Team:Heidelberg/Modeling/miBSdesigner

From 2010.igem.org

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Seed sequence (1-8) </span></div>
Seed sequence (1-8) </span></div>
<div class="option"><SELECT name="seed" onchange="chMd1()" disabled="disabled">
<div class="option"><SELECT name="seed" onchange="chMd1()" disabled="disabled">
 +
                <OPTION value="0">
<OPTION value="6mer">6mer                (2-7 paired)
<OPTION value="6mer">6mer                (2-7 paired)
<OPTION value="7merA1">7merA1          (1-7 paired)
<OPTION value="7merA1">7merA1          (1-7 paired)
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Supplementary region </span></div>
Supplementary region </span></div>
<div class="option"><SELECT name="comp" onchange="chMd2()" disabled="disabled">
<div class="option"><SELECT name="comp" onchange="chMd2()" disabled="disabled">
 +
                <OPTION value="0">
<OPTION value="3">3                  (14-16 paired)
<OPTION value="3">3                  (14-16 paired)
<OPTION value="4">4                  (13-16 paired)
<OPTION value="4">4                  (13-16 paired)

Revision as of 18:52, 25 October 2010

BS designer for miRNA
Sequence name

microRNA Sequence ( 5' -> 3')

Spacer (inert sequence)


Perfect Binding Site
Imperfect Binding Site with 4 nt bulge (9-12)
Personalized Binding Site

Seed sequence (1-8)
Customized MISMATCH position

Supplementary region
Customized MATCH positions (input numbers from 9 to 22)


Modify AU content
A in position -1
A in position 0
A in position 1
A in position 8
A in position 9
A in position 10


Sticky ends for integration in plasmid:
Customized: 5' 3'



Construction of microRNA binding sites





Name of primer 1


Sequence of primer 1


Name of primer 2


Sequence of primer 2