© 2004, snu biointelligence lab, joining and rotating data with molecules masanori arita, masami...

© 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


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


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


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


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


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)



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



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


Simple polymerization

Using overlapping region which anneals at low temperature

Not a good resultRFU value was less

than 20Time consuming


PCR from single-stranded templates

Direct amplification of dsDNA from the ssDNA templates


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 …


Using bridge primers

Concatenation with bridges


Rotation


DNA favors circularization rather than polymerization in diluted solution

inverse PCR on circular DNA produces rotated data

Rotation in diluted solution

unexpected ligation


Rotation with biotin

Use biotin to avoid unexpected ligation


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

© 2004, snu biointelligence lab, joining and rotating data with molecules masanori arita, masami...

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