> Because nucleic acids have a polarity like protein, too (biosynthesis), > which run from *.O5* to *.O3* a small arrowhead on the 3* end would be > nice and I like the rendering of the bases as plates like MIDAS or > MolMol do, e.g. on: > http://www.imb-jena.de/cgi-bin/ImgLib.pl?CODE=264d
I don't really understand this. I have never seen MIDAS nor MolMol.
Please see http://www.umass.edu/microbio/rasmol/molmol.gif This illustrates the nucleic acid base plates. I agree that (eventually) doing these plates in Jmol would be very very nice.
I also agree that arrowheads points on the 3' ends of backbones would be good.
To understand 5' vs. 3', please see the chime images at
http://molvis.sdsc.edu/dna/index.htm
specifically the chapter Ends and Antiparallellism
http://molvis.sdsc.edu/dna/fs_ends.htm
unprimed numbers refer to atoms in the base, while primed numbers refer to atoms in the ribose. Synthesis and reading of the code go from 5' to 3', cf. for proteins synthesis goes from N terminus to C terminus.
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