Team:UIUC-Illinois/Project/Future/Scaffold
From 2012.igem.org
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<center><img src="https://static.igem.org/mediawiki/2012/3/3e/D0_Scaffold.png" height=75% width=75%><br/></center><br/> | <center><img src="https://static.igem.org/mediawiki/2012/3/3e/D0_Scaffold.png" height=75% width=75%><br/></center><br/> | ||
- | <b>Fig. | + | <b>Fig. 3.</b> |
The corresponding image of the d0 RNA secondary structure as predicted by the <a href="http://rna.informatik.uni-freiburg.de:8080/LocARNA.jsp">LocARNA tool of Freiburg RNA Tools</a>. The software accurately depicts what the d0 structure looks like in the literature, therefore it was a reliable program which could be used to modify and visualize RNA secondary structures. | The corresponding image of the d0 RNA secondary structure as predicted by the <a href="http://rna.informatik.uni-freiburg.de:8080/LocARNA.jsp">LocARNA tool of Freiburg RNA Tools</a>. The software accurately depicts what the d0 structure looks like in the literature, therefore it was a reliable program which could be used to modify and visualize RNA secondary structures. | ||
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<center><img src="https://static.igem.org/mediawiki/2012/5/5c/Modified_d0_Sequence_with_PUF_Binding_Sites_--3.png" width=100% ><br/></center><br/> | <center><img src="https://static.igem.org/mediawiki/2012/5/5c/Modified_d0_Sequence_with_PUF_Binding_Sites_--3.png" width=100% ><br/></center><br/> | ||
- | <b>Fig. | + | <b>Fig. 4.</b> |
Modifications to the d0 sequence were made by replacing the PP7 and MS2 binding sites with WT PUF-PIN and 6-2/7-2 PUF-PIN binding sites. | Modifications to the d0 sequence were made by replacing the PP7 and MS2 binding sites with WT PUF-PIN and 6-2/7-2 PUF-PIN binding sites. | ||
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<br/><br/><br/> | <br/><br/><br/> | ||
- | <center><img src="https://static.igem.org/mediawiki/2012/d/d1/Freiburg_RNA_Tools_Website_Modifiedd_d0_-1.png" width= | + | <center><img src="https://static.igem.org/mediawiki/2012/d/d1/Freiburg_RNA_Tools_Website_Modifiedd_d0_-1.png" height=75% width=75%><br/></center><br/> |
- | <b>Fig. | + | <b>Fig. 5.</b> |
The resulting scaffold of the changed sequence. | The resulting scaffold of the changed sequence. | ||
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- | <center><img src="https://static.igem.org/mediawiki/2012/d/d2/IDT_miniGene_Scaffold_-1_--4.png" | + | <center><img src="https://static.igem.org/mediawiki/2012/d/d2/IDT_miniGene_Scaffold_-1_--4.png" width=100%><br/></center><br/> |
- | <b>Fig. | + | <b>Fig. 6.</b> |
The scaffold was further modified after research suggested that PUF binds best to nucleotides with an angle of curvature similar to its own of approximately 20o turn per repeat*. The hairpin loops were changed in order to accommodate this from 8 nucleotides to 18 nucleotides achieving a 20o turn per nucleotide effect. Sequences of the stem loop were further modified in order to keep GC content from being too high and to make a more stable structure. This DNA sequence was then synthesized through IDT’s miniGENE option. | The scaffold was further modified after research suggested that PUF binds best to nucleotides with an angle of curvature similar to its own of approximately 20o turn per repeat*. The hairpin loops were changed in order to accommodate this from 8 nucleotides to 18 nucleotides achieving a 20o turn per nucleotide effect. Sequences of the stem loop were further modified in order to keep GC content from being too high and to make a more stable structure. This DNA sequence was then synthesized through IDT’s miniGENE option. | ||
Revision as of 07:58, 3 October 2012