Team:Heidelberg/Parts

From 2010.igem.org

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__NOTOC__
__NOTOC__
-
=Parts=
+
=miBricks - Parts submitted to the registry=
-
We assembled a lot of '''miBricks''' (i. e. basic parts) to composite parts that were then used to built up our final constructs. The submitted parts are listed below. We did not categorize the parts according to different subprojects since they are universally applicable or clearly denoted through their names. Some binding site patterns, which were created via [... miraPCR], are listed separately.
+
<br>
-
<br/>
+
-
== Basic parts ==
+
The parts we submit belong to the two core aims our project: Reaching regulatory control (1) and specificity (2) of gene expression of any gene of interest in any target cell or tissue of choice. Therefore we engineered parts, that address these two aims on two different regulatory levels.
 +
 
 +
First, we engineered gene therapy vectors based on synthetic adeno associated viruses (AAVs). On parts level, we provide about 50 plasmids that can be used for creating shuffled AAV libraries or even rationally designed, recombinant AAV vectors. Those parts we refer to as virobytes, are designed in a format directly applicable for the [http://2010.igem.org/Team:Heidelberg/Project/Capsid_Shuffling/ViroBytes Virobytes Assembly] protocol we develop.
 +
 
 +
On RNA level we provide the [http://2010.igem.org/Team:Heidelberg/Project/miRNA_Kit miTuner toolkit] consisting of roughly 60 parts enabling gene expression control based on synthetic or cell-specific endogenous microRNAs. This toolkit consists of three main constructs: The '''pSMB_miMeasure''' binding site characterization standard and '''two pSMB_miTuner''' expression controlling plasmids. Furthermore, it contains 12 basic and 28 intermediate construction parts, synthetic, single microRNA binding sites as well as binding site patterns in BB-2 (RFC 12, Tom Knight) standard. This enables maximum flexibility for applications in many different contexts.
 +
 
 +
 
 +
==Main Measurement Constructs - Engineered==
 +
<center>
 +
{| class="wikitable sortable" border="0" style="text-align: left"
 +
|-bgcolor=#cccccc
 +
|+ align="top, left"|
 +
|width=40px| ID||width=600px|Content||width=100px|Registry link||width=100px|Name
 +
|-
 +
|K3||BGH(rc)/shRNA10(rc)/RSV(rc)/CMV/Luc2_sv40/CMV/Kozag_hRluc_BGH||[http://partsregistry.org/Part:BBa_K337036 BBa_K337036]|| pSMB_miTuner Plasmid HD3
 +
|-
 +
|K4||BGH(rc)/shRNA10(rc)/RSV(rc)/CMV_TetO2/Luc2_sv40/CMV/Kozag_hRluc_BGH||[http://partsregistry.org/Part:BBa_K337038 BBa_K337038]|| pSMB_miTuner Plasmid HD4
 +
|-
 +
|miM||sv40ter(rc)/eBFP(rc)/biCMV/eGFP(fw)/sv40ter(fw)||[http://partsregistry.org/Part:BBa_K337049 BBa_K337049]|| pSMB_miMeasure
 +
|-
 +
|}
 +
</center>
 +
 
 +
 
 +
==Synthetic Single Binding Sites==
 +
<center>
 +
{| class="wikitable sortable" border="0" style="text-align: left"
 +
|-bgcolor=#cccccc
 +
|+ align="top, left"|(Physical DNA not submitted)
 +
|width=60px| Design||width=300px|Content||width=100px|Registry link||width=100px|Name
 +
|-
 +
|KD:97%||perfect binding site||[http://partsregistry.org/wiki/index.php?title=Part:BBa_K337052 BBa_K337052]||shRNA miRhaat
 +
|-
 +
|KD:69%||imperfect binding site: point mut 11||[http://partsregistry.org/wiki/index.php?title=Part:BBa_K337053 BBa_K337053]||shRNA miRhaat
 +
|-
 +
|KD:28%||imperfect binding site: bulge 16-18||[http://partsregistry.org/wiki/index.php?title=Part:BBa_K337054 BBa_K337054]||shRNA miRhaat
 +
|-
 +
|KD:96%||perfect binding site||[http://partsregistry.org/wiki/index.php?title=Part:BBa_K337055 BBa_K337055]||miR122
 +
|-
 +
|KD:64%||imperfect binding site:||[http://partsregistry.org/wiki/index.php?title=Part:BBa_K337056 BBa_K337056]||miR122
 +
|-
 +
|KD:24%||imperfect binding site:||[http://partsregistry.org/wiki/index.php?title=Part:BBa_K337057 BBa_K337057]||miR122
 +
|-
 +
|}
 +
</center>
 +
 
