<Noxz>
came across nano pores to sequence dna in my random internet searching today
<pie_>
i figured something like ...lets say our primitive is square tiles (which will behave like puzzle pieces, as explained in the following)
<pie_>
by some method we implant a specific seed tile
<pie_>
each tile has 4 sides, and each side is different, so only a matching component can bind
<pie_>
so by evacuating the chamber and swapping the ambient gas and doing your process/whatever
<pie_>
you could do some cindof combinatory thing to build out the stuff
<pie_>
like a puzzle in the classical sense
<pie_>
of course in this formulation thats impractical due to a lot of things, and depends on being able to create the appropriate molecules
<pie_>
so maybe you can only use premade tiles instead of actual atomic/micromolecular construction
<pie_>
(i mean if you need to make big tiles)
<pie_>
which raises the question of how to make the tiles to begin with
<pie_>
and then theres also the question of how to clean the surface when cycling the gas etc....
<pie_>
but thos eare "engineering problems" ;P
<pie_>
i guess question is whether you can do this combinatory constructive approach at all
<pie_>
for starters
<Noxz>
well, are we building a puzzlor, say, dna ?
<Noxz>
having 'just' AGCT to work with, 4 diff kinds that is, may simply things a bit
<Noxz>
oh, and linear
<pie_>
i didnt say how many you need because idk what the geometry would impose but for the sake of argument i guess we could just say two things
<Noxz>
so, A and B, if linear you would have to be able to map when you want AA, AB, BB and BA connections, yeah?
<Noxz>
also, you only want one AA if there is a B next and not do AAAAAAAAAAAAAAAAA..
<Noxz>
or something
<pie_>
so you seed A
<pie_>
then set ambience to A, B, A, B, A, A ,A in that sequence
<pie_>
you get AABABAAA on your substrate
<Noxz>
sure, but how do you limit?
<pie_>
well ok technically youd have to do some kind of inactivation or something
<pie_>
so add an implicit C
<Noxz>
that's actually a good idea there
<pie_>
AC,BC,AC,BC,AC,AC
<pie_>
im stealing from how CVD works iirc
<Noxz>
and after you connect, you then cleave all Cs
<pie_>
yeah
<Noxz>
sure
<pie_>
at this point i think this may be no different mostly than cvd/ald
<pie_>
the interesting part would be controlling tiling by the sequence
<Noxz>
well, what about biologically?
<pie_>
yeah but thats cheating
<Noxz>
I've been looking at genes making proteine in my freetime lately ;)
<Noxz>
hahaa
<pie_>
well i guess its not quite cheating actually
<Noxz>
they actually made/use a certain proteine for the nanopore stuff here and there
<Noxz>
to drive the dna through, and th epore itself
<pie_>
ok so what i want to say is this was one of my sitting-on-the-crapper-for-an-hour ideas for possible methods to do extremely precise stuff with extremely crude tools
<Noxz>
the john is usually where I workout the process flow for a reaction
<pie_>
lol
<pie_>
only extremely tangentially related, are you familiar with penrose tilings?
<pie_>
the short story is you can make a nonrepeating tiling from two tiles with special edge interfaces
<pie_>
Noxz, at a quick glance, seems neat!
<pie_>
thing is, once you start growing up from babbys first spherical cow representations (which is rather hard reach apparently...i mean doing th ework itself is hard, but just getting exposed to the ideas at all..) the non-idealites are terrifying :O
<pie_>
like how flat is not actually flat.
<Noxz>
graphene is starting to be use for nanopores, which is interesting because I am highly interested in graphene, mainly for the electric fields
<pie_>
funny thing btw
<pie_>
if i can find it...
<pie_>
http://paperscape.org/ condensed matter is the brown at the bottom (pff phrasing)
<pie_>
half the most cited papers are graphene graphene graphene lol
<pie_>
thats for all of condensed matter on arxiv
<pie_>
is graphene ever gonna do anything interesting macro-scale
<pie_>
?
<pie_>
or nanotubes
<SpeedEvil>
That rather depends on production.
<SpeedEvil>
It could be tomorrow someone works out how to make long aligned nanotubes at $100/kg, at which time everything gets real interesting
<pie_>
bioengineer somebacteria to do it lol
<pie_>
(whatCouldPossiblyGoWrong.jpg)
<pie_>
also gonna be a tangled mess
<SpeedEvil>
Because suddenly cables with ~10* the best tensile strength become available for example
<pie_>
or righ tyou said /aligned/
<pie_>
thats gonna be great for bondage eh
<nmz787>
Noxz: I am not an expert in nanopores, but I have been researching DNA read/write for ~10 years... so I can try to answer any questions
<Noxz>
I mean, it was more so stumbling across it from the minION
<Noxz>
I was interested in general bio stuff, and why the gene I am looking at online didnt have UTR stuff
<Noxz>
and apparently it came down to missing information
<Noxz>
plus lack of information published
<Noxz>
really annoying to get to that conclusion
<Noxz>
like, how are people supposed to replicate if the full genome isnt available
<Noxz>
have to have it sequenced yourself?
<Noxz>
so then I came across biohackers sequencing using the minION
<Noxz>
then I looked at what a nanopore was
<Noxz>
and here I am watching this vid
<Noxz>
:)
<Noxz>
friday night
<nmz787>
I probably know that guy with the minION
<nmz787>
Sebastian
<nmz787>
minION isn't really the best method of sequencing
<nmz787>
they use a neural net to process the data
<nmz787>
because the nanopore is taller than a single DNA base
<nmz787>
so the transconductance current depends on many bases blocking current flow during a read event
<nmz787>
thus you gotta use a lot of context to try and determine what the next base should be
<Noxz>
yes, Sebastian
<nmz787>
so they have for example, some known sequence that they ligate to the DNA-of-interest, so that's a known sequence to start baselining reads from
<nmz787>
and they can sort of "diff" the signal after their sequence ends, iteratively
<nmz787>
sanger sequencing is different in that it amplifies the DNA and then separates it in to bands electrophoretically, but the signal is large enough to be detected optically because of the earlier amplification process
laintoo has quit [Ping timeout: 268 seconds]
<Noxz>
but it cant do large bp
<Noxz>
it is very accurate, gold standard, but takes a long time
<Noxz>
and rather expensive
<Noxz>
but yeah, the opticall method is neat, but I looked into it earlier
<Noxz>
today is only so lng, and that is nearly all I learned today ;)
<nmz787>
solid-state nanopores are why I'm interested in getting Atomic Layer Deposition equipment
<Noxz>
oh?
<Noxz>
good topic to bring up then
<nmz787>
if you can make an atomically-thick electrode layer, you can use tunnelling current /through/ the DNA base, and voila you have single-base resolution
<nmz787>
(i saw graphene mentioned earlier)
<Noxz>
the only pore like thing I was looking at before was more so a micropore formed from aluminum and phosphoric acid, making more or less filter discs
<Noxz>
and could control the size of the pore with varius conditions
<Noxz>
was looking at that the 'filter' off graphene into a sheet