I conducted the RFLP and electrophoresis experiment, and i analyzed the size of every band by image J. after i calculated the size of every band, i found the size of PCR product is 434 bp, and the band of restriction enzyme digestion is 238 and 156 bp, respectively. Here comes my question, aren't the size of PCR product and that of the sum of its RFLP product the same? what factors cause such difference?
If you had a second cut site of about 30 bases it might be too weak to show on agarose gel. To answer your question ...no the sum of the parts is not always equal to the whole fragment. The speed of fragments running in agarose depends on run voltage,size and shapeof the dna fragment...the last 2 changing the viscosity of the molecule in the gel. Once you have cut the fragment then the 2 cut fragments have single stranded ends and are smaller than the original so they can fold and form different conformations in non denaturing agarose. The ends may stick out of the folded dna and change both shape and total solvation of the fragment causing it to run differently from expectation.
You can also see a similar effect with different concentrations of agarose when running marker dyes which will run at different sizes in different gel concentrations and also the different sizes of the same plasmid dna in agarose gels which depends on shape and not size
In theory, the smaller fragments should add up to the size of the larger band. But, as Paul Rutland said, DNA doesn't always migrate just based on it's size.
Also, double-check that you don't have a error in estimating the expected sizes of your PCR products. 238 + 156 = 394. You could easily be off by 100 bases.
the smaller fragments should add up to the size of the larger band
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