 +
==synthetic microRNA binding Site patterns against endogenous miRNA==
 +
<center>
 +
 
 +
 
 +
{| class="wikitable sortable" border="0" style="text-align: left"
 +
|-bgcolor=#cccccc
 +
|+ align="top, left"|
 +
|width=40px|  ID||width=350px|Content||width=100px|Registry link
 +
|-
 +
|1.3||hsa-miR-122 Binding site pattern (3BS)||[http://partsregistry.org/Part:BBa_K337000 BBa_K337000]
 +
|-
 +
|1A||hsa-miR-122 Binding site pattern (4BS)||[http://partsregistry.org/Part:BBa_K337003 BBa_K337003]
 +
|-
 +
|1-5||hsa-miR-122 Binding site pattern (2BS)||[http://partsregistry.org/Part:BBa_K337004 BBa_K337004]
 +
|-
 +
|3.7||hsa-miR-122 Binding site pattern (2BS - additional 10bp Spacer)||[http://partsregistry.org/Part:BBa_K337005 BBa_K337005]
 +
|-
 +
|1.5||hsa-miR-122 Binding site pattern (2BS) with randomized nt9-12||[http://partsregistry.org/Part:BBa_K337006 BBa_K337006]
 +
|-
 +
|1.8||hsa-miR-122 Binding site pattern (2BS) with randomized nt9-12||[http://partsregistry.org/Part:BBa_K337007 BBa_K337007]
 +
|-
 +
|3.1||hsa-miR-122 Binding site pattern (2BS) with randomized nt9-12||[http://partsregistry.org/Part:BBa_K337008 BBa_K337008]
 +
|-
 +
|4.5||hsa-miR-122 Binding site pattern (2BS) with randomized nt9-12||[http://partsregistry.org/Part:BBa_K337009 BBa_K337009]
 +
|-
 +
|4.6||hsa-miR-122 Binding site pattern (2BS) with randomized nt9-12||[http://partsregistry.org/Part:BBa_K337010 BBa_K337010]
 +
|-
 +
|mir221-10L2||hsa-miR-221 Binding site pattern (2BS)||[http://partsregistry.org/Part:BBa_K337011 BBa_K337011]
 +
|-
 +
|}
 +
</center>
 +
 
 +
==miTunig Kit - Basic Parts==
<center>
<center>
{| class="wikitable sortable" border="0" style="text-align: left"
{| class="wikitable sortable" border="0" style="text-align: left"
|-bgcolor=#cccccc
|-bgcolor=#cccccc
-
|+ align="top, left"|'''Table 1''': Our miBricks. Listed ID refers to internal nomenclature.
+
|+ align="top, left"|
|width=40px|  ID||width=100px|Content||width=100px|Registry link|| width=300px|Comment
|width=40px|  ID||width=100px|Content||width=100px|Registry link|| width=300px|Comment
|-
|-
Line 82: Line 159:
|}
|}
</center>
</center>
 +
<html>
 +
<div class="backtop">
 +
<a href="#top">&uarr;</a>
 +
</div>
 +
</html>
-
== Composite Parts ==
+
==miTuning Kit -  Intermediate Parts 1==
<center>
<center>
{| class="wikitable sortable" border="0" style="text-align: left"
{| class="wikitable sortable" border="0" style="text-align: left"
|-bgcolor=#cccccc
|-bgcolor=#cccccc
-
|+ align="top, left"|'''Table 2''': Our composite parts from subsequent assembling steps. Listed ID refers to internal nomenclature.
+
|+ align="top, left"|
|width=40px|  ID||width=300px|Content||width=100px|Registry link||width=450px|Purpose of the cassette  
|width=40px|  ID||width=300px|Content||width=100px|Registry link||width=450px|Purpose of the cassette  
|-
|-
Line 135: Line 217:
</center>
</center>
-
== Final Constructs ==
+
 
