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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 - PowerPoint PPT Presentation
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© 2004, SNU Biointelligence Lab, http://bi.snu.ac.kr/
Joining and Rotating Data with Molecules
Masanori Arita, Masami Hagiya and Akira Suyama
Summarized by Sung-Kyu Kim
© 2004, SNU Biointelligence Lab, http://bi.snu.ac.kr/
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
© 2004, SNU Biointelligence Lab, http://bi.snu.ac.kr/
Computer Database
Tuples
OperationsSelection, Projection, Union, Difference, Catesian pr
oduct (or join)
StudentID Name
S0001 Tom
S0002 July
StudentID Subject Score
S0001 Math 100
S0002 English 70
S0002 Math 60
tuples
© 2004, SNU Biointelligence Lab, http://bi.snu.ac.kr/
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 GoldOutput graph with RFU (relative fluorescence unit)measures the amount of dsDNA
© 2004, SNU Biointelligence Lab, http://bi.snu.ac.kr/
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
© 2004, SNU Biointelligence Lab, http://bi.snu.ac.kr/
Each tuple was made from ssDNA of 60 or 45 bpPrimer sequence can be either 15 or 30 bpDNA sequences for the experiments
Data Representation (1/3)
© 2004, SNU Biointelligence Lab, http://bi.snu.ac.kr/
Data Representation (2/3)
Data: striped blockTag: shaded block
indicates what kind of data is stored after or before it
Can be used as target sites for PCR primers
© 2004, SNU Biointelligence Lab, http://bi.snu.ac.kr/
Data Representation (3/3)
Concatenated sequence of seq1, seq2 and seq31-2-3
ssDNA has a header (fwd or rev) before a sequence of numbersFwd: 5’ →3’Rev: 3’ →5’e.g) fwd 1-2-3-4, rev 4-5-6
dsDNA has no header
© 2004, SNU Biointelligence Lab, http://bi.snu.ac.kr/
Simple polymerization
Using overlapping region which anneals at low temperature
Not a good resultRFU value was less
than 20Time consuming
© 2004, SNU Biointelligence Lab, http://bi.snu.ac.kr/
PCR from single-stranded templates
Direct amplification of dsDNA from the ssDNA templates
© 2004, SNU Biointelligence Lab, http://bi.snu.ac.kr/
Concatenation of overlapping sequences
Concatenation of three templates tupleA(B) + seq7seq6 + tupleC(D) + seq13seq12 + tupleEWith primers fwd1,
rev18
Output: A-C-Eor A-D-E or B-C-Eor …
© 2004, SNU Biointelligence Lab, http://bi.snu.ac.kr/
Using bridge primers
Concatenation with bridges
© 2004, SNU Biointelligence Lab, http://bi.snu.ac.kr/
Rotation
© 2004, SNU Biointelligence Lab, http://bi.snu.ac.kr/
DNA favors circularization rather than polymerization in diluted solution
inverse PCR on circular DNA produces rotated data
Rotation in diluted solution
unexpected ligation
© 2004, SNU Biointelligence Lab, http://bi.snu.ac.kr/
Rotation with biotin
Use biotin to avoid unexpected ligation
© 2004, SNU Biointelligence Lab, http://bi.snu.ac.kr/
Tuple management using PCR techniqueReliable realization of catesian product op
erationThis method can be useful for building initi
al population of PLM library and updating library
Discussion