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Help - Why can't DNA be parallel?

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Help - Why can't DNA be parallel?

Postby keetner » Sun Sep 30, 2012 4:56 am

Hello, I just have a question in regards to DNA's directionality...

Why can't it be parallel? I understand the reason why they're anti-parallel is because of the numbering of the ribose sugars.
The thing I am confused about is when you look at the two strands, for the one from 3'-5', the base is flipped horizontally (so it can base pair, yes) but THEN the ribose and phosphate are flipped upside down. But the thing is, couldn't they still technically base pair if both strands are 5'-3'? Here is a really lame Paint thing I made up. First image is it normally, the second is my interpretation:

Image

All I did was copy and paste the strand, and flipped it horizontally. I also changed the base pairs so they would match up...
Do you guys see what I mean? I feel like 5'-3' would still theoretically work. As in, it literally seems like it's a simple horizontal flip.

I just don't understand the significance of why the ribose/phosphate must be upside down. I'm guessing I'm just missing something horribly here.

One more thing: how do the riboses flip upside down any way? Is it just from a simple twist of the single bond between the base + ribose?

Thanks in advance for any help! I do appreciate it.
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Postby Cat » Sun Sep 30, 2012 2:55 pm

They are antiparallel in nature. DNA normally condenses during cell division; your version most likely would not. I am sure a biochemist can explain this much better...
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Postby keetner » Sun Sep 30, 2012 6:18 pm

^Thanks for your response.

I would imagine so, I just wanted to know specifically what might happen or why it doesn't occur.
Looking at it again though, I realized, does it have to do with the RH/LH-ness of the helix? Cause if you look at the phosphates of bottom image (my version), one strand will be twisting to the right, while the other strand will be to the left. As a result, these won't quite base pair correctly...or if they do, I imagine it wouldn't be very stable.

Anyone else have thoughts on this? One of the many times a 3-D model would be handy.
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Re: Help - Why can't DNA be parallel?

Postby JackBean » Sun Sep 30, 2012 10:01 pm

Nice question :)

Unfortunately, 3D picture would not help here. I was thinking, why couldn't DNA anneal in parallel configuration after denaturation in vitro. The answer is pretty simple - because it is not capable to do so. Look on this picture
Image
(taken from http://users.rcn.com/jkimball.ma.ultranet/BiologyPages/B/BasePairing.html)

Are you able to form hydrogen bonds after flipping the bases?
http://www.biolib.cz/en/main/

Cis or trans? That's what matters.
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Re: Help - Why can't DNA be parallel?

Postby Cat » Sun Sep 30, 2012 10:48 pm

JackBean wrote:
Are you able to form hydrogen bonds after flipping the bases?



But, theoretically, you do not "flip the base" since it should rotate freely (single bond to sugar)...
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Postby JackBean » Mon Oct 01, 2012 10:06 am

Couldn't becuase of sterical reasons and mesomeric effect
http://www.biolib.cz/en/main/

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Re: Help - Why can't DNA be parallel?

Postby keetner » Tue Oct 02, 2012 9:07 pm

JackBean wrote:Nice question :)

Unfortunately, 3D picture would not help here. I was thinking, why couldn't DNA anneal in parallel configuration after denaturation in vitro. The answer is pretty simple - because it is not capable to do so. Look on this picture
Image
(taken from http://users.rcn.com/jkimball.ma.ultranet/BiologyPages/B/BasePairing.html)

Are you able to form hydrogen bonds after flipping the bases?


I'm not talking about flipping the bases though. If you look at my image I posted (the first DNA), you'll see that with the 3'-5' strand, the bases have been flipped horizontally compared to the 5'-3' strand. I understand this, otherwise there is no way they could base pair. However, they have NOT been flipped UPSIDE DOWN, unlike the riboses/phosphates which have been.

The thing I don't understand (ish, now), is why you can't have that ribose/phosphate backbone flipped right side up in the 3'-5' strand? That is what I tried to convey in the second part of my Paint image. I have kept the bases normally paired, but changed the ribose/phosphate orientation.

Also, I am horrible with chemistry related type things...so how would mesomeric effects play a part in this? Assuming you're talking about intermediates that could occur...? I'm a bit lost on here.
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Postby JackBean » Wed Oct 03, 2012 2:09 pm

because the ATP, CTP, GTP and UTP have certain conformation in the cell.

Moreover, if you had parallel strains, you've had to have something like negative-DNA-intermediate for replication.
http://www.biolib.cz/en/main/

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