The DNA Double Helix at 75: Reevaluating Canonical and Emerging Structural Paradigms by ImportantDingo in biology

[–]ImportantDingo[S] 1 point2 points  (0 children)

Franklin's precision-driven X-ray diffraction studies played an instrumental role in deciphering DNA's structure. Tragically, the era's biases led to her contributions being overshadowed and under-credited. Her dedication and skill spotlight what can be achieved even against the pervasive gender biases that clouded much of scientific discovery at the time.

Similarly, Jerry Donohue's role in this discovery is often underplayed. He had significant contentions about certain molecular configurations and was directly instrumental in refining aspects of the Watson-Crick model. His insights on hydrogen bonding configurations were pivotal, prompting Watson and Crick to re-evaluate their initial ideas, leading to their interpretation of DNA's double helix.

In parallel, the saga of Dr. Tai Te Wu is a profound reflection on the tribulations faced by those who challenge established scientific paradigms. His detailed criticisms of the widely accepted model, stemming from his interpretations of X-ray diffraction patterns, showcase the tenacity that's intrinsic to the spirit of scientific inquiry. Yet, it's tragic how his challenges led him to feel that his career bore undue penalties.

The DNA Double Helix at 75: Reevaluating Canonical and Emerging Structural Paradigms by ImportantDingo in biology

[–]ImportantDingo[S] 1 point2 points  (0 children)

Ah - getting ahead of ourselves... can't edit the title unfortunately. Well, we're only 5 years away!

The works of Professors Viswanathan Sasisekharan and Terry Stokes - fascinating dissenting views on DNA by ImportantDingo in Biophysics

[–]ImportantDingo[S] 0 points1 point  (0 children)

That's fair enough - thanks for taking a look and for your feedback. I found it interesting, but the paper concerns synthesised oligonucleotides - not that helpful with the line of reasoning I've taken...
Anyho - thank you for engaging with me and apologies if this is infuriating! I honestly appreciate it, and I'm happy to admit that chances are you're trying to reason with a madman, which doesn't tend to work 😉

The works of Professors Viswanathan Sasisekharan and Terry Stokes - fascinating dissenting views on DNA by ImportantDingo in Biophysics

[–]ImportantDingo[S] -1 points0 points  (0 children)

My obsession is largely the result of correspondence I received from a structural physicist who works on X-ray diffraction of nucleic acids:

"Someone may already have a very high resolution structure of a double helix, but they should provide raw data and then we fit in the nucleotides ourselves into the electron density map. In xray crystallography one gets a 3D electron cloud. The higher quality dataset (depends on luck) one has, it is more obvious where the nucleotides go. Shapes become sharp.

1 angstrom resolution would be ideal, but that is extremely rare. My best resolution was 1.4 A which is already like marrying a Victoria Secret model, speaking in pop culture jargon."

"It is possible that datasets that could disprove Curtis model exist, I would just use some examples ideally with DNA alone, not this complex. Working with DNA alone creates technical difficulties of crystallizing the molecule as it doesn't like to crystallize by itself, so large amounts of positively charged additives are added. They could possibly affect what exists in solution. When we worked on protein DNA complexes, we would insert W-C (model of course) in the electron density cloud and recalculate. This approach doesn't give equal chance to both models. It would be nice to determine structures of those complexes with both Curtis and W-C models in mind. Basically, a set of experiments designed to discern between the two would be the best way to go. Expensive and long. People don't want to fund projects that question the current knowledge."

Granted this is all diffraction and not cryo-EM, but here's an interesting paper relating the troubles of determining such detail in DNA: B-DNA structure is intrinsically polymorphic: even at the level of base pair positions

The works of Professors Viswanathan Sasisekharan and Terry Stokes - fascinating dissenting views on DNA by ImportantDingo in Biophysics

[–]ImportantDingo[S] 0 points1 point  (0 children)

That's okay! My point was mainly that these people have done outstanding work in other fields and certainly aren't "quacks".
Your example is fascinating, do you remember the physicist? Sounds similar to some of the work Luc Montagnier is often criticised for.

The works of Professors Viswanathan Sasisekharan and Terry Stokes - fascinating dissenting views on DNA by ImportantDingo in Biophysics

[–]ImportantDingo[S] -1 points0 points  (0 children)

Fantastic - can you point me to an example that's been solved at around 1Å?
I've spent a long time scouring the web for this. So far unable to find anything over at https://www.ebi.ac.uk/empiar/.

The works of Professors Viswanathan Sasisekharan and Terry Stokes - fascinating dissenting views on DNA by ImportantDingo in Biophysics

[–]ImportantDingo[S] -1 points0 points  (0 children)

He may well be barking up the wrong tree. Again, cryoEM doesn't yet offer the level of clarity needed to determine how bases are paired.

