Expanding Clollin's nano machine idea (wild thinking)

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Just thinking about it Clollin's comments in the nano machine puzzle (just a bit in a slightly crazy manner)

I think probably the easiest? change to a molecule from an 'rna probe' is appending a single base at the end of a molecule.

so build your stable nano machine with a chain of 79 bases
and then re enter the same sequence on a design of 80 bases - and decide what the final extra base is going to be

and see if the shape can change significantly from appending the single base.

shape/no shape (a line) is probably the biggest change.

Anyway something to mess about with
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Edward Lane

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Posted 8 years ago

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clollin

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Glad I got you thinking about this concept!

If I understand your proposal correctly...you are suggesting to make the exact design with one less base - and stable! Then add the one base at the end and have the sequential shift of every base down to the one that creates the fold to also now be stable in the folded format. ???

the only way I can see that happening is if the loop that allows the movement was very close to the beginning so that not too many bases had to be shifted.

What do you think?

have you tried designing anything?
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Edward Lane

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Well I was thinking of something simpler to start with

imagine a sequence

GGGAAACCC that would clearly end up as a hairpin

can you create a sequence

GGGAAACCCX that is stable in a significantly different shape

at the moment that looks like it would be a hairpin - with a spare base on the end, unless the spare base was a C

but I was looking for a 'shape change' from maybe a line

so perhaps

GAAAAAAAAA might be the simplest example - it's a line unless you add a C

I guess that GAAAAAAAAAC takes up a lot more room than CGAAAAAAAAA

so adding C to the end of the chain ought to increase the volume of the GAAAAAAA by a bigger amount than just adding C would normally indicate

perhaps that has a mechanical - push effect, also it might change the density as a result. So that would seem to be a possible RNA 'machine'

but then I don't know quite where that would go - is it possible to extend that out to a much more complex shape?

Edward :)
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Edward Lane

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Had a further thought that perhaps this shape change (and thus density and volume change) affects internal cell pressures when RNA are synthesised in vitro ?
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clollin

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Not sure I follow you on the change in density and volume. Can you try to make the example as a puzzle?
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Edward Lane

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Well I imagine a line of just GGGGGGGGGGGGGGGG as a bit like a strand of raw spaghetti.

But stick a few CCC in the right place and it forms a loop, and go more complex and you have a big knotted molecule (that I think of as tagliatelli).

If I have 500 grams in neat strands of spaghetti they fit nicely together in the packet, compare that to the balls of tagliatelli that you get in the super market the same amount (weight) of pasta takes up a lot more space.

So if you were to think of a cell as a packet - with lots of spaghetti in it - and then you added a few bits to the end of those strings, and the spaghetti all coiled up into 'tagliatelli target shapes' , then (and I'm aware the scale is a bit off, but) if the same weight of what was spaghetti is all changed into tagliatelli, suddenly the packet (cell membrane) gets a bit too tight.

So perhaps (and this is me making a whole host of random guesses) the cell internal pressure increases slightly ?? If the cell pressure increases I'd guess the membrane either leaks a bit faster - or it just fills the 'bag' out a bit more, in which case the same weight of stuff is filling a larger volume, so the density of the RNA might even affect the density of the cell itself.

anyway busy day at work today - so I'll leave it at that for now :)