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DNA traversal

Discussion of all aspects of biological molecules, biochemical processes and laboratory procedures in the field.

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DNA traversal

Postby geoffrey » Wed Mar 25, 2009 1:09 am

How do the enzymes involved in DNA replication (and similar processes) traverse a strand of DNA? The more I think about this seemingly trivial question, the more problems I find:

- they need to maintain forward motion along the strand.

- some parts of the process need building blocks such as nucleotides from the surrounding environment. Surely they need to control the speed of traversal in case there's a shortage of resources?

- how do they avoid getting confused if there's a collision with another DNA strand?
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Postby MrMistery » Wed Mar 25, 2009 4:02 am

look up the trombone model of DNA replication. it's too complicated to explain here.
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Re: DNA traversal

Postby geoffrey » Wed Mar 25, 2009 6:27 pm

Thanks for the suggestion, I've been able to find a few more details about the process with that term. However I haven't been able to find anything that explains how the speed of traversal is regulated.
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Postby MrMistery » Thu Mar 26, 2009 1:56 am

Speed of traversal? You mean how fast DNA polymerase moves along DNA? That's mostly dependent on the inherent properties of each DNA polymerase, and for some polymerases ( the main one for DNA replication included) it is greatly increased by the sliding clamp.
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Re: DNA traversal

Postby geoffrey » Thu Mar 26, 2009 6:28 pm

It's not so much the speed of traversal as how that speed is controlled.

Logically, in order to perfectly copy the DNA it's critical that the polymerase moves along the strand no faster than it's able to attach nucleotides. I would imagine the rate at which is attaches nucleotides is variable (since it has to gather them from the surrounding environment). Is there a (known) mechanism for regulating the speed, or does it perhaps just move relatively slowly and hope for the best?

I'm still stuck on a more basic point as well - what powers the movement of the polymerase in the first place.
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