Difference between revisions of "Team:IIT-Madras/Design"

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= RIBOS =
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== Introduction ==
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In order to make precise and predictable biological devices, which can be controlled at will, we have designed a ribo-regulatory switch and named it RIBOS (RNA Inducible Boolean Output like Switch). RIBOS works on the principle of Watson-Crick base pairing between '''trigger RNA''' and '''switch mRNA'''. There are two sub-types of RIBOS, <span class="riboson">RIBOSON</span> and <span class="ribosoff">RIBOSOFF</span>, which activates and represses the translation process of downstream protein coding mRNA respectively in the presence of corresponding '''trigger RNA'''. The validation and functional optimization of RIBOS switches have been done with the help of 'Nupack' software by taking the thermal stability of RNA secondary structures and various other parameters into account. We have designed RIBOS such that the difference between it's ON and OFF states for both sub-types of switches are large enough to make them reliable in cell environment. Owing to the special designs of RIBOS, the base pairing between trigger and switch can range from 10 nucleotide to around 25 nucleotide, which makes it very orthogonal in principle. RIBOS can be used at the place of RBS parts in our expression systems, which can be controlled by supplying '''trigger RNA''' molecules. It's applications range from detection and quantification of mRNA molecules to the design of independent and modular genetic circuits in limitless number using forward engineering. As a deliverable, the algorithm can be used by future iGEM teams to design <span class="riboson">RIBOSON</span> and <span class="ribosoff">RIBOSOFF</span> for any trigger sequence.
  
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== RIBOSON ==
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<h3>★  ALERT! </h3>
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[[Image:SingleMolDet_iGEM16.png|900px|center]]
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<p>This page is used by the judges to evaluate your team for the <a href="https://2016.igem.org/Judging/Awards#Special_Prizes"> design special prize</a>. </p>
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<gallery widths=275px heights=275px 'frameless'>
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File:RIBOSON_s1.svg|Initial State
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File:RIBOSON_s2.svg|Intermdiate State
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File:RIBOSON_s3.svg|Final State
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</gallery>
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== RIBOSOFF ==
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[[Image:SingleMolDet_iGEMRIBOSoff.png|900px|center]]
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<gallery widths=275px heights=275px 'frameless'>
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File:RIBOSOFF_s1.svg|Initial State
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File:RIBOSOFF_s2.svg|Intermediate State
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File:RIBOSOFF_s3.svg|Final State
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</gallery>
  
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<p> Delete this box in order to be evaluated for this medal. See more information at <a href="https://2016.igem.org/Judging/Pages_for_Awards/Instructions"> Instructions for Pages for awards</a>.</p>
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Given below are animations which describe the working of <span class="riboson">RIBOSON</span> and <span class="ribosoff">RIBOSOFF</span> respectively.
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<video width="49%" controls>
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  <source src="https://static.igem.org/mediawiki/2016/4/48/Ribosplus.mp4">
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  <source src="https://static.igem.org/mediawiki/2016/9/98/Ribosminus.mp4">
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By talking about your design work on this page, there is one medal criterion that you can attempt to meet, and one award that you can apply for. If your team is going for a gold medal by building a functional prototype, you should tell us what you did on this page.
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<p>This is a prize for the team that has developed a synthetic biology product to solve a real world problem in the most elegant way. The students will have considered how well the product addresses the problem versus other potential solutions, how the product integrates or disrupts other products and processes, and how its lifecycle can more broadly impact our lives and environments in positive and negative ways.</p>
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If you are working on art and design as your main project, please join the art and design track. If you are integrating art and design into the core of your main project, please apply for the award by completing this page.
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<p>Teams who want to focus on art and design should be in the art and design special track. If you want to have a sub-project in this area, you should compete for this award.</p>
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Latest revision as of 23:59, 19 October 2016


RIBOS

Introduction

In order to make precise and predictable biological devices, which can be controlled at will, we have designed a ribo-regulatory switch and named it RIBOS (RNA Inducible Boolean Output like Switch). RIBOS works on the principle of Watson-Crick base pairing between trigger RNA and switch mRNA. There are two sub-types of RIBOS, RIBOSON and RIBOSOFF, which activates and represses the translation process of downstream protein coding mRNA respectively in the presence of corresponding trigger RNA. The validation and functional optimization of RIBOS switches have been done with the help of 'Nupack' software by taking the thermal stability of RNA secondary structures and various other parameters into account. We have designed RIBOS such that the difference between it's ON and OFF states for both sub-types of switches are large enough to make them reliable in cell environment. Owing to the special designs of RIBOS, the base pairing between trigger and switch can range from 10 nucleotide to around 25 nucleotide, which makes it very orthogonal in principle. RIBOS can be used at the place of RBS parts in our expression systems, which can be controlled by supplying trigger RNA molecules. It's applications range from detection and quantification of mRNA molecules to the design of independent and modular genetic circuits in limitless number using forward engineering. As a deliverable, the algorithm can be used by future iGEM teams to design RIBOSON and RIBOSOFF for any trigger sequence.

RIBOSON

SingleMolDet iGEM16.png
  • Error creating thumbnail: File missing

    Initial State

  • Error creating thumbnail: File missing

    Intermdiate State

  • Error creating thumbnail: File missing

    Final State

RIBOSOFF

SingleMolDet iGEMRIBOSoff.png
  • Error creating thumbnail: File missing

    Initial State

  • Error creating thumbnail: File missing

    Intermediate State

  • Error creating thumbnail: File missing

    Final State

Given below are animations which describe the working of RIBOSON and RIBOSOFF respectively.