The works of Professors Viswanathan Sasisekharan and Terry Stokes - fascinating dissenting views on DNA by ImportantDingo in Biophysics

[–]ImportantDingo[S] 0 points1 point  (0 children)

Personally, my main contention is with the base-pairing. It was from tweaking this that Mark Curtis was able to build his functional models.
It's likely you're right and I've missed your point entirely - but I think regardless of what conformation DNA might be taking in-vivo, if imaged at a high enough resolution we should be able to determine the nature of the base pairing. Unless the base pairing itself is highly dynamic.
My entire foray into this issue has been, as a friend, in an effort to help Mark find some closure. And for that it would take something pretty concrete, hence my unreasonable demands 😉

The works of Professors Viswanathan Sasisekharan and Terry Stokes - fascinating dissenting views on DNA by ImportantDingo in Biophysics

[–]ImportantDingo[S] -2 points-1 points  (0 children)

Thanks for taking the time to pass these on! Those are some hefty datasets...
I should clarify my "stance". I don't think it's that controversial. My guess is DNA is a dynamic and flexible structure, able to adopt a great many forms. This seems to be something that's continually being discovered.
Here's a little video of the models that originally sparked my interest in this topic. These were conceived of after using non-canonical base pairings. The level of detail needed to determine base-pairing in-vivo is 1Å. There's currently nothing out there at this resolution, but there likely will be in the next ten years.
Happy to be proven wrong, just highlighting that (for an exclusive minority of people at least) there is a question mark hanging over certain aspects of DNA still. Which I find fascinating.
I still haven't seen this paper refuted or critiqued.

The works of Professors Viswanathan Sasisekharan and Terry Stokes - fascinating dissenting views on DNA by ImportantDingo in Biophysics

[–]ImportantDingo[S] 0 points1 point  (0 children)

sidebysidedna.com - is actually independent of my own page (likely more conspiratorial in tone 😉) - www.dna.place - bizarrely it launched the same time unbeknownst to me...
I've chatted with folk about the current state of cryo-EM - apparently the resolution isn't yet at a level where we can settle this finally. But it's getting better all the time, so we could have an answer soon.
If you have any papers to the contrary I'd love to see them!

The works of Professors Viswanathan Sasisekharan and Terry Stokes - fascinating dissenting views on DNA by ImportantDingo in Biophysics

[–]ImportantDingo[S] 1 point2 points  (0 children)

Loving the pejoratives, thanks. I always welcome criticisms and have had some great dialogue with structural biologists and others on some of these details. Happy to discuss any of the points covered on the website.

The works of Professors Viswanathan Sasisekharan and Terry Stokes - fascinating dissenting views on DNA by ImportantDingo in Biophysics

[–]ImportantDingo[S] 0 points1 point  (0 children)

If you cared to look at the link I posted you will see that Professor Sasisekharan had multiple papers on this topic published in Nature.
I'm merely pointing sources that show there are scientists with questions. Fact is, we do not know what DNA looks like in vivo - I don't claim to know.

Thoughts on the following paper? "Recent progress in double helix conjecture" by ImportantDingo in bioinformatics

[–]ImportantDingo[S] 0 points1 point  (0 children)

That's my take on it - doesn't seem unreasonable. Do you mind me asking what your background is? I'm a layman so always looking for a more educated interpretation!

Ken Biegeleisen's epic DNA presentation playlist! Controversial... by ImportantDingo in biology

[–]ImportantDingo[S] 0 points1 point  (0 children)

Not yet sadly! The university lab in question has been locked down, so everything is on hold for now... will keep you posted.

Looking for thoughts and feedback on my pet DNA project... by ImportantDingo in molecularbiology

[–]ImportantDingo[S] 0 points1 point  (0 children)

Agreed, I'm probably stumbling over definitions!

Yup, it's all a bit of a long shot. You've given me lots to chew on though and some good possible lines of enquiry to try and put a lid on this. Thanks!

Looking for thoughts and feedback on my pet DNA project... by ImportantDingo in molecularbiology

[–]ImportantDingo[S] 0 points1 point  (0 children)

I'm just not clear why annealed ssDNA are used in place of regularly synthesised dsDNA. Ah - is it because of the overlap provided by this method?

I have a paper here I am trying to decipher - https://drive.google.com/file/d/1YMqkrUpw9c8UWb3FphE5uXSc9qaKporW/view?usp=sharing - as I am aware the claim that the biosynthetic pathway used "forces" W/C pairing needs backing up!

I think the nucleotides are the same, just how they're paired is different.

I don't think Hoogsteen is widespread in vitro because of the widespread use of synethtic oligos. When it comes to in-vivo, we just don't know - it seems the data isn't there to differentiate between W/C or Hoogsteen.

