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Discussion of all aspects of biological molecules, biochemical processes and laboratory procedures in the field.
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DNA 3' end & 5' end

Tue Jul 19, 2011 1:50 am

I can't quite grasp the "ends" of DNA.
When we say "3' end", does it mean that we can only add the nucleotides to the 5's, and not the 3's?
Also, why are there "ends" in the first place?

Tue Jul 19, 2011 6:16 am

because the strands are not indefinite? ;)

What do you mean by "When we say "3' end", does it mean that we can only add the nucleotides to the 5's, and not the 3's?"? (that's kind of contrary, isn't it?

Tue Jul 19, 2011 11:00 pm

Do you know about phosphodiester linkages? Each nucleotide is bound to the other (in the same chain) by these, and they are between the phosphate groups and terminal hydroxyl groups. The end starting with the phosphate is the 5' end and the terminal hydroxyl end is the 3' end. DNA runs antiparallel. When DNA is being constructed nucleotides are most easily added to the 3' end, so that is the direction of chain elongation. Think of it like a stream, which is also why the terms upstream and downstream are used. 5' is the waterfall. Each strand has its end, but they are opposite of each other. Does that help?

Wed Jul 20, 2011 1:40 pm

Sorry for jumping in the discussion. The explanation of plasmodesmata11 is complete for me to understand Yuuki's question. But it raises an other related question: so the DNA molecule has two strands twisting together and orienting in opposite directions (3' -> 5' and 5' -> 3'). It looks to me that the double DNA is symmetric in two directions, so why it again twists itself in only one direction of the clock, but not the other way around? And apart from the twisting structure, is there any other asymmetry biological effect the double strand DNA molecule, say for example: replication in one direction (of the double strand, say from the long arm of chromosomes to the short arm of chromosomes, I do not mean the difference between lagging and leading strand...) is better than the other?
Hope I did not drive the topic so far away...
Thanks.

Wed Jul 20, 2011 3:13 pm

actually, the DNA can be both left-turning and right-turning, look for forms of DNA (A, B and Z;)

Both strands are transcribed, equally I would say.

Wed Jul 27, 2011 1:36 am

Yeah, to add to what Jack said there are several forms of DNA, usually depending on how hydrated they are or what nitrogenous bases they contain. There can be left or right hand helices, the measurements between the bases can be wide or short, etc. There are forms B (biological), A (dehydrated), C (more dehydrated), D and E (no guanine), P (interior phosphates), and Z, which has only C-G bonds

Sat Jul 30, 2011 6:05 pm

interior phosphates? Do you have any paper about the helices D, E and P? Is it natural or only something artificial?
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