|MadSci Network: Genetics|
Really, the best way to answer this question is to ask your professor! It is really impossible for someone else to know exactly what he or she was thinking. However, since you asked us, I will offer some possible explanations.
First, a brief summary of the differences between DNA and RNA. I assume that you already know these, and I am enumerating them here only for emphasis. If you aren't familiar with these differences, you should review related answers in the archives, and a biochemistry and molecular biology textbook.
The differences are both chemical and functional. Chemically, the ribose sugars in RNA molecules have one more hydroxyl (-OH) group on the than the deoxyribose sugars in DNA molecules. This is why RNA stands for ribonucleic acid, while DNA stands for deoxyribonucleic acid.
Where dexoyribose has a 3' and a 5' -OH group, ribose has a 2', 3' and a 5' -OH group. It is the presence of this 2' -OH that makes the RNA molecule much less stable than the DNA molecule. Under high-pH conditions, the 2' -OH can spontaneously interfere with the phosphodiester bond between the 3' -OH and the phospate group in the RNA molecule, essentially breaking the RNA polymer into monomers. There are also many RNase enzymes in the environment that will rapidly degrade RNA using this mechanism.
So, chemically, RNA is simply harder to work with than DNA because it is less stable. It takes more effort and precaution to work with RNA than DNA, so that makes DNA more attractive for studies.
Functionally, DNA is used to store all of the information in an organism's genome for the long term (the life of the organism), while RNA is only used to transport information transiently, and it is only used to transport information for genes that are being expressed. Expressed genes make up only a small fraction of the information in an organism's genome, so while the expressed genes may be an important part of the genome, you cannot easily survey all of the organism's genome using RNA.
In addition, mature RNA is spliced, which means that the intron-sequences have been removed. So, you are going to see even less of the information associated with a gene.
Perhaps most importantly, because the information in expressed genes is so crucial, those genes and their products are under a very strong selection pressure. In some cases, this selection pressure can obscure the relationships between organisms, making two organisms seem more or less related to each other than they actually are. When we look for genetic markers to study the relatedness between organisms, we want to identify markers that are not under selection (so-calle neutral markers). Considered in the aggregate, these markers will give us the best idea of the degree of relatedness between two organisms.
It just happens that the part of the genome that does not include genes does include quite a lot of these neutral markers. This is not simply a coincidence; there is a much lower selection pressure in much of the non-coding portion of the genome. So, a large number of these neutral markers are never copied from DNA to RNA, and they would never be seen in RNA molecules.
So, there are my three reasons why DNA is more useful for studying relationships between organisms than RNA. First, DNA is easier to work with than RNA. Second, RNA represents only a limited portion of an organism's genome, while DNA represents all of it. Third, there are many more neutral markers (which are useful for determining relatedness) available in DNA molecules, because the DNA represents the entire genome, than in RNA.
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