[HN Gopher] DNA turbine powered by a transmembrane potential acr...
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DNA turbine powered by a transmembrane potential across a nanopore
Author : bookofjoe
Score : 61 points
Date : 2023-10-30 16:49 UTC (6 hours ago)
(HTM) web link (www.nature.com)
(TXT) w3m dump (www.nature.com)
| matheusmoreira wrote:
| A man-made ATP synthase?! Very cool!
| jcims wrote:
| First thing that came to mind.
|
| One of many mindblowing molecular genetic animation by Drew
| Barry - https://www.youtube.com/watch?v=OT5AXGS1aL8
|
| Zoomed out electron transport chain -
| https://www.youtube.com/watch?v=nmoLoiFakxY
| Zee2 wrote:
| For some reason, what actually stands out to me in this paper is
| the method in which they verified the rotational motion. They
| used single-molecule fluorescence and optically tracked the
| circular trajectories that the single molecule traced out while
| spinning. That's the most impressive part, in my opinion... I
| didn't know we could even resolve fluorescing particles on that
| scale, much less track their trajectories over time.
| foota wrote:
| See the section titled "Fluorescence microscopy data analysis".
| Basically, when you have a single molecule fluorescing you
| "just" need to do some math to figure out the center of the
| samples over time. See
| https://www.microscope.healthcare.nikon.com/products/super-r...
| for an overview
| panabee wrote:
| thanks for sharing.
|
| since you sound like an expert, do you know if this technique
| would work for imaging small RNA molecules (< 200
| nucleotides)?
|
| or would tagging such a small molecule potentially alter
| biological processes and contaminate results?
| w10-1 wrote:
| FISH works for both DNA and RNA. When articles have pretty
| colors lighting up the inside of a cell, it's likely FISH.
|
| First google hit is a 2020 summary of RNA-FISH, "Technical
| review and guide to RNA fluorescence in situ
| hybridization":
| https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7085896/
| panabee wrote:
| thanks for the link. i saw this already; it's very
| useful.
|
| to clarify, the question was meant for live imaging and
| the risk of altering biological processes for target RNA
| molecules < 200 nucleotides.
| foota wrote:
| I am not exactly an expert, I just happened to do a deep
| dive into microscopy techniques a couple years ago :-)
|
| The general term for these types of techniques (e.g., ones
| that let you image things below the "diffraction limit",
| which is roughly half the wavelength of light being used to
| image, see [1]), is super resolution microscopy[2]. There
| are a few other types you might find interesting.
|
| 1: https://en.wikipedia.org/wiki/Diffraction-limited_system
| 2: https://en.wikipedia.org/wiki/Super-
| resolution_microscopy
| dr_coffee wrote:
| https://www.nature.com/articles/s41586-019-1397-7
|
| this paper came out a few years ago using super resolution
| fluorescence and dna origami to track unwinding of dna by
| single helicase enzymes! its not an easy technique but it is
| doable with the right equipment (the 2014 Nobel Prize in
| chemistry was for super resolution microscopy)
| suzzer99 wrote:
| Here's something I've been wondering that maybe some smart
| hackernews-ian can explain to me. I watched a spider build a web
| last night. A ton of extremely complicated engineering went into
| it, all driven by pure instinct, presumably coded in DNA
| somewhere.
|
| If you gave me enough time I could lay out how a semi-conducting
| material turns into a T-gate transistor, which can be chained
| with other transistors to create AND, OR, NOT and NOR gates,
| which are executed in the CPU by machine language code, which is
| created by compiling down from higher-level C code, which is
| executed by Javascript code running in the browser, which uses
| React to power the Facebook front end. Maybe I missed a step in
| there, but you get the idea.
|
| Is that how DNA tells a spider how to build a web? Or tells me I
| should drink water when I feel thirsty? Does it all boil down to
| ones and zeros stored in protein sequences? And if so, are there
| layers of abstraction like in computer code? Or is there some
| other fundamental mechanism?
| jxramos wrote:
| biology and physics operate at more dimensions where physical
| forces conspire to be leveraged by some neat tricks. Chemical
| gradients, various pressures, mechanical forces, electrostatic
| gradients, all sorts of differences out there to ride--some are
| passive, some are actively produced and take energy.
| reginaldo wrote:
| Also interested in the answer, and I thought a bit about this
| and have a hypothesis that DNA does not encode everything,
| instead it depends on implicit assumptions about the
| environment.
|
| To give an example, gravity is likely not encoded in the DNA,
| but instead, there are many encoded behaviors that would make
| sense only on an environment where gravity is present. The same
| for the presence of predators, wind, solar radiation, etc.,
| i.e. many of the things that we take for granted.
|
| That's how you would get more than 750MB of behavior on 750MB
| of DNA data [1]
|
| [1]
| https://en.wikipedia.org/wiki/Human_genome#Information_conte...
| captainclam wrote:
| Interesting! I like that thought. I enjoy thinking about how
| surprisingly good we are at predicting trajectories, good
| enough that we can throw, catch, and dodge small objects with
| remarkable accuracy. I wonder if our internal calculations of
| acceleration due to gravity is purely learned, or future
| space-faring infants will be surprised by how their block
| castles react when they knock them over.
| ertgbnm wrote:
| Here is not a very good answer to your question, but think
| about how you know how to walk. It's something that is not
| entirely conscious. You legs just move between places that you
| desire to go without any thought to the angle of your knee or
| tension in your gluts. You feel unbalanced when you center of
| gravity is too far forward despite having no conscious
| understanding of where exactly your center of gravity is in the
| first place.
|
| Spiders likely have a similar feeling but even further refined.
| They don't know how to build a truss, but they do end up
| building analogous structures because in their tiny bug brains
| it just feels right. This is the same way a human knows they
| are more stable with their legs spread apart and knees slightly
| bent. Part of that certainly comes from learning but a lot of
| it is built into our biology too.
| adr1an wrote:
| You are looking to emergent properties of biological systems
| from a reductionist philosophical perspective. It's pretty
| common to have that view. I believe the nature-nurture debate
| of the 80s (iirc) will be of your interest.
| w10-1 wrote:
| (warning: ignorant curiosity from someone with no chemical
| engineering background)
|
| This is a nice design: the chiral DNA turbine follows a leading
| leash into the nanopore, and the trailing cap keeps it from
| flowing through. The ion/electrical differential drives the
| turbine blades to turn (presumably the cap/leash assymmetry
| requires unidirectional flow).
|
| What's unclear is how this can be converted to work in the
| presence of ionic flow.
|
| It's unclear if the cap or leash could be repurposed; they're
| presumably spinning along with the turbine. That leaves the
| chiral arms, passing by the nanopore walls. I could see some
| charge-dependent reaction resulting from passing a charged arm-
| tip proximal to the nanopore-wall (enzyme), but by hypothesis
| we're in a charged flow so that seems like a no-go.
|
| The converse question is whether a charged DNA arms could be
| induced to spin by the nanopore; that could actually drive flow
| (albeit likely not against any ionic or osmotic current, so it
| would be hard to see how it could be useful).
|
| On the other hand, something like this might be useful not as a
| motor but as a discrete gating factor, e.g., to serialize flow of
| other molecules through a nanopore. E.g., to improve quality in
| the current nanopore DNA sequencing, a slow rotation time (5/s
| here) could enable an upstream nanopore to select one segment of
| DNA to be read by a downstream nanopore without the interaction
| of the to-be-processed segment tail with other DNA molecules near
| the nanopore entry. (but that might already be a solved problem
| for all I know.)
| rsynnott wrote:
| Today in apparently real things which sound suspiciously like
| Star Trek technobabble...
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