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Scrambled sequence?


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#1 cathyolive

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Posted 29 October 2013 - 07:42 AM

I have made a number of enhancer variants and need to insert a scramble/nonsense sequence to test one of my hypotheses. The sequence needs to be 23bp long, and ideally not contain any sequences for any known transcription factor binding sites.

 

Can anyone help me with how to do this or where to look?

 

 



#2 jerryshelly1

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Posted 29 October 2013 - 10:53 AM

Can you use the sequence of a well known epitope tag? Flag, myc, HA?



#3 phage434

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Posted 29 October 2013 - 01:16 PM

As far as I am aware, there is not a comprehensive list of transcription factors available anywhere (many are probably not known). Your best bet is to make a random sequence, and go from there. A non-computer easy way would be to label 23 identical items (coins?) with each of the nucleotides, mix them up, and pull them out in a random order. If you wanted to be sure, you could do this twice.



#4 cathyolive

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Posted 30 October 2013 - 04:34 AM

Thank you both!






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