|MadSci Network: Molecular Biology|
Dear Man, This is a question whose answer can only be opinion - informed opinion, hopefully, but I think it is opinion nonetheless. Let me give you mine, based on my own thinking. If I were you, I would run this question past some other people to get their ideas as well. Not only is the genetic code read in the 5-3 direction, its also replicated in that direction. One strand (the leading strand) is copied linearly, and the other (the lagging strand) is copied in a series of short pieces (called Okazaki fragments after their discoverer) which are then ligated into a single long molecule. I suspect that the main reason DNA is both transcribed and replicated in the 5-to-3 direction is that if these processes could proceed in either chemical direction, you would obviously have a terrible problem. Genes encoded by DNA sequences would be ambiguous instead of specific and replication would be much more problematic if you could start at either end and/or go in either direction. While some organisms (especially in the viral world) may make use of both strands of a given stretch of DNA to encode proteins and even use "nested" sequences to read more than one message in different frames from a given sequence, they always follow only the 5-to-3 direction when reading or replicating the genome of that strand. Since reading and replicating in both directions wouldnt work, evolution had to favor a system that was uni-directional. Im not certain there are any inherent chemical advantages in going 5 to 3 rather than 3 to 5 that one could determine a priori, that is before the evolution of directional polymerases. I would guess that it just worked out that way based on some extremely early evolutionary events. The success of the directed use of DNA (or perhaps it was RNA in the primordial evolutionary events) then became locked into the evolutionary program by virtue of its success. In an analogous case, we have only the l-amino acids, not their d-isomers, used universally in protein synthesis by all of life. Again, no one is certain why one was "chosen" by evolution, but I believe it probably reflects another very early evolutionary solution to a serious problem of ambiguity. I hope this helps, and keep thinking! Paul Odgren Cell Biology Univ. of Massachusetts Medical School Worcester MA USA
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