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This question already has an answer here:

Why is it that DNA strands are running in anti-parallel fashion? Given the chemical base-pairing, they could have been parallel just as well.

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marked as duplicate by WYSIWYG Aug 22 '15 at 15:21

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    $\begingroup$ How could they run parallel instead of anti-parallel when they need to be complementary to each other, and at the same time have the same structure? Having them parallel and complementary would need them to be enantiomers, and that's biochemically a huge mess. I'm not posting it as answer because I can't really justify it $\endgroup$ – Athe Aug 21 '15 at 13:38
  • $\begingroup$ This is a similar question in Biology SE biology.stackexchange.com/questions/27839/… $\endgroup$ – falsum Aug 22 '15 at 2:09
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Parallel DNA helix can exist and this has been observed experimentally. However these structures are stabilized by Hoogsteen type base pairing [1,2] and not the usual Watson-Crick type pairing because the parallel conformation does not allow the latter (See the figure below).

Hoogsteen base

This elongates the hydrogen bonds and also causes a loss of one hydrogen bond in the GC pair. Because of these differences, the parallel double helix is structurally weaker than the anti-parallel double helix.

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    $\begingroup$ I think your last comment is the clincher. When the two strands run anti-parallel, they organize in a way that the hydrogen bonds stabilize the molecule in a low energy state. By the way, Watson addresses this pretty clearly in his book, The Double Helix. $\endgroup$ – johntreml Aug 21 '15 at 20:30
  • $\begingroup$ @johntreml Haven't read that book actually. Thanks for mentioning. $\endgroup$ – WYSIWYG Aug 21 '15 at 20:33
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This is more chemistry than Biology.

Both strands of DNA are 5' to 3' direction. Why so? because the direction is determined in terms of the direction in which purine or pyrimidine bases are added.

The four bases that exist in DNA are Adenine, Guanine, Thymine and Cytosine. They are referenced under Purine and Pyrimidine links posted above.

This molecule is added to the end of a new DNA molecule. It will be added to the 3' end of a new growing DNA molecule.

Skeletal formula of ATP
"Adenosintriphosphat protoniert" by NEUROtiker - Own work. Licensed under Public Domain via Commons.

What is the 3' and 5' end? Deoxyribose and Ribose sugar

The ribose sugar at position two will lose the OH, the 5' position is the one where the long chain of phosphates are added in the top image and this phosphate at position 5' will be bonded to the OH at position 3' seen in the deoxyribose molecule, this reaction will generate a phosphodiester bond.

Phosphodiester Bond Diagram.svg
"Phosphodiester Bond Diagram" by File:Enlace fosfodiéster.png, File:PhosphodiesterBondDiagram.png: User:G3pro (talk) Original uploader was User:G3pro at en.wikipedia.org Derivative work: User:Merops (talk) Derivative work: User:Deneapol (talk) Derivative work: User:KES47 (talk) Text tweaks: Incnis Mrsi (talk) Text tweaks: DMacks (talk)) - File:Enlace fosfodiéster.png. Licensed under CC BY-SA 3.0 via Commons.

And here's the complete reaction

phosphodiester linkage

If you have noticed the negative charge on the Oxygen, then you will notice that Oxygen has one more electron to donate for a covalent linkage. So this electron attacks the O-H bond at the 3' OH of the deoxy-ribose sugar to generate the phosphodiester bond.

So the 3' OH is always a requirement for addition of new bases to a DNA strand. The 5' refers to the dangling 5' end of the first Phosphate, while the 3' refers to the 3' OH of the Ribose sugar at the last base of the DNA. The entire reaction is catalysed by DNA Polymerase

P.S. They are not really free, there are many modifications which make them inert.

So that is why DNA is anti-parallel.

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    $\begingroup$ This answers why DNA strand have polarity but not why they form anti-parallel helices. $\endgroup$ – canadianer Aug 21 '15 at 15:19
  • $\begingroup$ Is there any other way in which DNA polymerase can polymerize the polymerization reaction? $\endgroup$ – FoldedChromatin Aug 21 '15 at 15:23
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    $\begingroup$ Nucleic acids must be added to the 3' OH forming the phosphodiester bond, which is the basis for 5' to 3' direction of DNA, there must always be a 3' OH to add more bases to which is why a Primer is added during replication, or else DNA will not have been replicated, so is that not reason enough for anti-parallelism? $\endgroup$ – FoldedChromatin Aug 21 '15 at 15:33

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