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Name: George
Status: student
Grade: other
Location: Outside U.S.
Country: USA
Date: N/A 


Question:
WHY are DNA strands twisted?



Replies:
The reason for the double stranded DNA is neither obvious nor simple. The reasons are a subtle interaction of the component nucleic acids, sugar, phosphate components with each other and with water. To my knowledge it defies a “one line” explanation. The website

http://www.thetech.org/genetics/ask.php?id=109

provides a reasonably accurate and comprehensible explanation.

Vince Calder


We can only surmise, based on observation, but I'd offer that a first need is that our cells (which contain DNA in nuclei and mitochondria) be small ....this due to the surface area requirement being optimized in small, not large, cells. In order for the DNA to actually fit within the small size of cells, there is the need for a compact structure, and one could argue that a straight-line structure of DNA would necessitate very large cells. We would probably not see organisms in their current form if cells needed to be that large.

As far as a structural reason for the coiling, one could surmise that due to the hydrogen bonding between purines and pyrimidines, and their required paring based on base chemical structure, the coiling is the only real way a stable molecule could be built.

The short answer: compactness and a stable structure is accomplished by the coiling.

During replication, and the needed coupling of complimentary base pairs, the coiling needs to be temporarily un-done. Once the replication is complete, the coiling returns.

Thanks for using NEWTON!

Ric Rupnik


George,

The very short answer is that the twisted ladder is a low-energy state, but without context, that answer is not a very good one. I'm not sure of your grade level, so please respond if my more detailed answer below is unclear or if you have more questions. And forgive me, as it's quite long.

First, let me note that double-stranded DNA is what we're talking about -- the structure of single-stranded DNA is a completely different story (and one I'll save for a different day...).

Based on your question, I'm assuming you already know the primary structure of DNA -- the bases, sugars, and phosphates. When you combine two strands of DNA, the "rungs" of the ladder (the bases) attract each other -- just like the opposite-pole magnets in the example. This is known as DNA hybridization. You might also know that the connections between the bases are very weak -- its easy to "melt" DNA (cause the strands to separate). The reason DNA is anti-parallel is because when the bases pair up, they bond more tightly (=lower energy) when arranged in anti-parallel fashion than when parallel.

The base pair story is pretty famous, but for DNA shape, the base-pairs are not the whole story. DNA also has a backbone made of sugar (deoxyribose) and a very important Phosphate group (it's important chemically because it's highly charged). You must remember also that the the whole DNA molecule is surrounded by water. It turns out, the sum of the DNA-DNA and DNA-water interactions determine the shape of the DNA.

When DNA is in water, the twisted helix has lower energy than an untwisted one. DNA "likes" itself, more than it "likes" water. By twisting on itself, it makes more DNA-DNA connections, and fewer DNA-water connections. The result is fewer repulsive interactions and more attractive ones (and this means lower energy).

Specifically, the charged phosphates repulse each other and try to space themselves as far apart as they can (with an untwisted ladder, they are closer together), and the hydrophobic parts (meaning they repel water) of the base pairs are more shielded from the water by the backbone twisting around it.

If more water was touching more hydrophobic parts of the DNA, then the DNA would be a higher energy state. The DNA, through random fluctuations, ends up in a configuration to avoid those kinds of interactions. When you add up all the small energy effects of the base pairs, the backbone, and the water, it turns out that the twisted helix is the favored (=low-energy) state.

It's interesting to note that DNA only forms a double-helix in water, and only if it's the right balance of salt, and not too high a temperature. If you have too much salt, or you put the DNA in ethanol (e.g. not water), or if you heat the water too much, the DNA "denatures" -- meaning it loses its twisted, helical shape. DNA is *not* a double-helix all the time!

It's also interesting that DNA has at least three *different* stable helical shapes (they're all twisted, but they're not all twisted the same way). Although the most famous (beta-helix) is the most common, other helices have been discovered in chemically-modified DNA (changing the atoms changes the energy, which changes the shape) and dehydrated DNA (less water means different energy which means different shape).

In terms of energy, this introduces a concept of "stability". A "stable" molecule is one that tends to stay like it is -- whereas an unstable molecule tends to change to something else. In terms of energy, this means that the small vibrations of the molecule all result in higher-energy states -- which means the vibrations tend to lead back to the original configuration, or in other words it is "stable". You can imagine a stable molecule as a marble inside a bowl. If you nudge it around, regardless of which direction, it tends to just end up back where it started. On the other hand, if you flip that bowl over and place the marble on top of it, if you push the marble, it's is going to roll off and end up somewhere else. That's like an "unstable" molecule. In energy terms, an unstable molecule is one where small vibrations lead to configurations that are lower energy, which means the molecule will not tend to revert to its original configuration.

OK, George, if you're still with me, I commend you.

Now, this answer assumes you know what 'energy' means in the context of molecular configuration. If not, here's an 'appendix' on that subject...

The structure of DNA (and any molecule) really needs to be understood in terms of energy. Chemical molecules are constantly vibrating and moving around (thermal energy). A fundamental property of matter is that it's constantly moving toward a lower-energy state (which is related to entropy and the second law of thermodynamics). Very large molecules like DNA or proteins have lots of possible shapes they might be in -- but they tend toward the shape(s) that minimize their energy. With this in mind, your question might be restated as, "why do twisted strands of DNA have lower energy than untwisted ones?"

Let me start by explaining the concept of energy of a molecule. To understand the "energy" of a molecule's configuration, imagine two magnets. If you push opposite poles together, the magnets "stick". You have to pull on them to get them apart. In other words, you have to do work (pull them apart) to separate them. In contrast, if you push the same poles together, you have to push to keep them close, and if you let go, they separate. You have to do work (you have to expend energy) to get them together.

You may know from basic physics that doing work on an object means you are adding energy to it (if you push a ball, it starts rolling, it gains kinetic energy, etc.). The same is true for the magnets -- by doing work on the magnets, you are moving them into a higher energy state. When you push two same-pole magnets together, the magnets are at a higher energy state than if you have opposite-pole magnets together.

So how does this relate to molecules? A DNA molecule is made up of lots of atoms, each with different connections (chemical bonds, or just proximity) to other atoms. All of these atoms are vibrating around. Just like magnets might push or pull on each other, so do the molecules push and pull on each other. As the molecule is vibrating, it tends to creep toward the configuration with the lowest energy (recall the magnet example -- here, "lower energy" means more atoms "pulling" on each other and fewer atoms "pushing" away).

It's commonly known that "oil and water don't mix" -- in molecules, atoms have a cloud of electrical charge around them that depends on the type of atom (element) and how it's bonded with other atoms near it. With atoms, positive charges attract negative charges. But also, uncharged atoms tend to attract other uncharged atoms (this is like oil-oil mixing). A uncharged atom next to an charged atom also repels (this is like the oil-water repulsion). So in addition to positive-negative attraction, you could say that atoms with "compatible" charge properties (oil-oil) tend to attract each other, while atoms with "incompatible" charge properties tend repel each other (oil-water).

I hope this is helpful,
Burr



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