 +
==miTuning Kit -  Intermediate Parts 2==
<center>
<center>
{| class="wikitable sortable" border="0" style="text-align: left"
{| class="wikitable sortable" border="0" style="text-align: left"
|-bgcolor=#cccccc
|-bgcolor=#cccccc
-
|+ align="top, left"|'''Table 3''': Our final constructs. Listed ID refers to internal nomenclature.
+
|+ align="top, left"|
|width=40px|  ID||width=600px|Content||width=100px|Registry link||width=100px|Name  
|width=40px|  ID||width=600px|Content||width=100px|Registry link||width=100px|Name  
|-
|-
Line 145: Line 228:
|-
|-
|K2||BGH(rc)/shRNA10(rc)/sv40(rc)/CMV/Luc2_sv40/CMV/Kozag_hRluc_BGH||[http://partsregistry.org/Part:BBa_K337035 BBa_K337035]|| pSMB_miTuner Plasmid HD2  
|K2||BGH(rc)/shRNA10(rc)/sv40(rc)/CMV/Luc2_sv40/CMV/Kozag_hRluc_BGH||[http://partsregistry.org/Part:BBa_K337035 BBa_K337035]|| pSMB_miTuner Plasmid HD2  
-
|-
+
-
|K3||BGH(rc)/shRNA10(rc)/RSV(rc)/CMV/Luc2_sv40/CMV/Kozag_hRluc_BGH||[http://partsregistry.org/Part:BBa_K337036 BBa_K337036]|| pSMB_miTuner Plasmid HD3
+
-
|-
+
-
|K4||BGH(rc)/shRNA10(rc)/RSV(rc)/CMV_TetO2/Luc2_sv40/CMV/Kozag_hRluc_BGH||[http://partsregistry.org/Part:BBa_K337038 BBa_K337038]|| pSMB_miTuner Plasmid HD4
+
|-
|-
|K5||BGH(rc)/shRNA10(rc)/sv40(rc)/RSV/Luc2_sv40/RSV/Kozag_hRluc_BGH||[http://partsregistry.org/Part:BBa_K337040 BBa_K337040]|| pSMB_miTuner Plasmid HD5  
|K5||BGH(rc)/shRNA10(rc)/sv40(rc)/RSV/Luc2_sv40/RSV/Kozag_hRluc_BGH||[http://partsregistry.org/Part:BBa_K337040 BBa_K337040]|| pSMB_miTuner Plasmid HD5  
Line 157: Line 237:
|-
|-
|K8||BGH(rc)/shRNA10(rc)/RSV(rc)/CMV_TetO2/Luc2_sv40/RSV/Kozag_hRluc_BGH||[http://partsregistry.org/Part:BBa_K337046 BBa_K337046]|| pSMB_miTuner Plasmid HD8  
|K8||BGH(rc)/shRNA10(rc)/RSV(rc)/CMV_TetO2/Luc2_sv40/RSV/Kozag_hRluc_BGH||[http://partsregistry.org/Part:BBa_K337046 BBa_K337046]|| pSMB_miTuner Plasmid HD8  
-
|-
 
-
|miM||sv40ter(rc)/eBFP(rc)/biCMV/eGFP(fw)/sv40ter(fw)||[http://partsregistry.org/Part:BBa_K337049 BBa_K337049]|| pSMB_miMeasure
 
