Question about principle of PCR - (Oct/06/2010 )

Lets say i have a set of primer to amplify a 100 bp fragment. The forward primer binds and extend. But what makes it stop at the 100th base of my interest? Why doesn't it extend further? OR it does extend further? If so, why is the product 100bp and not longer than that?

Even if the forward primer bind to the fragment created by reverse primer to synthesis a 100 bp fragment, fragments longer than 100 bp from direct priming with original template will continue to exist. Original template will also be repeatedly amplify to produce fragment longer than 100bp. Why does agarose gel show only 1 band? Does this make gel excision purification more efficient than column purification?

It does extend onwards for the first couple of rounds as the template DNA is mostly from the genome. However, each time a primer binds to a strand produced by the PCR, it results in a product as below and from then on, can get no longer so with each cycle you end up producing more and more strands of the same size...

TTT= forward primer, GGG=reverse primer >>>>> = pcr product

Genomic sequence: CTCGTAGTCTGCTCAAACGGATTA......TCAGCTACGACGATGGGGGATCGTACGATCGTAGC
1st product: TTT>>>>>>>>>>>>>>>>>>>>>>>>>>>>>CCC>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>
2nd product: AAA<<<<<<<<<<<<<<<<<<<<<<<<<<<<<GGG


bob1 on Fri Oct 8 01:50:03 2010 said:

Correct, too small an amount of DNA is produced by the first product to be seen on a gel, though amounts of this will be produced at each cycle, so you will get roughly 30 copies (assuming one copy at the start).

In theory the product could be as long as the strand of DNA it is on. However, in practise this is limited by extension time and the type of polymerase used. With Taq the maximum product size is a about 10 kbp I think.