[dna? (OP)]

Deep into this rabbit hole, soon to be collaborating with a researcher who will carry out extensive molecular modelling on these proposed structures.

Part shameless plug but also looking for feedback - I've been working at getting my thoughts together on a website - dna.place

These ideas seem to illicit some upset responses from people - not my intention! I just have a genuine curiosity and reserve the right to be completely wrong about all this...

[Kryptid]

If you have an idea, you are supposed to post the idea here for discussion (not link other pages about it, which looks like advertising).

[dna? (OP)]

If you have an idea, you are supposed to post the idea here for discussion (not link other pages about it, which looks like advertising).

Understood! It's a tricky concept to get across in a single forum post, will try and copy and paste the basics over (edit - pictures proving tricky...) :

This site serves as my attempt to curate resources relating to the structure of DNA and the work of Tai Te Wu, Ken Biegeleisen, Lev I. Verkhovsky,  Mark Curtis - and others. My hope is to provide a starting point for anyone interested in researching these ideas. It may evolve as time goes by...
My fascination with this topic began after meeting artist Mark Curtis in 2017. Driven by his interest in nature and the depiction of space, Curtis began an investigation into structure of DNA in 1995. The resulting artwork was later used for a Royal Mail 'Millennium Collection' stamp, commemorating the discovery of DNA.

The following is taken from New Scientist, 16 May 1998 - Deconstructing DNA:

After many attempts, he found he couldn't make sense of the two and three-dimensional representations he found in textbooks. They seemed to contradict one another. Frustration finally forced him back to what he refers to as "geometrical first principles", and in the manner of Renaissance perspectival artists such as Paolo Uccello, he began by making careful scale drawings of DNA.

DNA has ten base pairs to each turn of the helix, so, using these centuries-old methods, Curtis began with a decagon-a 10-sided figure. He then placed a pentagon for each base around it. The pentagon is the only regular shape that can fit round a decagon in this way without leaving any space. And according to Curtis, this figure of 10 pentagons oriented about a decagon is the only geometrical configuration that enables one to create a helix with the known dimensions of DNA. Add some thickness to each of the pentagons, and the 10 pentagons telescope out to form a helix. To build a structurally sound double helix, Curtis reasoned that he would need not just one pentagon, but two joined together. With this insight he was finally able to produce the drawings and paintings that he had originally planned.

This kind of reasoning may seem obscure by modern standards. But for Curtis, it established that a double helix of 10 turns had to be made of twinned pentagons. At this point in his work, he was still thinking in terms of the traditional Watson and Crick structure. But he faced a contradiction: in the standard Watson and Crick chemistry, the base pairs join through hexagonal regions in their structures. Then came Curtis's moment of truth: "I sat down on the sofa one night and I thought, hang on a second, the molecular structures of the bases also have pentagons in them. And here was I, with two pentagons, building a consistent helix that conformed to the dimensions of the DNA double helix." By connecting the bases differently, Curtis found that he could naturally form pairs of pentagons in each base pair. "It was placed in my lap. I wasn't trying to prove anybody wrong. I wasn't even thinking then that they've got it wrong. I was just playing, like artists play."


In Curtis's painting, ten pentagons arranged around a decagon form a helix with the known dimensions of DNA


Striking similarities to Curtis' pentagonal stacking, from: Structure of the DNA Duplex d(ATTAAT)2 with Hoogsteen Hydrogen Bonds

It was later brought to Curtis' attention that he had inadvertently created base pairs discovered by Karst Hoogsteen in 1959.

There is a growing body of work on Hoogsteen base pairs. The following is from a 2019 paper - Infrared Spectroscopic Observation of a G–C+ Hoogsteen Base Pair in the DNATATA‐Box Binding Protein Complex Under Solution Conditions:

Hoogsteen DNA base pairs (bps) are an alternative base pairing to canonical Watson–Crick bps and are thought to play important biochemical roles. Hoogsteen bps have been reported in a handful of X‐ray structures of protein–DNA complexes. However, there are several examples of Hoogsteen bps in crystal structures that form Watson–Crick bps when examined under solution conditions. Furthermore, 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.

Through subsequent research I came across Professor Tai Te Wu. Wu sent me the document Politics Dictates Scientific Truth which gives an overview of his experience. All of Wu's publications along with correspondence between Wu and Maurice Wilkins can be found on this page.





