Valid Shapes of DNA: Is A Reasonable?

[DaveC426913]

TL;DR Summary

Are both these valid representations of the DNA double helix?

I'm designing a ... let's call it a sculpture. It represents DNA.

I just realized there are (at least) two ways helices can spiral together:

A has two helices that are concentric but with different radii. They are also "in phase".
B has two identical helices that are "out-of-phase" by 180 degrees.

A is what I started with - and what I want - but I don't know if it is a valid representation of DNA (if you uncurled it, the inner helix is shorter than the outer helix. It would curve around to form a "wagon wheel" pattern.

Or am I being persnickety? After all, if DNA is bendy enough, and if the radii in A were long enough, in theory, the length disparity would effectively disappear. In other words, sufficient unfurlification of B would result in A.

So, my question is: is A a reasonable representation of DNA - i.e. perhaps odd but not wrong?

 

[BillTre]

Its more like B than A.
However, there is a major groove and a minor grove, like this:

The backbone parts are charged and coil around the outside.

The backbones of the two strands go in opposite directions chemically along the molecule (anti-parallel). Probably doesn't matter to your model though.

 

[Hornbein]

TL;DR Summary: Are both these valid representations of the DNA double helix?

I'm designing a ... let's call it a sculpture. It represents DNA.

I just realized there are (at least) two ways helices can spiral together:

View attachment 315948

A has two helices that are concentric but with different radii. They are also "in phase".
B has two identical helices that are "out-of-phase" by 180 degrees.

A is what I started with - and what I want - but I don't know if it is a valid representation of DNA (if you uncurled it, the inner helix is shorter than the outer helix. It would curve around to form a "wagon wheel" pattern.

Or am I being persnickety? After all, if DNA is bendy enough, and if the radii in A were long enough, in theory, the length disparity would effectively disappear. In other words, sufficient unfurlification of B would result in A.

So, my question is: is A a reasonable representation of DNA - i.e. perhaps odd but not wrong?

Form A does not appear in real life.

 

[Hornbein]

Form A does not appear in real life.

I am amazed that such a thing is theoretically possible (though pardon me that I'm not 100% confident in your assertion).

 

[DaveC426913]

I am amazed that such a thing is theoretically possible...

Not sure what you mean. 'splain?

 

[Hornbein]

Not sure what you mean. 'splain?

? I dunno, it's just a very weird possibility.

 

[DaveC426913]

? I dunno, it's just a very weird possibility.

Oh, you mean impossible specifically for DNA.

 

[BillTre]

One of the major problems with the "A" version would be the location of the sugar-phosphate backbone. It has electrical (static) charges. The bases (nucleosides, nucleotides include bases sugars and phosphates) are not or only weakly charged. The two strands will be most stable with the charges as far a apart as possible within the molecule. Thus, the two backbones would be as far apart as possible. the bases that do the pair bonding are in the middle snuggled up to each other.

The B form of DNA is what people usually think of, but there are other forms:
A-DNA: twists in the same direction as B-DNA, but the base orientation is idfferent
there are also other weird forms or DNA possible. there is an
Z-DNA: twists in the opposite direct from A and B-DNA. I think this form depends on certain sequences. It is definitely affected by supercoiling of the double helix (which puts twisting tension on the molecule).

Just to make things more confusing, there are also some 3 and 4 strand DNA structures:

 

[DaveC426913]

Cool.
That answers a question I had when I saw this:

I wondered how this was possible, if both strands were identical and the structure were axially symmetric. I started thinking about what it would do to the nucleotides.

But this shows how it's possible:

The two ends of the nucleotides are staggered along the length (the vertical axis). That's what leads to the alternating major/minor groove. Right?

TIL.

 

[Hornbein]

Oh, you mean impossible specifically for DNA.

Yeah, incompatible with its function.

 

[DaveC426913]

OK, more stuff.

This diagram

indicates that the nucleotide pairs span the minor groove, not the major groove.

I'm interested to know what the "phase" difference of the two strands are. If it were 180 degrees, the two gaps would be identical.

More to-the-point, I'm interested in knowing what the arc (of a full circle) of a given nucleotide pair is.

This diagram suggests that it might be around 135 degrees.

I'm not looking for exact numbers, just the gist.

 

[Hornbein]

OK, more stuff.

This diagram
View attachment 316653
indicates that the nucleotide pairs span the minor groove, not the major groove.

Aha that explains it. It's hard to see that.

I'm interested to know what the "phase" difference of the two strands are. If it were 180 degrees, the two gaps would be identical.

More to-the-point, I'm interested in knowing what the arc (of a full circle) of a given nucleotide pair is.

This diagram suggests that it might be around 135 degrees.

View attachment 316654
View attachment 316655
I'm not looking for exact numbers, just the gist.

I'd call that the pitch of the helix. Not that I'm any expert.

 

[DaveC426913]

Nope. Turns out I was completely wrong and the diagram is highly misleading.

From the specific angle of the diagram, the two helices are exactly 180 degrees out of phase. It only looks like the helices are unevenly-spaced:

And the asymmetry is not about the nucleotides either. Here is an outline of the helices - the nucleotides do not produce the asymmetry in the grooves - at least, not at this angle:

But if I measure the helices at a point 90 degrees rotated, you can see that they are not even; it's a 5:7 ratio.

This suggests that the major/minor groove is a product of the bumpiness of the helices themselves.