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].
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.
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.
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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.
I have vague memories of a college professor who had spent a lot of time working out the exact places water would tend to coordinate on the DNA strand as part of his early prior research. His rant on the role of hydrogen bonding in the molecule was memorable.
The authors state their contribution as, "specific longitudinal unstacking in a hydrophobic environment has to our best knowledge never been reported before."
A little background on one of the authors: Carlos Bustamante (there are two science-famous ones, this one is NOT the one who analyzed Elizabeth Warren's DNA test) is a pioneer in structural analysis of DNA, particularly using optical tweezers to study how DNA (and later proteins) behave. As part of that work he has been interested in how tension or compression or other perturbations propagate through the DNA helix. The longitudinal unstacking is part of that.
Full disclosure: in graduate school I worked in a lab that published a paper that contradicted some of his previous work. It was a different part of the lab so I only know the high level overview of the controversy. He's a giant in the field though.
It may not be disingenuous. Judging by all the repetition in the article it was probably by written by someone who had no idea what the researchers were talking about.
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.
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.
"Often overlooked" might be a better term. This seems to be well-known to biophysicists studying nucleic acids but doesn't trickle down to the genetics/biology side of things.
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) "
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.
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.
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.
No. "Ionizing radiation" is not a reference to breaking hydrogen bonds. It _can_ affect covalent bonds (introducing them or breaking them), but hydrogen bonds are not the same thing.
This research likely has no direct impact on how we understand the effects of EM radiation on DNA.
[1] https://academic.oup.com/nar/article/36/suppl_2/W163/2505801
[2] https://www.pnas.org/content/116/35/17169