
DNA is held together by hydrophobic forces - hhs
https://scitechdaily.com/scientists-were-wrong-about-dna-it-is-actually-held-together-by-hydrophobic-forces/
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entee
Extensive studies on the thermodynamics of DNA helix formation have long shown
that there's a very important contribution for base stacking [1]. This isn't
news. What is new in this study is that they explore how hydrophobic
interactions could play a role in DNA binding interactions with proteins by
varying the solvent hydrophobicity. The title and linked article are quite
misleading, the paper itself is making very different claims [2].

[1]
[https://academic.oup.com/nar/article/36/suppl_2/W163/2505801](https://academic.oup.com/nar/article/36/suppl_2/W163/2505801)

[2]
[https://www.pnas.org/content/116/35/17169](https://www.pnas.org/content/116/35/17169)

~~~
arthurcolle
Every pop sci article about a new journal article in some publication is
always the same; personal question: doesn't it get frustrating needing to give
an addenda of all the misleading commentary?

Pop science publications literally do more harm than good by miscommunicating
the actually novel aspect of a particular discovery, irrespective of
superficial intent (popularizing science topics). Oh wait, why do they even
exist to begin with? Assumption: to soak up all the advertising dollars go
around.

How unproductive can an industry really be? The cost alone in wasted human-
hours time analyzing and post-processing to discern what is real and what is
hype and nonsense must be huge.

~~~
_Nat_
Pop-science journalism is still neat to observe!

The thing's that, as far as I can tell, economic/political journalism seems to
be at least as corrupted (intellectually; not talking about moral corruption),
where explanations of complex phenomena are grossly oversimplified beyond
recognition. Despite knowing that, it's hard to make a precise study of that
sort of corruption because the actual underlying truth is unclear.

By contrast, it seems reasonable to read pop-science journalism and then
compare it to a corresponding scientific story. We can then try to understand
the nature of media twisting, then apply that understanding to helping us
interpret journalism covering economics/politics, where the underlying truth
isn't as easily otherwise-determined.

In short, it's neat to see pop-science journalism in action as it helps to put
other sorts of journalism into perspective.

\---

Separately, I'd note the expression that " _There 's no such thing as bad
publicity._".

While science-journalism may not be particularly successful in informing the
public about science, it might have a positive effect on public-relations with
the scientific community, helping the community to feel more connected to the
scientific establishment.

I mean, it seems to work in, say, sports, where local communities will cheer
on competitors from their community despite not having any real direct
attachment to the competitors' efforts. It's my understanding that this sort
of emotional connection helps to keep professional sports well-funded, driving
public interest in their activities.

Then ditto for stuff like the expensive Apollo missions to put someone on
Luna, which I've heard that Americans took to be a national victory (and
perhaps others found it to be a human victory).

In short, science journalism might help drive public support for the sciences,
even if it fails to convey actual science.

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vedtopkar
This coverage is incredibly disingenuous. It's been known for a long time that
base stacking is the dominant force in keeping a double helix together.

Literally the first sentence of the abstract is "Hydrophobic base stacking is
a major contributor to DNA double-helix stability."

~~~
et2o
So this sentence is uncontroversial? Somehow I never came across this idea in
my genetics PhD.

> The main stabilizer of the DNA double helix is not the base-pair hydrogen
> bonds but coin-pile stacking of base pairs, whose hydrophobic cohesion,
> requiring abundant water, indirectly makes the DNA interior dry so that
> hydrogen bonds can exert full recognition power.

~~~
entee
That statement is uncontroversial, though keep in mind it's also not
completely rejecting the importance of H-bonds. A GC basepair is still more
stable than an AT basepair due to 3 H-bonds on the GC and only 2 for the AT.
However, to compute DNA helix stability you must take into account the
stacking of basepairs. Modern melting point calculators have correction terms
that take stacking between different pairs of base pairs (AT stacking on a GC,
AT stacking on a TA, etc.). They also take into account salt concentration,
which is absolutely critical to maintaining helix stability. This is because
the salt coordinates with the phosphate backbone, stabilizing the helix.