|-
|-
|}
|}
</center>
</center>
-
== Binding Site Patterns ==
+
==ViroBytes==
 +
 
 +
These parts are not submitted in the standardized form.
<center>
<center>
{| class="wikitable sortable" border="0" style="text-align: left"
{| class="wikitable sortable" border="0" style="text-align: left"
|-bgcolor=#cccccc
|-bgcolor=#cccccc
-
|+ align="top, left"|'''Table 4''': Binding site patterns generated by miraPCR.
+
|+ align="top, left"|
-
|width=40px|  ID||width=350px|Content||width=100px|Registry link
+
|width=40px|  ID||width=150px|Part name||width=100px|Registry link||width=300px|Description
|-
|-
-
|1.3||hsa-miR-122 Binding site pattern (3BS)||[http://partsregistry.org/Part:BBa_K337000 BBa_K337000]
+
|1||Fragment 1 of wt AAV1||[http://partsregistry.org/Part:BBa_K337058 BBa_K337058]||flanked with Bsa1 sites at both ends
|-
|-
-
|1A||hsa-miR-122 Binding site pattern (4BS)||[http://partsregistry.org/Part:BBa_K337003 BBa_K337003]
+
|2 ||Fragment 2 of wt AAV1||[http://partsregistry.org/Part:BBa_K337059 BBa_K337059]||flanked with Bsa1 sites at both ends
|-
|-
-
|1-5||hsa-miR-122 Binding site pattern (2BS)||[http://partsregistry.org/Part:BBa_K337004 BBa_K337004]
+
|3 ||Fragment 3 of wt AAV1||[http://partsregistry.org/Part:BBa_K337060 BBa_K337060]||flanked with Bsa1 sites at both ends
|-
|-
-
|3.7||hsa-miR-122 Binding site pattern (2BS - additional 10bp Spacer)||[http://partsregistry.org/Part:BBa_K337005 BBa_K337005]
+
|4 ||Fragment 4 of wt AAV1||[http://partsregistry.org/Part:BBa_K337061 BBa_K337061]||flanked with Bsa1 sites at both ends
|-
|-
-
|1.5||hsa-miR-122 Binding site pattern (2BS) with randomized nt9-12||[http://partsregistry.org/Part:BBa_K337006 BBa_K337006]
+
|5 ||Fragment 5 of wt AAV1||[http://partsregistry.org/Part:BBa_K337062 BBa_K337062]||flanked with Bsa1 sites at both ends
|-
|-
-
|1.8||hsa-miR-122 Binding site pattern (2BS) with randomized nt9-12||[http://partsregistry.org/Part:BBa_K337007 BBa_K337007]
+
|6 ||Fragment 6 of wt AAV1||[http://partsregistry.org/Part:BBa_K337063 BBa_K337063]||flanked with Bsa1 sites at both ends
|-
|-
-
|3.1||hsa-miR-122 Binding site pattern (2BS) with randomized nt9-12||[http://partsregistry.org/Part:BBa_K337008 BBa_K337008]
+
|7 ||Fragment 7 of wt AAV1||[http://partsregistry.org/Part:BBa_K337064 BBa_K337064]||flanked with Bsa1 sites at both ends
|-
|-
-
|4.5||hsa-miR-122 Binding site pattern (2BS) with randomized nt9-12||[http://partsregistry.org/Part:BBa_K337009 BBa_K337009]
+
|8 ||Fragment 8 of wt AAV1||[http://partsregistry.org/Part:BBa_K337065 BBa_K337065]||flanked with Bsa1 sites at both ends
|-
|-
-
|4.6||hsa-miR-122 Binding site pattern (2BS) with randomized nt9-12||[http://partsregistry.org/Part:BBa_K337010 BBa_K337010]
+
|9 ||Fragment 1 of wt AAV2||[http://partsregistry.org/Part:BBa_K337066 BBa_K337066]||flanked with Bsa1 sites at both ends
|-
|-
-
|mir221-10L2||hsa-miR-221 Binding site pattern (2BS)||[http://partsregistry.org/Part:BBa_K337010 BBa_K337010]
+
|10 ||Fragment 2 of wt AAV2||[http://partsregistry.org/Part:BBa_K337067 BBa_K337067]||flanked with Bsa1 sites at both ends
|-
|-
 +
|11 ||Fragment 3 of wt AAV2||[http://partsregistry.org/Part:BBa_K337068 BBa_K337068]||flanked with Bsa1 sites at both ends
 +
|-
 +
|12 ||Fragment 4 of wt AAV2||[http://partsregistry.org/Part:BBa_K337069 BBa_K337069]||flanked with Bsa1 sites at both ends
 +
|-
 +
|13 ||Fragment 5 of wt AAV2||[http://partsregistry.org/Part:BBa_K337070 BBa_K337070]||flanked with Bsa1 sites at both ends
 +
|-
 +
|14 ||Fragment 6 of wt AAV2||[http://partsregistry.org/Part:BBa_K337071 BBa_K337071]||flanked with Bsa1 sites at both ends
 +
|-
 +
|15 ||Fragment 7 of wt AAV2||[http://partsregistry.org/Part:BBa_K337072 BBa_K337072]||flanked with Bsa1 sites at both ends
 +
|-
 +
|16 ||Fragment 8 of wt AAV2||[http://partsregistry.org/Part:BBa_K337073 BBa_K337073]||flanked with Bsa1 sites at both ends
 +
|-
 +
|17 ||Fragment 1 of wt AAV5||[http://partsregistry.org/Part:BBa_K337074 BBa_K337074]||flanked with Bsa1 sites at both ends
 +
|-
 +
|18 ||Fragment 2 of wt AAV5||[http://partsregistry.org/Part:BBa_K337075 BBa_K337075]||flanked with Bsa1 sites at both ends
 +
|-
 +
|19 ||Fragment 3 of wt AAV5||[http://partsregistry.org/Part:BBa_K337076 BBa_K337076]||flanked with Bsa1 sites at both ends
