Power tool analogue in MolBio.

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Yuriy

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Oct 31, 2015, 3:13:18 PM10/31/15
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Hello everyone.


I’ll try to be as brief as possible, given the lack of knowledge on the subject. I don’t know where to start. That’s why I came here with the question.


I was looking at my drill and it dawned on me that there isn’t anything like it, to my knowledge, in molecular biology. It is a tool that alone has no use but given the proper fittings and combination of tool:fittings (adapters), can get the job done. The drill bit end for example, has six sides that accommodate the adjustable chuck. That’s what I was looking into for the last few days.


Is there a good, on both transcribed, antibody to antigen fitting to adapt fitting to a molecular tool?


If yes do they have to be on termini? Or can it jet out of aa design via linkers?


I essentially need the tool that will be stable in vivo, while the adapters can undergo a higher turnover under different environmental ques.


Just looking for a good non-bulky-lock and key to be encoded for the tool set.


-Yuriy

Matt Lawes

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Oct 31, 2015, 3:18:56 PM10/31/15
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Biotin / streptavidin come to mind .... Just at first pass. ....
>matt

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Yuriy

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Oct 31, 2015, 3:55:12 PM10/31/15
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Biotin is not transcribed, is it?

Matt Lawes

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Oct 31, 2015, 4:55:05 PM10/31/15
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No but biotinylation of a protein is easy peasy

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Koeng

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Oct 31, 2015, 5:58:49 PM10/31/15
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What exactly do you want it to do? There are leucine zippers or TALENS or CRISPR, inteins and GS linkers, his tags or FLAG tags, biotin and streptavidin, introns or ribozymes... Each has a specific purpose. And for the termini, yes most likely, unless you want to go through some protein engineering and structure analysis to see if it would fold correctly.

Maybe this will be a lead for the inteins, if you just want a specific protein to fuse to something modularly - http://2014.igem.org/Team:Heidelberg/Parts .

-Koeng

Mega [Andreas Stuermer]

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Oct 31, 2015, 6:58:32 PM10/31/15
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Like what Koeng said. Leucin zippers seem what you're looking for?
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Yuriy

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Nov 5, 2015, 2:47:12 AM11/5/15
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"Biotinylation of a protein is easy peasy" In Vivo?

Just as in any of these I am hesitant about is if the fit is too good and the turnover too slow. From skim readings I understood that there might be some off target activity in both bacterial and mammalian systems by the Biotinylation enzyme.

Looks like I missed a couple of deleted messages, shame. Maybe we've got like minded ideas :)

After doing some further digging I found something called nano-bodies, turns out camels and lamas produce them. I figure with alpaca farms popping up this might be the way to go. They are 15 kDa still bulky but not as bulky as the set of tools I'd like to test them against.

FLAG-tag (1.5 kDa) + M2 (150 kDa?): I just read it. I like this one. I might just try it out. Thank you for bringing that to my attention, Koeng.

Also there seems to be at least two aa antibody target guessing software, given an input. They are called Bishop (download) and AbDesigner (online via NIH website). I am not completely sure how the second one works but I know that the post translational modification and 3D structures are not taken into consideration. Although mods are predicted in output page.

As for the rest, I am still digging through literature on all of that.

The purpose is to make your lives easier. Other than that don't mind the purpose for now. I'll let you know later.

-Yuriy

Mega [Andreas Stuermer]

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Nov 5, 2015, 4:47:47 PM11/5/15
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The deleted messages were mine. My browser froze and sent it off three times. 
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