Difference between revisions of "Part:BBa K779120"
Line 3: Line 3:
  
  
−
Binds to [[Part:BBa_K779116]] to form a RNA reporter complex (rRep6). Has an unquenched Alexa fluorophore.
+
Binds to [[Part:BBa_K779116]] to form a RNA reporter complex (rRep6). Has an unquenched Alexa 488 fluorophore.
  
−
<!-- Add more about the biology of this part here
 
−
===Usage and Biology===
 
  
 +
===Usage===
 +
<p>
 +
This part works in concert with a complementary strand ([[Part:BBa_K779116]]). When the parts are annealed, RQ will quench ROX on the opposite strand, while Alexa continues to fluoresce at all times.
 +
</p>
 +
<p>
 +
[[Part:BBa_K779118]] can act as an input to the formed reporter, whereas [[Part:BBa_K779119]] is used as a negative control input. The mechanism by which the input strands react with the reporter, toehold-mediated strand displacement, is described in more detail on the [http://2012.igem.org/Team:MIT MIT iGEM 2012 Wiki page].
 +
</p>
 +
<p>
 +
[[Image:MIT2012_Alexa_Emission_Excitation_small.png]]<br/>
 +
<em>Excitation / emission spectrum for the Alexa 488 fluorophore in BBa_K779120</em>. Obtained by the MIT iGEM 2012 team using a Tecan Safire II plate reader (see [http://2012.igem.org/Team:MIT/MaterialsAndMethods#iv2bio instrument settings], note that excitation and emission scans were performed instead of fixed wavelength measurements).
 +
</p>
 +
<p>
 +
[[Image:MIT2012_Alexa_dilutions_medium.png]]<br/>
 +
<em>Dilutions of BBa_K779120 as a free strand or in complex with BBa_K779116</em>. Measurements carried out on a Tecan Safire II plate reader (see [http://2012.igem.org/Team:MIT/MaterialsAndMethods#iv2bio protocol]).
 +
</p>
 +
<p>
 +
[[Image:MIT2012_In_vitro_SD_with_Alexa_medium.png]]<br/>
 +
In vitro <em>strand displacement reaction using the BBa_K779116:BBa_K779120 complex with input strands BBa_K779118, BBa_K779119 as described above</em>. The results indicate that the Alexa 488 fluorophore does not prevent strand displacement from happening, although it could theoretically inhibit toehold binding and branch migration initiation. Measurements carried out on a Tecan Safire II plate reader (see [http://2012.igem.org/Team:MIT/MaterialsAndMethods#iv2bio protocol]).
 +
</p>
 +
<br/>
 
<!-- -->
 
<!-- -->
−
<span class='h3bb'>Sequence and Features</span>
+
==Sequence and Features==
 
<partinfo>BBa_K779120 SequenceAndFeatures</partinfo>
 
<partinfo>BBa_K779120 SequenceAndFeatures</partinfo>
  
  
−
<!-- Uncomment this to enable Functional Parameter display  
+
<!-- Uncomment this to enable Functional Parameter display -->
 +
<!--
 
===Functional Parameters===
 
===Functional Parameters===
 
<partinfo>BBa_K779120 parameters</partinfo>
 
<partinfo>BBa_K779120 parameters</partinfo>
 +
-->
 
<!-- -->
 
<!-- -->

Revision as of 04:22, 2 October 2012

RNA Reporter top strand with quencher (RQ) and tag fluorophore (Alexa 488) MammoBlock


Binds to Part:BBa_K779116 to form a RNA reporter complex (rRep6). Has an unquenched Alexa 488 fluorophore.


Usage

This part works in concert with a complementary strand (Part:BBa_K779116). When the parts are annealed, RQ will quench ROX on the opposite strand, while Alexa continues to fluoresce at all times.

Part:BBa_K779118 can act as an input to the formed reporter, whereas Part:BBa_K779119 is used as a negative control input. The mechanism by which the input strands react with the reporter, toehold-mediated strand displacement, is described in more detail on the [http://2012.igem.org/Team:MIT MIT iGEM 2012 Wiki page].

MIT2012 Alexa Emission Excitation small.png
Excitation / emission spectrum for the Alexa 488 fluorophore in BBa_K779120. Obtained by the MIT iGEM 2012 team using a Tecan Safire II plate reader (see [http://2012.igem.org/Team:MIT/MaterialsAndMethods#iv2bio instrument settings], note that excitation and emission scans were performed instead of fixed wavelength measurements).

MIT2012 Alexa dilutions medium.png
Dilutions of BBa_K779120 as a free strand or in complex with BBa_K779116. Measurements carried out on a Tecan Safire II plate reader (see [http://2012.igem.org/Team:MIT/MaterialsAndMethods#iv2bio protocol]).

MIT2012 In vitro SD with Alexa medium.png
In vitro strand displacement reaction using the BBa_K779116:BBa_K779120 complex with input strands BBa_K779118, BBa_K779119 as described above. The results indicate that the Alexa 488 fluorophore does not prevent strand displacement from happening, although it could theoretically inhibit toehold binding and branch migration initiation. Measurements carried out on a Tecan Safire II plate reader (see [http://2012.igem.org/Team:MIT/MaterialsAndMethods#iv2bio protocol]).


Sequence and Features


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]