Key rule of thumb for pretty much any biological structure: it's the entropy
not the enthalpy that dominates. Entropy in this context is the stacking of
base pairs, enthalpy is formation of electrostatic or similar bonds (like an
H-bond between DNA bases). Essentially every biological molecule is "greasier"
than water, so it likes to hide that "grease" from the water much the same way
oil likes to form droplets with itself in water because doing so reduces the
"order" and therefore the boosts the total entropy of the solution.

Why you ask? It's complicated but my general understanding is that water that
is interacting with "grease" has to adopt a fair amount of structure. By
reducing the number of water molecules contacting your "grease" you reduce the
amount of structure the water has, which means the total system is more
disordered even as the grease itself adopts a higher degree of structure.

This is all a little handwavy, it's been a while since thermo, but it's a
decent overall framework for general understanding.

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rolph
research of scientific calibre avoids reporting salient facts such as pure
water at STP is clear and colourless liquid.

    
    
      The authors state their contribution as, "specific longitudinal unstacking in a hydrophobic environment,
     has to our best knowledge never been reported before."
    

reporting such is akin to reporting oil is immiscible with water.

have a look here:

"Water and counterions are crucial to screen the electrostatic repulsion among
charged phosphates and also favor the apolar stacking of bases. Accordingly,
the large impact of solvent modification on the properties of DNA is not
surprising. For example, a subtle change in the neutralizing cation can lead
to a dramatic conformational change(8, 9) or even to a complete alteration in
the sequence-stability rules of the duplex.(10) "

[https://pubs.acs.org/doi/full/10.1021/jp503816r](https://pubs.acs.org/doi/full/10.1021/jp503816r)

[https://www.ncbi.nlm.nih.gov/pmc/articles/PMC1904262/](https://www.ncbi.nlm.nih.gov/pmc/articles/PMC1904262/)

these articles predate the submission and stand firmly on exploitation of
solvent effects upon DNA helix stability.

50+years of Biochemistry have produced many DNA manipulation techniques wholly
dependent, on solvent selection.

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bodeadly
As other's have pointed out, yes, bases align like two parallel stack of
plates. This is for two reasons. One is that the aromatic rings of bases are
mostly carbon and thus not polar like water. Meaning they're hydrophobic. Duh.
But also the rings stack because of the "pi stacking" which is A Thing.

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dwighttk
I thought I learned this in HS biology 25 years ago.

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archarios
I'm curious if this changes how we think about how EM waves affect dna? My
understanding before was that we defined ionizing radiation as radiation that
could break that hydrogen bond.

~~~
Ultimatt
Your understanding before wasn't quite right. The ionizing in ionizing
radiation is the key, its about knocking off an electron to form an ion. So
that's something like a UV photon exciting an electron and breaking a covalent
chemical bond. Hydrogen bonds are weaker electrostatic interactions between
molecules where the charge is distributed in two molecules such that they have
a weak + and - charge arrangement. So pure water for example, the hydrogens
from one molecule have a bit more + and the oxygen has a bit more - within
each molecule. If you think about how that works with a bunch of magnets fixed
on a peg board they all try and match up their N and S if you move one they
all wobble around to find a new arrangement to minimise the energy across the
board. Thats hydrogen bonding all the H and O between different molecules try
and match their charges. In DNA there are either 2 or 3 of those kinds of
bonds to match up. Covalent bonds are more like how the magnets are fixed on
the peg board. So if you split a magnet off its way more chaos right? That
magnet will fly off and stick to another one and all bets are off on how
everything else will interact.

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capableweb
Read this as "DNS is held together by hydrophobic forces" and still thought
"yeah, that makes sense actually"

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rdlecler1
I wonder if this changes anything with respect to how we manipulate DNA or the
conditions by which DNA is, can be preserved.

~~~
lez
Looking forward to learn about healing retrovirus infections.

