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Is it because heterozygotes have a greater base pair length? (And if they do, why is that?) Or is it because recessive alleles are moving slower than the dominant alleles in the gel?

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    $\begingroup$ If a loci is heterozygous there are two different alleles coding for the same Protein. The alleles may differ in their lengths. With a gel electrophoreses you split DNA fragments by their length. Homozygous -> same alleles -> same length -> one band. | Heterozygous -> different alleles -> different length -> two bands Is this what your question was about? $\endgroup$
    – Oli4
    Feb 4, 2015 at 21:54
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    $\begingroup$ Your question is the answer. Hetero = different, thus you have two different bands, representing two versions/alleles of one gene. Homo = equal, thus you only have one version of a gene. These alleles may differ in length and/or restriction sites, resulting in different bands, because electrophoresis is based on molecular weights. $\endgroup$ Feb 4, 2015 at 22:12
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    $\begingroup$ It depends what molecule you are running on the gel and how it was treated beforehand. Are you referring to restriction fragment length polymorphisms of DNA, or another type of assay? You need to understand the method to understand the result! $\endgroup$
    – Teige
    Feb 5, 2015 at 0:31
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    $\begingroup$ Okay @ChrisStronks, boss is away today and no work pending. So passing time by digging old unanswered questions :) Will post it as an answer. $\endgroup$
    – WYSIWYG
    Feb 26, 2015 at 9:52
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    $\begingroup$ @ChrisStronks Thanks. I had tried to answer some other old questions. Please have a look at them and let me know if anything else is needed. The answered question had gone down by 1% : so all this effort :P $\endgroup$
    – WYSIWYG
    Feb 26, 2015 at 10:31

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A heterozygous locus has two different alleles and therefore it is possible that their DNA sequence lengths are different. However, it is unlikely that they are so different so as to be clearly resolved in a gel electrophoresis. Agarose gels can at best resolve 20bp; polyacrylamide gels can resolve smaller differences but it is only done for small DNA fragments.

I think upto 50bp difference is possible between alleles. But such huge insertions/deletions are rare and the difference between the alleles is usually a point mutation or small insertions/deletions(indels). Big indels are possible when a transgene is inserted specifically in one chromosome; these cases are mostly experimental.

If you consider paralogs as alleles then they can be of different lengths and can be resolved in agarose gels— usually the difference is in the untranslated regions. If you are doing Southern blot and using a probe that can bind to both paralogs then you will end up getting two bands.

Having said that, it is possible to see a difference in gel bands even if there is no size difference. This is possible by a technique called RFLP. In this technique the DNA is digested using a restriction enzyme which basically cuts the DNA at a specific sequence (usually a hexamer). If a point mutation abolishes or creates a restriction site then the fragment length would be different between the alleles. This is detectable on the gel.

A similar technique is AFLP.

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  • $\begingroup$ the restriction enzyme analyses are an interesting addition for sure $\endgroup$
    – AliceD
    Feb 26, 2015 at 10:26
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Heterozygous loci have both alleles present at a given time, for example Aa (considering diploid organism), where as homozygous have only one type (AA or aa). Generally, both alleles have different sequence lengths due to deletions, insertions etc. so if any locus is homozygous, it will produce only one length but heterozygous will produce two different lengths. That is why you will only see one band in case of homozygous and two in heterozygous.

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    $\begingroup$ Why would AA, Aa, and aa produce different lengths if they each contain two alleles? Shouldn't they each project two different bands on the gel? $\endgroup$ Mar 1, 2015 at 22:49
  • $\begingroup$ Only Aa would produce two bands but AA and aa would produce only one band. Imagine, for example, allele 'A' has length 100bp, allele 'a' has length 95bp. So if an individual is only AA, it will produce two bands, one for each A and A but since both of them are same length, they will overlap and appear as only one band on gel. Similar is the case for 'aa' individual. However, when Aa individual produce two bands they differ in length, so it will produce one band at 100bp and one at 95bp. Hope this helps. $\endgroup$
    – nsinghphd
    Mar 16, 2015 at 4:58

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