I have a question related to the orientation of DNA antiparallel strains. DNA strains are called antiparallel because one strain is orientated from 5' to 3' and the other one from 3' to 5'. Regarding the phosphate-sugar chains that would be equivalent to say that the chains are rotated 180 degrees with respect to each other. However, in textbooks, 3' to 5' nitrogeneous bases are not shown as rotated with respect to 5' to 3' nitrogenous bases.

Why is this? If it would be the case then A-T would still make two hydrogen bonds but G-C would not make three but just one hydrogen bond!

PD: if needed I could make a picture to show my point.

  • 2
    $\begingroup$ Welcome to Chemistry StackExchange! My advise for you would be to stare at various 3D images or interactive models of DNA structure long enough to resolve any misunderstandings you have about the actual structure :-) $\endgroup$
    – Domen
    Jan 24, 2022 at 19:15
  • $\begingroup$ Thank you! Now it makes much more sense :) $\endgroup$
    – DOMiguel
    Jan 24, 2022 at 19:52

1 Answer 1


The bases are roughly perpendicular to the axis of the double helix. In two-dimensional figures, the structure is flattened to make it easier to see.

The two strands are in the same conformation, just rotated by 180 degrees around an axis perpendicular to the helix axis. You can see this nicely in a palindromic duplex such as the one below, where the two strands (shown with black and gray carbon atoms) are rotated from the double helix orientation to a superimposed orientation and back again.

enter image description here

To get an interactive view of the same DNA (but without the artificial rotation to superimpose the two strands), see e.g. Proteopedia. (To run the superposition yourself, click on the "load full" button, right-click on the Jmol window, open a console, and issue the command "compare {1-12} {13-24} ATOMS{1-12}{13-24} ROTATE TRANSLATE").

It is not easy to find a 2D drawing that captures this symmetry. Here is an example, though, where the left and the right strand look like they have the same conformation:

enter image description here Source: https://universe-review.ca/I01-06-DNA.jpg


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