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 [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.