Difference between revisions of "Part:BBa K3657022:Design"

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<ol>
 
<ol>
 
   <li>Generate a random DNA sequence containing adenine, cytosine and guanine. You sequence should be longer than 19 base pairs and preferably should not contain thymine.</li>
 
   <li>Generate a random DNA sequence containing adenine, cytosine and guanine. You sequence should be longer than 19 base pairs and preferably should not contain thymine.</li>
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   <li>Use the following script to generate RNA: <a href="https://github.com/igemsoftware2020/Heidelberg_2020/blob/main/CoNcoRDe/rnasupport/scripts/design_rna_triple_helix.py">link.</a> <br>Corresponding bases in the script are the pairs that create strongest bonds according to Kunkler et al.</li>
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   <li>Use the following script to generate RNA: <a href="https://github.com/igemsoftware2020/Heidelberg_2020/blob/main/CoNcoRDe/CoNcoRDe/rnasupport/scripts/design_rna_triple_helix.py">link.</a> <br>Corresponding bases in the script are the pairs that create strongest bonds according to Kunkler et al.</li>
 
   <li> Attention! If you are adding other parts to your RNA, for example hairpins that interact with RNA binding proteins, makes sure that the added parts don't create a stable secondary structure with the triple helix part. Otherwise it may disturb the formation of the triple helix.</il>
 
   <li> Attention! If you are adding other parts to your RNA, for example hairpins that interact with RNA binding proteins, makes sure that the added parts don't create a stable secondary structure with the triple helix part. Otherwise it may disturb the formation of the triple helix.</il>
 
</ol>
 
</ol>
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===Source===
 
===Source===
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Kunkler CN, Hulewicz JP, Hickman SC, Wang MC, McCown PJ, Brown JA. Stability of an RNA•DNA-DNA triple helix depends on base triplet composition and length of the RNA third strand. Nucleic Acids Res. 2019; 47(14):7213-7222.
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<i>Homo sapiens</i>
  
 
===References===
 
===References===
 
Kunkler CN, Hulewicz JP, Hickman SC, Wang MC, McCown PJ, Brown JA. Stability of an RNA•DNA-DNA triple helix depends on base triplet composition and length of the RNA third strand. Nucleic Acids Res. 2019; 47(14):7213-7222.
 
Kunkler CN, Hulewicz JP, Hickman SC, Wang MC, McCown PJ, Brown JA. Stability of an RNA•DNA-DNA triple helix depends on base triplet composition and length of the RNA third strand. Nucleic Acids Res. 2019; 47(14):7213-7222.

Latest revision as of 23:07, 27 October 2020


RNA Part of an RNA·DNA-DNA triple helix


Assembly Compatibility:
  • 10
    COMPATIBLE WITH RFC[10]
  • 12
    COMPATIBLE WITH RFC[12]
  • 21
    COMPATIBLE WITH RFC[21]
  • 23
    COMPATIBLE WITH RFC[23]
  • 25
    COMPATIBLE WITH RFC[25]
  • 1000
    COMPATIBLE WITH RFC[1000]


Design Notes

Sequence of this part was published by the Kunkler et al.

Part Design

You can generate analogical parts yourself as following:

  1. Generate a random DNA sequence containing adenine, cytosine and guanine. You sequence should be longer than 19 base pairs and preferably should not contain thymine.
  2. Use the following script to generate RNA: link.
    Corresponding bases in the script are the pairs that create strongest bonds according to Kunkler et al.
  3. Attention! If you are adding other parts to your RNA, for example hairpins that interact with RNA binding proteins, makes sure that the added parts don't create a stable secondary structure with the triple helix part. Otherwise it may disturb the formation of the triple helix.

Source

Homo sapiens

References

Kunkler CN, Hulewicz JP, Hickman SC, Wang MC, McCown PJ, Brown JA. Stability of an RNA•DNA-DNA triple helix depends on base triplet composition and length of the RNA third strand. Nucleic Acids Res. 2019; 47(14):7213-7222.