In Secondary Structures Of DNA, Wu proposes an alternative structure to explain the diffraction pattern in Photo 51:

Through systematic search, a four-stranded structure that gives predicted diffraction patterns in agreement with the experimental result at 92 per cent relative humidity has been obtained. It is schematically illustrated in Figure 3. The solid lines represent one base-paired double helix, which can be considered as a stretched-out version of the conventional double helix. Its pitch is 67.2 A, and the separation between base-pairs is 6.4 A. The pairing is of the Hoogsteen type. The other identical double helix is represented by dotted lines. It is located symmetrically opposite to the helical axis. These two double helices are held together by partial base-pair intercalation. As a result, the effective pitch is reduced to 33.6 A, and the effective separation between base-pairs is 3.2 A.

The comparison between experiment and theory is shown in Figure 4. Since the pitch of the helices is twice that of the conventional one, there should be twice the number of layer lines. But, by symmetry, the intensities on odd-layer lines vanish within the region of interest. The theoretical 0, 2nd, 4th, and 6th layer lines therefore correspond to the experimental 0, 1st, 2nd, and 3rd layer lines. The agreement is indeed remarkable. A comparison with Figure 2 clearly indicates that the predicted diffraction patterns based on the present model can only fit the experimental result obtained at 92 per cent relative humidity but not at 66 per cent.



Curtis' models adopting the intercalated structure proposed by Tai Te Wu

Dr Ken Biegeleisen developed Wu's ideas further. His papers can also be found here, along with accompanying video presentations.

Wu and Biegeleisen are mainly concerned with the net helicity and tertiary structure of DNA. Wu published the paper - "A novel intact circular dsDNA supercoil" in 1996 which has been largely ignored:

The combination of the above theoretical model and experimental results strongly suggests that there is an alternative structure of DNA which does not have the usual difficulty of unwinding, rewinding and requiring numerous covalent bond breakages and ligations during semiconservative replication.

Biegeleisen proposes a different means to test this theory in Methods for Non-Destructively Separating or Reannealing the Strands of Circular Duplex DNA Chromosomes.

I was intrigued to discover that Curtis' models are able to adopt all the forms put forward by Wu and uploaded a brief video demonstrating this.

[Kryptid]

So is the idea here that the commonly-depicted structure of DNA is wrong? Or is it that there is just an alternative configuration that has not been discovered before?

[dna? (OP)]

So is the idea here that the commonly-depicted structure of DNA is wrong? Or is it that there is just an alternative configuration that has not been discovered before?

It's mainly that the canonical Crick and Watson pairings may not be correct. I have never been able to find x-ray diffraction data at a high enough resolution of "fibre" DNA (ie, native - not a synthesised oligonucleotide) to determine the base pairing. I have had other people trawl databases - no luck! That would definitely put this to bed.

[Kryptid]

Unfortunately, I'm not particularly well-versed on alternatives to the Watson-Crick model nor the specific spectrographic evidence used to support it. Someone else might be able to better respond with the relevant expertise. I also don't have the means to perform any experiments (I'm not actually a scientist, just a science enthusiast and college graduate).

[Bored chemist]

"fibre" DNA (ie, native - not a synthesised oligonucleotide)

Why do you think that matters?
We put synthetic DNA in cells, and it works- so we know the configuration must be right.

[puppypower]

The DNA depicted in textbooks is not correct, since the entire working structure of DNA also contains a double helix of water within the major and minor grooves of the double helix. DNA by itself is not bioactive without this water. There is no other solvent, besides water, that can be substituted and make DNA active.

The organic-centric depiction of DNA, in textbooks, without water, leads to a lot of confusion and is why casino science is still being used in biology. The water becomes the invisible wild card for the organic aspects of the DNA. This requires dice and roulette. In reality, the water-DNA composite  follows logical principles.

If you look at the base pairs, there are more hydrogen bonding sites within the bases than are needed between the organic bases. This is shown below in the first pictures.These extra sites are earmarked for water. Water also binds other water molecules within the major and minor grooves. The water also extends outwards covering the surface phosphate groups. Among other things this water serves as finger prints for the aqueous covered bases helping to target enzyme attachment. The water also contains free energy critical to DNA function; cooperative hydrogen bonding. The second picture depicts the water within the minor groove.

[Bored chemist]

The DNA depicted in textbooks is not correct, since the entire working structure of DNA also contains a double helix of water within the major and minor grooves of the double helix. DNA by itself is not bioactive without this water. There is no other solvent, besides water, that can be substituted and make DNA active.

The organic-centric depiction of DNA, in textbooks, without water, leads to a lot of confusion and is why casino science is still being used in biology. The water becomes the invisible wild card for the organic aspects of the DNA. This requires dice and roulette. In reality, the water-DNA composite  follows logical principles.