 +
|-
 +
|20 ||Fragment 4 of wt AAV5||[http://partsregistry.org/Part:BBa_K337077 BBa_K337077]||flanked with Bsa1 sites at both ends
 +
|-
 +
|21 ||Fragment 5 of wt AAV5||[http://partsregistry.org/Part:BBa_K337078 BBa_K337078]||flanked with Bsa1 sites at both ends
 +
|-
 +
|22 ||Fragment 6 of wt AAV5||[http://partsregistry.org/Part:BBa_K337079 BBa_K337079]||flanked with Bsa1 sites at both ends
 +
|-
 +
|23 ||Fragment 7 of wt AAV5||[http://partsregistry.org/Part:BBa_K337080 BBa_K337080]||flanked with Bsa1 sites at both ends
 +
|-
 +
|24 ||Fragment 8 of wt AAV5||[http://partsregistry.org/Part:BBa_K337081 BBa_K337081]||flanked with Bsa1 sites at both ends
 +
|-
 +
|25 ||Fragment 1 of wt AAV6||[http://partsregistry.org/Part:BBa_K337082 BBa_K337082]||flanked with Bsa1 sites at both ends
 +
|-
 +
|26 ||Fragment 2 of wt AAV6||[http://partsregistry.org/Part:BBa_K337083 BBa_K337083]||flanked with Bsa1 sites at both ends
 +
|-
 +
|27 ||Fragment 3 of wt AAV6||[http://partsregistry.org/Part:BBa_K337084 BBa_K337084]||flanked with Bsa1 sites at both ends
 +
|-
 +
|28 ||Fragment 4 of wt AAV6||[http://partsregistry.org/Part:BBa_K337085 BBa_K337085]||flanked with Bsa1 sites at both ends
 +
|-
 +
|29 ||Fragment 5 of wt AAV6||[http://partsregistry.org/Part:BBa_K337086 BBa_K337086]||flanked with Bsa1 sites at both ends
 +
|-
 +
|30 ||Fragment 6 of wt AAV6||[http://partsregistry.org/Part:BBa_K337087 BBa_K337087]||flanked with Bsa1 sites at both ends
 +
|-
 +
|31 ||Fragment 7 of wt AAV6||[http://partsregistry.org/Part:BBa_K337088 BBa_K337088]||flanked with Bsa1 sites at both ends
 +
|-
 +
|32 ||Fragment 8 of wt AAV6||[http://partsregistry.org/Part:BBa_K337089 BBa_K337089]||flanked with Bsa1 sites at both ends
 +
|-
 +
|33 ||Fragment 1 of wt AAV8||[http://partsregistry.org/Part:BBa_K337090 BBa_K337090]||flanked with Bsa1 sites at both ends
 +
|-
 +
|34 ||Fragment 2 of wt AAV8||[http://partsregistry.org/Part:BBa_K337091 BBa_K337091]||flanked with Bsa1 sites at both ends
 +
|-
 +
|35 ||Fragment 3 of wt AAV8||[http://partsregistry.org/Part:BBa_K337092 BBa_K337092]||flanked with Bsa1 sites at both ends
 +
|-
 +
|36 ||Fragment 4 of wt AAV8||[http://partsregistry.org/Part:BBa_K337093 BBa_K337093]||flanked with Bsa1 sites at both ends
 +
|-
 +
|37 ||Fragment 5 of wt AAV8||[http://partsregistry.org/Part:BBa_K337094 BBa_K337094]||flanked with Bsa1 sites at both ends
 +
|-
 +
|38 ||Fragment 6 of wt AAV8||[http://partsregistry.org/Part:BBa_K337095 BBa_K337095]||flanked with Bsa1 sites at both ends
 +
|-
 +
|39 ||Fragment 7 of wt AAV8||[http://partsregistry.org/Part:BBa_K337096 BBa_K337096]||flanked with Bsa1 sites at both ends
 +
|-
 +
|40 ||Fragment 8 of wt AAV8||[http://partsregistry.org/Part:BBa_K337097 BBa_K337097]||flanked with Bsa1 sites at both ends
 +
|-
 +
|41 ||Fragment 1 of wt AAV9||[http://partsregistry.org/Part:BBa_K337098 BBa_K337098]||flanked with Bsa1 sites at both ends
 +
|-
 +
|42 ||Fragment 2 of wt AAV9||[http://partsregistry.org/Part:BBa_K337099 BBa_K337099]||flanked with Bsa1 sites at both ends
 +
|-
 +
|43 ||Fragment 3 of wt AAV9||[http://partsregistry.org/Part:BBa_K337100 BBa_K337100]||flanked with Bsa1 sites at both ends
 +
|-
 +
|44 ||Fragment 4 of wt AAV9||[http://partsregistry.org/Part:BBa_K337101 BBa_K337101]||flanked with Bsa1 sites at both ends
 +
|-
 +
|45 ||Fragment 5 of wt AAV9||[http://partsregistry.org/Part:BBa_K337102 BBa_K337102]||flanked with Bsa1 sites at both ends
 +
|-
 +
|46 ||Fragment 6 of wt AAV9||[http://partsregistry.org/Part:BBa_K337103 BBa_K337103]||flanked with Bsa1 sites at both ends
 +
|-
 +
|47 ||Fragment 7 of wt AAV9||[http://partsregistry.org/Part:BBa_K337104 BBa_K337104]||flanked with Bsa1 sites at both ends
 +
|-
 +
|48 ||Fragment 8 of wt AAV9||[http://partsregistry.org/Part:BBa_K337105 BBa_K337105]||flanked with Bsa1 sites at both ends
 +
|-
 +
|}
|}
</center>
</center>
<!-- <groupparts>iGEM010 Heidelberg</groupparts> -->
<!-- <groupparts>iGEM010 Heidelberg</groupparts> -->
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<div class="backtop">
 +
<a href="#top">&uarr;</a>
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{{:Team:Heidelberg/Single_Bottom}}
{{:Team:Heidelberg/Single_Bottom}}

