexpected ligation

  16. Discussion • Tuple management using PCR technique • Reliable realization of catesian product operation • This method can be useful for building initial population of PLM library and updating library

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