If you look at the base pairs, there are more hydrogen bonding sites within the bases than are needed between the organic bases. This is shown below in the first pictures.These extra sites are earmarked for water. Water also binds other water molecules within the major and minor grooves. The water also extends outwards covering the surface phosphate groups. Among other things this water serves as finger prints for the aqueous covered bases helping to target enzyme attachment. The water also contains free energy critical to DNA function; cooperative hydrogen bonding. The second picture depicts the water within the minor groove.

The grown-ups know that life is 70% water.
Stop banging on about it.

[dna? (OP)]

"fibre" DNA (ie, native - not a synthesised oligonucleotide)

Why do you think that matters?
We put synthetic DNA in cells, and it works- so we know the configuration must be right.

This is a good point and an area I need help in understanding! I am looking for clear-cut examples of synthetic oligonucleotides being inserted into living cells and then functioning properly. Wrapping my head around this article - "Creation of a Bacterial Cell Controlled by a Chemically Synthesized Genome" - can't insert link so you'll have to try googling...

Starts off synthesising oligonucleotide snippets, that from what I can make out - are joined together in increasingly longer lengths then used as templates for PCR, and later finished off via homologous recombination in yeast.

Now, this is a bit of a stretch on my part - but perhaps base pairing doesn't matter so much in PCR. Canonical Crick and Watson pairing function perfectly well as a template, but what is the resulting base pairing downstream of these steps?

[dna? (OP)]

The DNA depicted in textbooks is not correct, since the entire working structure of DNA also contains a double helix of water within the major and minor grooves of the double helix. DNA by itself is not bioactive without this water. There is no other solvent, besides water, that can be substituted and make DNA active.

The organic-centric depiction of DNA, in textbooks, without water, leads to a lot of confusion and is why casino science is still being used in biology. The water becomes the invisible wild card for the organic aspects of the DNA. This requires dice and roulette. In reality, the water-DNA composite  follows logical principles.

If you look at the base pairs, there are more hydrogen bonding sites within the bases than are needed between the organic bases. This is shown below in the first pictures.These extra sites are earmarked for water. Water also binds other water molecules within the major and minor grooves. The water also extends outwards covering the surface phosphate groups. Among other things this water serves as finger prints for the aqueous covered bases helping to target enzyme attachment. The water also contains free energy critical to DNA function; cooperative hydrogen bonding. The second picture depicts the water within the minor groove.

Absolutely!

Attached is a model of a duplex using Curtis' base pairs, again showing the multitude of hydrogen bonds. (Sugar phosphate chain omitted...)

[Bored chemist]

Now, this is a bit of a stretch on my part - but perhaps base pairing doesn't matter so much in PCR.

The polymerase they use in PCR is the same polymerase that is used by cells.
And enzymes (like that one) are extremely specific.
It simply isn't plausible that it would do things the "wrong" way round while used for lab DNA synthesis but the "right" way in nature.

We also know that degradation of DNA gives fragments (nucleotides) where there is a sugar molecule (ribose or deoxyribose) connected to the 5 membered ring.
These bits have other uses in the body. The best known is probably ATP.

So, while it's an interesting idea, there's just no way that the DNA could be "inside out" in the way you are suggesting.

[dna? (OP)]

I am looking for clear-cut examples of synthetic oligonucleotides being inserted into living cells and then functioning properly. Wrapping my head around this article - "Creation of a Bacterial Cell Controlled by a Chemically Synthesized Genome" - can't insert link so you'll have to try googling...

Starts off synthesising oligonucleotide snippets, that from what I can make out - are joined together in increasingly longer lengths then used as templates for PCR, and later finished off via homologous recombination in yeast.

Now, this is a bit of a stretch on my part - but perhaps base pairing doesn't matter so much in PCR. Canonical Crick and Watson pairing function perfectly well as a template, but what is the resulting base pairing downstream of these steps?

Now, this is a bit of a stretch on my part - but perhaps base pairing doesn't matter so much in PCR.

The polymerase they use in PCR is the same polymerase that is used by cells.
And enzymes (like that one) are extremely specific.
It simply isn't plausible that it would do things the "wrong" way round while used for lab DNA synthesis but the "right" way in nature.

We also know that degradation of DNA gives fragments (nucleotides) where there is a sugar molecule (ribose or deoxyribose) connected to the 5 membered ring.
These bits have other uses in the body. The best known is probably ATP.

So, while it's an interesting idea, there's just no way that the DNA could be "inside out" in the way you are suggesting.

I'm probably not explaining myself very well. I acknowledge that the polymerase is the same. In PCR a synthesised oligonucleotide is used as a primer - the resulting nucleotide in my mind is probably the same as native DNA.