Latest revision as of 22:42, 27 October 2010

miBricks - Parts submitted to the registry


The parts we submit belong to the two core aims our project: Reaching regulatory control (1) and specificity (2) of gene expression of any gene of interest in any target cell or tissue of choice. Therefore we engineered parts, that address these two aims on two different regulatory levels.

First, we engineered gene therapy vectors based on synthetic adeno associated viruses (AAVs). On parts level, we provide about 50 plasmids that can be used for creating shuffled AAV libraries or even rationally designed, recombinant AAV vectors. Those parts we refer to as virobytes, are designed in a format directly applicable for the Virobytes Assembly protocol we develop.

On RNA level we provide the miTuner toolkit consisting of roughly 60 parts enabling gene expression control based on synthetic or cell-specific endogenous microRNAs. This toolkit consists of three main constructs: The pSMB_miMeasure binding site characterization standard and two pSMB_miTuner expression controlling plasmids. Furthermore, it contains 12 basic and 28 intermediate construction parts, synthetic, single microRNA binding sites as well as binding site patterns in BB-2 (RFC 12, Tom Knight) standard. This enables maximum flexibility for applications in many different contexts.


Main Measurement Constructs - Engineered

IDContentRegistry linkName
K3BGH(rc)/shRNA10(rc)/RSV(rc)/CMV/Luc2_sv40/CMV/Kozag_hRluc_BGHBBa_K337036 pSMB_miTuner Plasmid HD3
K4BGH(rc)/shRNA10(rc)/RSV(rc)/CMV_TetO2/Luc2_sv40/CMV/Kozag_hRluc_BGHBBa_K337038 pSMB_miTuner Plasmid HD4
miMsv40ter(rc)/eBFP(rc)/biCMV/eGFP(fw)/sv40ter(fw)BBa_K337049 pSMB_miMeasure


Synthetic Single Binding Sites

(Physical DNA not submitted)
DesignContentRegistry linkName
KD:97%perfect binding siteBBa_K337052shRNA miRhaat
KD:69%imperfect binding site: point mut 11BBa_K337053shRNA miRhaat
KD:28%imperfect binding site: bulge 16-18BBa_K337054shRNA miRhaat
KD:96%perfect binding siteBBa_K337055miR122
KD:64%imperfect binding site:BBa_K337056miR122
KD:24%imperfect binding site:BBa_K337057miR122

synthetic microRNA binding Site patterns against endogenous miRNA


IDContentRegistry link
1.3hsa-miR-122 Binding site pattern (3BS)BBa_K337000
1Ahsa-miR-122 Binding site pattern (4BS)BBa_K337003
1-5hsa-miR-122 Binding site pattern (2BS)BBa_K337004
3.7hsa-miR-122 Binding site pattern (2BS - additional 10bp Spacer)BBa_K337005
1.5hsa-miR-122 Binding site pattern (2BS) with randomized nt9-12BBa_K337006
1.8hsa-miR-122 Binding site pattern (2BS) with randomized nt9-12BBa_K337007
3.1hsa-miR-122 Binding site pattern (2BS) with randomized nt9-12BBa_K337008
4.5hsa-miR-122 Binding site pattern (2BS) with randomized nt9-12BBa_K337009
4.6hsa-miR-122 Binding site pattern (2BS) with randomized nt9-12BBa_K337010
mir221-10L2hsa-miR-221 Binding site pattern (2BS)BBa_K337011

