Team:Heidelberg/Notebook/BSDesign

From 2010.igem.org

(Difference between revisions)
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|'''25'''||'''26'''||'''27'''||'''28'''||'''29'''||'''30'''||'''31'''
|- style="background:#f2f2f2; color:#f09600"
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=Binding Site Design=
=Binding Site Design=
 +
 +
==Introduction==
 +
 +
To create binding site (BS) patterns for micro RNAs (miRNAs) , we used the random assembly PCR (raPCR) – method from iGEM2009-Heidelberg team ([http://2009.igem.org/Team:Heidelberg/Project_Synthetic_promoters#RA-PCR_protocol see here]) and adopted it to our purposes.
 +
The differences:
 +
*Sequences from 100 to 400 base pairs are requested.
 +
*Oligos span over a whole binding site for a certain miRNA and shuffling occurs on the level of pattern creation.
 +
 +
Several points need to be considered for setting up miRNA-binding site (miRBS) patterns:
 +
:*the right distance after the stop codon for efficient (or non-efficient) BS recognition
 +
:*distance and sequence between miRBS (the spacer)
 +
 +
 +
See on our Notebook pages how we created binding site patterns.
 +
 +
The adopted method for BS-patterns can be found on our [http://2010.igem.org/Team:Heidelberg/Notebook/Methods#random_assembly_PCR_.28raPCR.29 methods page].
 +
 +
On the [http://2010.igem.org/Team:Heidelberg/Parts#synthetic_microRNA_binding_Site_patterns_against_endogenous_miRNA Parts]-Page you can find standardized BS-patterns for hsa-mir-122 and has-mir-221, containing at least 2 binding sites.
 +
{{:Team:Heidelberg/Single_Bottom}}
{{:Team:Heidelberg/Single_Bottom}}

Latest revision as of 03:17, 28 October 2010

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Binding Site Design

Introduction

To create binding site (BS) patterns for micro RNAs (miRNAs) , we used the random assembly PCR (raPCR) – method from iGEM2009-Heidelberg team (see here) and adopted it to our purposes. The differences:

  • Sequences from 100 to 400 base pairs are requested.
  • Oligos span over a whole binding site for a certain miRNA and shuffling occurs on the level of pattern creation.

Several points need to be considered for setting up miRNA-binding site (miRBS) patterns:

  • the right distance after the stop codon for efficient (or non-efficient) BS recognition
  • distance and sequence between miRBS (the spacer)


See on our Notebook pages how we created binding site patterns.

The adopted method for BS-patterns can be found on our methods page.

On the Parts-Page you can find standardized BS-patterns for hsa-mir-122 and has-mir-221, containing at least 2 binding sites.