12 years, 2 months agoHello, 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:
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.
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
(taken from http://users.rcn.com/jkimball.ma.ultranet/BiologyPages/B/BasePairing.html)Are you able to form hydrogen bonds after flipping the bases?
- quote JackBean: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
(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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