miTunig Kit - Basic Parts

IDContentRegistry linkComment
F1RSV fwBBa_K337012-
F2SV40 rcBBa_K337013-
F3RSV rcBBa_K337014-
F4BGH fwBBa_K337001-
F5BGH rcBBa_K337002 leads to insertion of BamHI site
F7microRNA 10HDBBa_K337016 template for creation of shRNA-like miRNA
F8CMV fwBBa_K337018-
F9FRT siteBBa_K337019-
F10hRlucBBa_K337025-
F16TetRBBa_K337028-
F17Luc2BBa_K337030 compatible for insertion of microRNA binding sites
biCMVbiCMVBBa_K337017-

miTuning Kit - Intermediate Parts 1

IDContentRegistry linkPurpose of the cassette
F6luc2_sv40terBBa_K337015 Luc2 reporter gene with terminator referring to SV40 promoter
F15CMV_TetO2BBa_K337027 CMV promoter under control of Tet Operator for regulation of gene expression
R1Sv40(rc)/RSV(fw)BBa_K337045 bidirectional hybrid promoter
R2Sv40(rc)/CMV(fw)BBa_K337047
R3RSV(rc)/CMV(fw)BBa_K337048
R4RSV(rc)/CMV_TetO2(fw)BBa_K337050
R5BGH(rc)/shRNA10(rc)BBa_K337051 synthetic microRNA template part
R13BGH(rc)/shRNA10(rc)/sv40(rc)/RSV(fw)BBa_K337020tuning construct cloning into reporter plasmid backbone containing a binding site against synthetic shRNA-like miRNA
R14BGH(rc)/shRNA10(rc)/sv40(rc)/CMV(fw)BBa_K337021
R15BGH(rc)/shRNA10(rc)/RSV(rc)/CMV(fw)BBa_K337022
R16BGH(rc)/shRNA10(rc)/RSV(rc)/CMV(fw)_TetO2(fw)BBa_K337023
R17BGH(rc)/shRNA6(rc)/sv40(rc)/RSV(fw)BBa_K337024
R18BGH(rc)/shRNA6(rc)/sv40(rc)/CMV(fw)BBa_K337026
R19BGH(rc)/shRNA6(rc)/RSV(rc)/CMV(fw)BBa_K337029
R20BGH(rc)/shRNA6(rc)/RSV(rc)/CMV_TetO2(fw)BBa_K337031tuning construct core containing Tet Operator for On-Targeting together with repressor construct
R21Luc2(rc)_sv40(rc)/CMV(fw)BBa_K337033 bidirectional hybrid promoter with Luc2 reference gene under control of SV40 promoter
R22Luc2(rc)_sv40(rc)/RSV(fw)BBa_K337034
R32Kozag_hRluc/BGH(fw)BBa_K337037reference reporter
R33TetR_mut(XhoI/XbaI)BBa_K337039mutagenized TetR including cutting sites to paste miRNA binding sites
T1BGH(rc)_CMV/TetR/BGH(fw)/BGH(rc)BBa_K337041repressor construct for On-Targeting together with tuning construct
T2BGH(rc)_RSV/TetR/BGH(fw)/BGH(rc)BBa_K337043


miTuning Kit - Intermediate Parts 2

IDContentRegistry linkName
K1BGH(rc)/shRNA10(rc)/sv40(rc)/RSV/Luc2_sv40/CMV/Kozag_hRluc_BGHBBa_K337032 pSMB_miTuner Plasmid HD1
K2BGH(rc)/shRNA10(rc)/sv40(rc)/CMV/Luc2_sv40/CMV/Kozag_hRluc_BGHBBa_K337035 pSMB_miTuner Plasmid HD2
K5BGH(rc)/shRNA10(rc)/sv40(rc)/RSV/Luc2_sv40/RSV/Kozag_hRluc_BGHBBa_K337040 pSMB_miTuner Plasmid HD5
K6BGH(rc)/shRNA10(rc)/sv40(rc)/CMV/RSV/Luc2_sv40/RSV/Kozag_hRluc_BGHBBa_K337042 pSMB_miTuner Plasmid HD6
K7BGH(rc)/shRNA10(rc)/RSV(rc)/CMV/Luc2_sv40/RSV/Kozag_hRluc_BGHBBa_K337044 pSMB_miTuner Plasmid HD7
K8BGH(rc)/shRNA10(rc)/RSV(rc)/CMV_TetO2/Luc2_sv40/RSV/Kozag_hRluc_BGHBBa_K337046 pSMB_miTuner Plasmid HD8

ViroBytes

These parts are not submitted in the standardized form.