That DNA adopts the Hoogsteen pairing doesn't conflict with your point about the known structure of nucleotides.

I came across this from Crick recently... The Biochemistry of Genetics, 1964 - page 124
"Two further points should be made. First, it does not follow that other base-pairs cannot occur in important places in certain situations, for example, in transfer RNA, or during the presumed combination of transfer RNA with messenger RNA. Second, the exact nature of the base-pairs is still not completely clear. There is little doubt about the pair (G + C). Three hydrogen bonds are formed between the bases, as mentioned tentatively by Watson and myself (48), but first clearly suggested by Pauling and Corey (49). This structure has now been found in two single crystals (50, 51).The uncertainty concerns the pair (A + T). The standard form suggested by Watson and myself is that shown in Fig. 2. However, the first single crystal of a base-pair to be solved, that of g-methyl adenine and l-methyl thymine, by Hoogsteen (52)) contained the pairing illutrated in Fig. 9. This pairing, or a variant of it, has since been found in three other crystals (53, 54). Neither of these two new base-pairs can easily be fitted into a double helix which also has G-C pairs without making the backbone the exact structure the double helix (poly A and poly U) and the triple helix (poly A and 2 poly U). A recent paper (55)) dealing with the infrared evidence, discusses this problem more fully."

My interpretation is that is that they were unable to build a duplex with a Hoogsteen AT pair and Watson/Crick GC pair... but they negated to attempt modelling a helix with both Hoogsteen AT and GC pairings.

R.E. Dickerson later found a duplex with both AT and GC Hoogsteen pairs was the best way to explain fibre X-ray diffraction patterns for a "D-DNA". Same conclusion reached by other researchers.

[Bored chemist]

If the only evidence we had was X Ray diffraction then that would be a more important point.
But there's chemical evidence too.
The sugar is stuck to the 5 member ring.
That's just chemistry.
Stuff like this
http://www.bmrb.wisc.edu/metabolomics/mol_summary/show_data.php?molName=ADP&id=bmse000004
There's no "wriggle room" here.

[dna? (OP)]

If the only evidence we had was X Ray diffraction then that would be a more important point.
But there's chemical evidence too.
The sugar is stuck to the 5 member ring.
That's just chemistry.
Stuff like this
newbielink:http://www.bmrb.wisc.edu/metabolomics/mol_summary/show_data.php?molName=ADP&id=bmse000004 [nonactive]
There's no "wriggle room" here.

I don't disagree and Hoogsteen isn't in conflict here (see attachment)

[puppypower]

"fibre" DNA (ie, native - not a synthesised oligonucleotide)

Why do you think that matters?
We put synthetic DNA in cells, and it works- so we know the configuration must be right.

This is a good point and an area I need help in understanding! I am looking for clear-cut examples of synthetic oligonucleotides being inserted into living cells and then functioning properly. Wrapping my head around this article - "Creation of a Bacterial Cell Controlled by a Chemically Synthesized Genome" - can't insert link so you'll have to try googling...

Starts off synthesising oligonucleotide snippets, that from what I can make out - are joined together in increasingly longer lengths then used as templates for PCR, and later finished off via homologous recombination in yeast.

Now, this is a bit of a stretch on my part - but perhaps base pairing doesn't matter so much in PCR. Canonical Crick and Watson pairing function perfectly well as a template, but what is the resulting base pairing downstream of these steps?

Biology is still too dependent on statistical models, which means even if most of the experiments do not work and one does, the one that works is called evidence. Things do no have to work all the time in statistical practice. Like in a casino, nobody wins all the time and this is acceptable practice.

Another thing to consider is the protein grid of a bacteria or cell is running the show. Proteins make all the enzymes and support molecules needed for the DNA to work. Water is also critical to the protein grid since the combination of water and protein defines placement within the grid, with the DA defining the position of lowest aqueous potential. DNA is really like a hard drive and not the CPU. If we place an aftermarket hard drive into a computer, it can still work since the mother board and CPU is running the show and they will integrate the new hard drive.

If we insert a DNA hard drive that is preprogrammed, with functionality that the rest of the cell does not use, there will be conflict.

During late in cell cycles, the DNA hard drive is packed  into chromosomes, and is therefore taken off line. Packed DNA is not functional; zip files. The mother cell's protein grid continues the processes needed to make two daughter cells. Each daughter cell will then unpack its DNA to get the hard drive back online.

