Team:Korea U Seoul/Notebook/Jun

From 2012.igem.org

Notebook : June

A. June, 4, 2012

Today, we discussed about main topic and preliminary topic which are bacterial logic gate and carbon fixation using carbonic anhydras

1) Idea development
Jeongmin Lee, Kyeongjin Kim: DNA logic gate

reviewed a paper on DNA gate by KAIST 2012

Possible to make logic gate (XOR, NOR, AND, OR) based on DNA

Mechanism: DNA hairpin: input DNA is complementary to output DNA which releases florescence.

Half adder possible, but requires further research on full adder

Hyunkee Kim

Deoxyribozyme based logic gate

Jang Kyeongwoo Jang

Progress on XOR logic gate

Possible candidate for XOR logic gate is .Lux R operon and Las R operon which is orthologous to each other

     Promoter design
      ① las - lux - output
      ② lux - las – output

output is the same protein. When two signals are simultaneously given, each operon inhibits transcription. In effect, this results in no transcription at all

Jihoon Jung

researched on output-input chemicals

One was substance that uses quorum sensing

For example, AHL(Acyl-homoserine lectone)

Since each bacteria uses different AHL, signal won’t mix up

Sanghoon Han

researched on output-input chemicals

2) Next meeting

Carbonic anhydrase : Byeongnam Min, Haerim Song, Ji Hyoung Nam

DNA logic gate : Jeongmin Lee, Kyeongjin Kim, Wonuk Lee

Plasmid logic gate : Hyunkee Kim, Jang Kyeongwoo Jang, Jihoon Jung, Sanghoon Han

Half adder, full adder completion: everyone

B. June 25, 2012

Today, we discussed about main topic and preliminary topic which are bacterial logic gate, Molecular Beacon, and carbon fixation using carbonic anhydrase.

1) Idea development
Jeongmin Lee, Kyeongjin Kim: DNA logic gate

Possible to make logic gate (XOR, NOR, AND, OR) based on DNA

Nearly impossible if more than half adder is used. (Note: longer DNA is required).

As DNA gets longer, price for synthesis is getting higher and even more when protein is attached to DNA.

Hyunkee Kim, Kyeongwoo Jang, Sanghoon Han, Jihoon Jung

need to unify input signal and output signal

Improvement on modeling of full gate.

If input and output are the same, these can interfere in signal transfer.

That is to say, input chemical must be destroyed once it gives signal to adjacent promoter..

Back up idea team ( Jihyong Nam, Byeongnam Min, Haerim Song, Dohoon Kwon)

Haerim Song: Inhibition of virulence of bacteria on plant – type 3 secretion

Sponsor (Dohoon Kwon, Wonuk Lee)

in order to get funding, we need to have presentation on our research or submit a report.

2) Next meeting

From next week, we will have our regular meeting on Wednesday 8p.m

Before next meeting, research the problems and limitations that we discussed during our regular meeting