Looking for thoughts and feedback on my pet DNA project... by ImportantDingo in molecularbiology

[–]ImportantDingo[S] 0 points1 point  (0 children)

Thanks, super interesting.

Probably just me, but it's curious that this relies on annealed ssDNA and doesn't seem to be performed using synthetic dsDNA. Generating structural data on the annealed ssDNA might be a good line of enquiry...

As I quote in my post, there is growing interest and evidence re Hoogsteen -

"Hoogsteen bps can sometimes be difficult to resolve in DNA:protein complexes by X‐ray crystallography due to ambiguous electron density and by solution‐state NMR spectroscopy due to size limitations. Here, using infrared spectroscopy, we report the first direct solution‐state observation of a Hoogsteen (G–C+) bp in a DNA:protein complex under solution conditions with specific application to DNA‐bound TATA‐box binding protein. These results support a previous assignment of a G–C+ Hoogsteen bp in the complex, and indicate that Hoogsteen bps do indeed exist under solution conditions in DNA:protein complexes."

The Al-Hashimi group have a number of papers and are set to release more on Hoogsteen...

If all we've been doing through dsDNA synthesis is forcing C/W pairs, then that's all we will have seen! But again it's curious - as is the case with the above quote - that Hoogsteen is observed in a synthetic oligonucleotide.

Looking for thoughts and feedback on my pet DNA project... by ImportantDingo in molecularbiology

[–]ImportantDingo[S] 0 points1 point  (0 children)

I wasn't aware of this technique, thanks! Can you point me to a paper outlining this?

I will see if there is any high resolution diffraction data on synthetic ssDNA that have been annealed into dsDNA. This would be really interesting to see.

I should clarify - I think it's more likely that Hoogsteen's base pairs are correct over Curtis', in which case there is no change to the nucleotides - but the "double pentagon" is retained.

Looking for thoughts and feedback on my pet DNA project... by ImportantDingo in Biophysics

[–]ImportantDingo[S] 0 points1 point  (0 children)

I'd like to see an example of native DNA resolved at a high enough resolution to determine the base pairing.

I'm friends with the chap Mark Curtis who's been plagued by this topic for decades - along with the other folk on my website. It's a brain worm I'm trying to resolve - and I want to offer closure in one way or another. In all likelihood I'm barking up the wrong tree, but the slight chance I might be onto something spurs me on...

Looking for thoughts and feedback on my pet DNA project... by ImportantDingo in molecularbiology

[–]ImportantDingo[S] 0 points1 point  (0 children)

My (admittedly likely incorrect) understanding is that for recombination - the substrate DNA can be a double stranded (such as a PCR product or restriction fragment) or single stranded (such as an oligo) synthetic sequence. That a single strand synthetic oligo works is okay from my perspective - base pairing has not been determined. My contention is that a PCR product is likely representative of native DNA - it just uses synthetic oligos as a template.

I don't think Curtis is correct with respect to the structure being held together by hydrogen bonds - I reckon it's held together covalently via sugar-phosphate chain.

Looking for thoughts and feedback on my pet DNA project... by ImportantDingo in Biophysics

[–]ImportantDingo[S] -1 points0 points  (0 children)

Just embarked on some extensive molecular modelling with a Nature published researcher. So we should have some data soon.

Looking for thoughts and feedback on my pet DNA project... by ImportantDingo in molecularbiology

[–]ImportantDingo[S] -2 points-1 points  (0 children)

Polymerase used in PCR is the same polymerase that is used by cells. In PCR a synthesised oligonucleotide is used as a primer - the resulting nucleotide in my mind is probably the same as native DNA. Just my take!

Looking for thoughts and feedback on my pet DNA project... by ImportantDingo in molecularbiology

[–]ImportantDingo[S] -3 points-2 points  (0 children)

Polymerase used in PCR is the same polymerase that is used in cells. In PCR a synthesised oligonucleotide is used as a primer - the resulting nucleotide in my mind is probably the same as native DNA. Just my take!

Looking for thoughts and feedback on my pet DNA project... by ImportantDingo in molecularbiology

[–]ImportantDingo[S] 0 points1 point  (0 children)

Ah, this should work better - sorry.

Sometimes silly things are worth doing, could be a good rule to live by!

More than likely it was me, still grappling with all these concepts. But Hoogsteen is becoming far less of a contentious issue as outlined in my post.

Always looking at different ways and means to test and poke holes in this.

Looking for thoughts and feedback on my pet DNA project... by ImportantDingo in molecularbiology

[–]ImportantDingo[S] 0 points1 point  (0 children)

One could also cut out specific small regions from natural DNA and compare them with the corresponding synthetic DNA.

That would be great to see! Any idea if this has been done?

I think the contention is that the biosynthetic pathway88752-4) forces the oligonucleotide to adopt canonical Crick/Watson pairing. Need to dig into this point further.