Team:Bologna/Project

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= Introduction =
= Introduction =
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Our goal is to create a logic gate based on a post-transcriptional regulation system in Escherichia coli, using RNA to silence gene expression. We inserted a cis-repressing sequence directly upstream of the rbs (ribosome binding site) to realize a "regulated rbs". We also designed the complementary trans-repressing sequence whose function is to recognize and cover the "regulated rbs" and prevent translation from it. Two versions of the trans- repressing sequence were designed with 2 different kinds of rbs covers. We want to use this short non-coding RNA segment placed in trans, to silence translation from dowstream the cis-repressing sequence.  
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Our goal is to create a logic gate based on a post-transcriptional regulation system in Escherichia coli, using RNA to silence gene expression. We inserted a cis-repressing sequence directly upstream of the rbs (ribosome binding site) to realize a "regulated rbs". We also designed the complementary trans-repressing sequence whose function is to recognize and cover the "regulated rbs" and prevent translation from it. Two versions of the trans-repressor sequence were designed with 2 different kinds of rbs covers. We want to use this short non-coding RNA segment placed in trans, to silence translation from dowstream the cis-repressing sequence.  
We developed a [[Team:Bologna/Software|bioinformatic tool]] to research the best sequences. Using the results of our software we changed some base pairs in order to minimize the free energy of the [[RNA secondary structures]].
We developed a [[Team:Bologna/Software|bioinformatic tool]] to research the best sequences. Using the results of our software we changed some base pairs in order to minimize the free energy of the [[RNA secondary structures]].
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Revision as of 15:45, 18 October 2009

ProvaBol2.png
HOME TEAM PROJECT SOFTWARE MODELING WET LAB PARTS HUMAN PRACTICE JUDGING CRITERIA


Introduction

Our goal is to create a logic gate based on a post-transcriptional regulation system in Escherichia coli, using RNA to silence gene expression. We inserted a cis-repressing sequence directly upstream of the rbs (ribosome binding site) to realize a "regulated rbs". We also designed the complementary trans-repressing sequence whose function is to recognize and cover the "regulated rbs" and prevent translation from it. Two versions of the trans-repressor sequence were designed with 2 different kinds of rbs covers. We want to use this short non-coding RNA segment placed in trans, to silence translation from dowstream the cis-repressing sequence. We developed a bioinformatic tool to research the best sequences. Using the results of our software we changed some base pairs in order to minimize the free energy of the RNA secondary structures.

These are the result sequences:


Cis-repressing sequence, inserted upstream of the target gene
Scar Cis-repressing Rbs Scar
TACTAGAG AACACAAACTATCACTTTAACAACACATTACATATACATTAAAATATTAC AAAGAGGAGAAA TACTAGAG


Trans-repressor sequence with a cover of 7 bases (long version)
Scar Cover Trans(long) Scar
TACTAGAG CCTCTTT GTAATATTTTAATGTATATGTAATGTGTTGTTAAAGTGATAGTTTGTGTT TACTAGAG


Trans-repressor sequence with a cover of 4 bases (short version)
Scar Cover Trans(short) Scar
TACTAGAG CTTT GTAATATTTTAATGTATATGTAATGTGTTGTTAAAGTGATAGTTTGTGTT TACTAGAG



When the TRANS-repressor element is present, it binds to the CIS-repressing, forming a RNA duplex and producing an obstruction that prevents the ribosome binding to the RBS:

Project3b.png



These are three genetic circuits that uses Cis-repressing and Trans-repressor:

Circuito with rRBS 1.jpg


Circuito with rRBS 1.1.jpg


Circuit2.jpg



We decided to realize and developed the third circuit and we started to characterize its parts.
(More information in the Wetlab section)