Difference between revisions of "Part:BBa K779120"
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Binds to [[Part:BBa_K779116]] to form a RNA reporter complex (rRep6). Has an unquenched Alexa 488 fluorophore. | Binds to [[Part:BBa_K779116]] to form a RNA reporter complex (rRep6). Has an unquenched Alexa 488 fluorophore. | ||
| − | '''Modifications:''' 5' Iowa Black RQ quencher, 3' Alexa 488 fluorophore, all bases modified with 2'O Methyl (ordered as a DNA oligo with Us instead of Ts | + | '''Modifications:''' 5' Iowa Black RQ quencher, 3' Alexa 488 fluorophore, all bases modified with 2'O Methyl (standard modification for increased stability of RNA); ordered as a DNA oligo with Us instead of Ts. |
'''IDT DNA Oligo Order:''' 5IAbRQ/mCmAmUmAmAmCmAmCmAmAmUmCmAmCmA/3AlexF488N/ | '''IDT DNA Oligo Order:''' 5IAbRQ/mCmAmUmAmAmCmAmCmAmAmUmCmAmCmA/3AlexF488N/ | ||
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===Usage=== | ===Usage=== | ||
<p> | <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. | + | 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 (Alexa is outside the quenching range of RQ, as by [http://idt.com IDT]). |
</p> | </p> | ||
<p> | <p> | ||
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<p> | <p> | ||
[[Image:MIT2012_Alexa_Emission_Excitation_small.png]]<br/> | [[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). | + | <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> | ||
<p> | <p> | ||
Latest revision as of 19:08, 7 October 2012
Status: 500 Content-type: text/html
Software error:
Not enough arguments for Range::range at /websites/parts.igem.org/cgi/lib/Range.pm line 250, near "range;" Unmatched right curly bracket at /websites/parts.igem.org/cgi/lib/Range.pm line 251, at end of line syntax error at /websites/parts.igem.org/cgi/lib/Range.pm line 251, near "}" Can't use global @_ in "my" at /websites/parts.igem.org/cgi/lib/Range.pm line 261, near "= @_" syntax error at /websites/parts.igem.org/cgi/lib/Range.pm line 282, near "}" Can't use global @_ in "my" at /websites/parts.igem.org/cgi/lib/Range.pm line 286, near "= @_" Global symbol "$course" requires explicit package name at /websites/parts.igem.org/cgi/lib/Range.pm line 288. syntax error at /websites/parts.igem.org/cgi/lib/Range.pm line 314, near "}" Compilation failed in require at /websites/parts.igem.org/cgi/lib/Part.pm line 16. BEGIN failed--compilation aborted at /websites/parts.igem.org/cgi/lib/Part.pm line 16. Compilation failed in require at /websites/parts.igem.org/cgi/partsdb/putout.cgi line 8. BEGIN failed--compilation aborted at /websites/parts.igem.org/cgi/partsdb/putout.cgi line 8.
For help, please send mail to this site's webmaster, giving this error message and the time and date of the error.
Binds to Part:BBa_K779116 to form a RNA reporter complex (rRep6). Has an unquenched Alexa 488 fluorophore.
Modifications: 5' Iowa Black RQ quencher, 3' Alexa 488 fluorophore, all bases modified with 2'O Methyl (standard modification for increased stability of RNA); ordered as a DNA oligo with Us instead of Ts.
IDT DNA Oligo Order: 5IAbRQ/mCmAmUmAmAmCmAmCmAmAmUmCmAmCmA/3AlexF488N/
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 (Alexa is outside the quenching range of RQ, as by [http://idt.com IDT]).
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].
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).
Dilutions of BBa_K779120 as a free strand or in complex with Part:BBa_K779116. Measurements carried out on a Tecan Safire II plate reader (see [http://2012.igem.org/Team:MIT/MaterialsAndMethods#iv2bio protocol]).
In vitro strand displacement reaction using the Part:BBa_K779116:BBa_K779120 complex with input strands Part:BBa_K779118, Part: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
Status: 500 Content-type: text/html
Software error:
Not enough arguments for Range::range at /websites/parts.igem.org/cgi/lib/Range.pm line 250, near "range;" Unmatched right curly bracket at /websites/parts.igem.org/cgi/lib/Range.pm line 251, at end of line syntax error at /websites/parts.igem.org/cgi/lib/Range.pm line 251, near "}" Can't use global @_ in "my" at /websites/parts.igem.org/cgi/lib/Range.pm line 261, near "= @_" syntax error at /websites/parts.igem.org/cgi/lib/Range.pm line 282, near "}" Can't use global @_ in "my" at /websites/parts.igem.org/cgi/lib/Range.pm line 286, near "= @_" Global symbol "$course" requires explicit package name at /websites/parts.igem.org/cgi/lib/Range.pm line 288. syntax error at /websites/parts.igem.org/cgi/lib/Range.pm line 314, near "}" Compilation failed in require at /websites/parts.igem.org/cgi/lib/Part.pm line 16. BEGIN failed--compilation aborted at /websites/parts.igem.org/cgi/lib/Part.pm line 16. Compilation failed in require at /websites/parts.igem.org/cgi/partsdb/putout.cgi line 8. BEGIN failed--compilation aborted at /websites/parts.igem.org/cgi/partsdb/putout.cgi line 8.
For help, please send mail to this site's webmaster, giving this error message and the time and date of the error.