IDPart nameRegistry linkDescription
1Fragment 1 of wt AAV1BBa_K337058flanked with Bsa1 sites at both ends
2 Fragment 2 of wt AAV1BBa_K337059flanked with Bsa1 sites at both ends
3 Fragment 3 of wt AAV1BBa_K337060flanked with Bsa1 sites at both ends
4 Fragment 4 of wt AAV1BBa_K337061flanked with Bsa1 sites at both ends
5 Fragment 5 of wt AAV1BBa_K337062flanked with Bsa1 sites at both ends
6 Fragment 6 of wt AAV1BBa_K337063flanked with Bsa1 sites at both ends
7 Fragment 7 of wt AAV1BBa_K337064flanked with Bsa1 sites at both ends
8 Fragment 8 of wt AAV1BBa_K337065flanked with Bsa1 sites at both ends
9 Fragment 1 of wt AAV2BBa_K337066flanked with Bsa1 sites at both ends
10 Fragment 2 of wt AAV2BBa_K337067flanked with Bsa1 sites at both ends
11 Fragment 3 of wt AAV2BBa_K337068flanked with Bsa1 sites at both ends
12 Fragment 4 of wt AAV2BBa_K337069flanked with Bsa1 sites at both ends
13 Fragment 5 of wt AAV2BBa_K337070flanked with Bsa1 sites at both ends
14 Fragment 6 of wt AAV2BBa_K337071flanked with Bsa1 sites at both ends
15 Fragment 7 of wt AAV2BBa_K337072flanked with Bsa1 sites at both ends
16 Fragment 8 of wt AAV2BBa_K337073flanked with Bsa1 sites at both ends
17 Fragment 1 of wt AAV5BBa_K337074flanked with Bsa1 sites at both ends
18 Fragment 2 of wt AAV5BBa_K337075flanked with Bsa1 sites at both ends
19 Fragment 3 of wt AAV5BBa_K337076flanked with Bsa1 sites at both ends
20 Fragment 4 of wt AAV5BBa_K337077flanked with Bsa1 sites at both ends
21 Fragment 5 of wt AAV5BBa_K337078flanked with Bsa1 sites at both ends
22 Fragment 6 of wt AAV5BBa_K337079flanked with Bsa1 sites at both ends
23 Fragment 7 of wt AAV5BBa_K337080flanked with Bsa1 sites at both ends
24 Fragment 8 of wt AAV5BBa_K337081flanked with Bsa1 sites at both ends
25 Fragment 1 of wt AAV6BBa_K337082flanked with Bsa1 sites at both ends
26 Fragment 2 of wt AAV6BBa_K337083flanked with Bsa1 sites at both ends
27 Fragment 3 of wt AAV6BBa_K337084flanked with Bsa1 sites at both ends
28 Fragment 4 of wt AAV6BBa_K337085flanked with Bsa1 sites at both ends
29 Fragment 5 of wt AAV6BBa_K337086flanked with Bsa1 sites at both ends
30 Fragment 6 of wt AAV6BBa_K337087flanked with Bsa1 sites at both ends
31 Fragment 7 of wt AAV6BBa_K337088flanked with Bsa1 sites at both ends
32 Fragment 8 of wt AAV6BBa_K337089flanked with Bsa1 sites at both ends
33 Fragment 1 of wt AAV8BBa_K337090flanked with Bsa1 sites at both ends
34 Fragment 2 of wt AAV8BBa_K337091flanked with Bsa1 sites at both ends
35 Fragment 3 of wt AAV8BBa_K337092flanked with Bsa1 sites at both ends
36 Fragment 4 of wt AAV8BBa_K337093flanked with Bsa1 sites at both ends
37 Fragment 5 of wt AAV8BBa_K337094flanked with Bsa1 sites at both ends
38 Fragment 6 of wt AAV8BBa_K337095flanked with Bsa1 sites at both ends
39 Fragment 7 of wt AAV8BBa_K337096flanked with Bsa1 sites at both ends
40 Fragment 8 of wt AAV8BBa_K337097flanked with Bsa1 sites at both ends
41 Fragment 1 of wt AAV9BBa_K337098flanked with Bsa1 sites at both ends
42 Fragment 2 of wt AAV9BBa_K337099flanked with Bsa1 sites at both ends
43 Fragment 3 of wt AAV9BBa_K337100flanked with Bsa1 sites at both ends
44 Fragment 4 of wt AAV9BBa_K337101flanked with Bsa1 sites at both ends
45 Fragment 5 of wt AAV9BBa_K337102flanked with Bsa1 sites at both ends
46 Fragment 6 of wt AAV9BBa_K337103flanked with Bsa1 sites at both ends
47 Fragment 7 of wt AAV9BBa_K337104flanked with Bsa1 sites at both ends
48 Fragment 8 of wt AAV9BBa_K337105flanked with Bsa1 sites at both ends