Team:Heidelberg/Notebook/BSDesign

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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.