In the case of inserting new DNA, chromosomes would be good time, since unpacking will occur independent on the DNA content. Although, the layers of unpacking, typically need to expose preliminary DNA hard drive data that reinforces the needs of the existing protein grid. The best bet for making this work is to duplicate original sequences and hope there are not too many typos. 

[puppypower]

The CPU of the cell is actually the interface between the water, protein grid and the DNA hard drive. Pure water will form a complex network of water-water hydrogen bonding that is very stable. This allows a small molecule like water to have an unusually high melting and boiling point. This is considered an anomaly of nature since it is very unique. Ammonia can form hydrogen bonds but boils at a much lower temperature more in tune with its size.

When we add the organics of life to the water to form cells, there is surface tension created; water and oil affect, which alters the hydrogen bonding grid of water and increases its potential. Water wants to get back to the stability of the pure state, while the organics by being covalently bonded, are very persistent. The compromise is a dynamic state of enzyme synthesis, metabolism and recycle that reflects the lingering potential between the protein grid, the DNA hard drive and the water. This is the CPU, with the water able to conduct information locally and globally through its hydrogen bonding grid.

Say we take out the old DNA hard drive from a cell and replace it with another. The water will surround the new hard drive and define a unique DNA-water potential distribution. This needs to align with the protein-water grid or else the cell will not be able to coordinate its global efforts.

When sperm fertilize an egg, the extra added male DNA alters the CPU potential near the DNA. The CPU will attempt to form a global equilibrium which results in cellular proliferation.

[dna? (OP)]

The CPU of the cell is actually the interface between the water, protein grid and the DNA hard drive. Pure water will form a complex network of water-water hydrogen bonding that is very stable. This allows a small molecule like water to have an unusually high melting and boiling point. This is considered an anomaly of nature since it is very unique. Ammonia can form hydrogen bonds but boils at a much lower temperature more in tune with its size.

When we add the organics of life to the water to form cells, there is surface tension created; water and oil affect, which alters the hydrogen bonding grid of water and increases its potential. Water wants to get back to the stability of the pure state, while the organics by being covalently bonded, are very persistent. The compromise is a dynamic state of enzyme synthesis, metabolism and recycle that reflects the lingering potential between the protein grid, the DNA hard drive and the water. This is the CPU, with the water able to conduct information locally and globally through its hydrogen bonding grid.

Say we take out the old DNA hard drive from a cell and replace it with another. The water will surround the new hard drive and define a unique DNA-water potential distribution. This needs to align with the protein-water grid or else the cell will not be able to coordinate its global efforts.

When sperm fertilize an egg, the extra added male DNA alters the CPU potential near the DNA. The CPU will attempt to form a global equilibrium which results in cellular proliferation.

Fascinating insights and food for thought. I've never seen it laid out like this before.

[puppypower]

Back in the 1950's an controversial observation was made in biology. It was discovered that proteins fold with exact folds. This was controversial then and even now because this observation was not anticipated by the statistical modeling of cells that had grown popular. The statistical models, then and now, assumed proteins should fold with average folds due to thermal vibrations and other randomization affects. It is almost 70 years later and there is still no good statistical explanation for this, even though it is a well established experimental fact. Something is still missing from the status quo explanations of life, which often raises questions in the minds of young scientists.

The explanation, which is still not mainstream, as evident by the DNA never shown with water in textbooks, is connected to water. The cellular water, in an attempt to lower its potential, is forcing the protein to assume minimal energy states, which make them ideal surface for the dynamics of catalysis; CPU. The CPU of the cell, is not into dice, but has a logical plan based on free energy, with evolution part of this plan.

Below is what is referred to as free energy landscape diagrams. This diagram show two states of a protein in water.

Image b represents a protein hot off the press, that has been synthesized. It is random in many sense. Image A shows the same protein after water packs it to minimize the free energy of the protein-water cooperative.

The hills and peaks in image b represent the various organic rich side groups that create the most potential in water; surface tension. These are packed first; core of the protein and thereby shielded  from the water, since the packing of these highest energy will minimize free energy the fastest.

Image A reflects the perfectly packed protein with a surface that is favorable to water; CPU. Water tries to do this everywhere with each type of protein and material having a different optimized potential. This sets priority and helps to establish the protein grid of the cell. The DNA is at lowest potential with the water. As the cell interacts with the environment and reduced materials enter; food, the global water potential increases, which increases the potential at the water and DNA hard drive. This gets the DNA into the game with its response tailored to the global and local CPU.

[dna? (OP)]

These are great nuggets, I think I get the gist but it's perhaps a bit beyond my understanding!

What's your background @puppypower ?

The reCAPTCHA on this forum is insane by the way...