Find the structure of nucleic acid from proportions of nucleotides

February 9, 2013 1:07 PM

How can you tell the physical and chemical structure of a nucleic acid based on a sample's proportions of nucleotides?

I've tried helping someone find information on the method you'd need to use to solve the problem above, but this is well beyond my understanding. I've pointed her towards some documents which I thought would help, but they didn't.

Yes, this is for a homework assignment, but I am not asking you to identify her samples--a general explanation of the method, or a pointer to one, would be plenty.

I hope it goes without saying that she's checked both her lecture notes and her textbook, and she did not find the answer there. She thinks maybe it was covered in one of the "optional" (not so optional!) books.

posted by johnofjack to science & nature (20 answers total)

Do you mean GC content?
posted by halogen at 1:12 PM on February 9

Can you be more specific? The physical property of a nucleic acid that most people care about in molecular biology is annealing temperature, and you can predict that from GC content. There are calculators online that will do it. They'll want the sequence, but she can just type in random strings with the specified nucleotide proportions.

If you're looking for secondary structure, DNA is almost always a helix (she can check Wikipedia for the two or three different helices) and RNA takes on a variety of shapes depending on its sequence. RNA folding is a major research topic, so there aren't any easy answers there.
posted by d. z. wang at 1:14 PM on February 9

So nucleic acids are always polymers of the same five nucleotides that differ only in the nucleic acid, except for the times they aren't that aren't relevant to you, and thus so long as you know the nucleic acid sequence you then know the chemical structure.

You cannot determine the chemical structure of a nucleic acid strand from just its proportion of nucleotides, generally referred to as its GC content, but you can roughly calculate a number of important properties of the strand. For example its melting temperature and what kind of critter it comes from.
posted by Blasdelb at 1:32 PM on February 9

Having more information about what you are looking for will help us figure out how to explain it.
posted by Blasdelb at 1:40 PM on February 9

I'm told this is the question before the sample results: "You are given three samples of nucleic acid and asked to determine each sample's chemical and physical identity. You use nucleases to completely degrade the samples into their constituent nucleotides and determine their approximate relative proportions. The results are as follows. What can you deduce and why?"
posted by johnofjack at 1:47 PM on February 9

Hello,
I decided to become a member. I would like to ensure my integrity on the matter. This is indeed a question from my assignment, but I am not trying to "cheat". Perhaps, I am misunderstanding the question. The course material does not offer me any help.
posted by iamcharity at 1:51 PM on February 9

Since the nucleases completely degrade the samples into individual nucleotides, I presume that the original sequence is not relevant to the question. Has she tried using OligoCalc? There are a number of parameters such as GC-content as mentioned by others. (But other information such as secondary structures and self-complementarity cannot be determined if the sample has been degraded.)
posted by angermanagement at 1:51 PM on February 9

So is this about DNA vs RNA? What are the listed results?
posted by halogen at 1:52 PM on February 9

I'm having a hard time parsing what "each sample's chemical and physical identity" means. Any hints if that refers to the actual elements that make up the nucleotides or if you're trying to figure out if the nucleotide is an RNA or DNA or something else?
posted by Mercaptan at 1:53 PM on February 9

This is the rest of the question verbatim. Please no spoilers if you can help it. Just tips, hints, suggestions.

Sample 1. dAMP 37% dCMP 12% dGMP 13% dTMP 38%


Sample 2. dAMP 43% dCMP 35% dGMP 15% dTMP 7%


Sample 3. dAMP 35% dCMP 15% dGMP 15% dTMP 10% UMP 25%

One thing that certainly makes no sense to me is that sample 3 has U and T.
posted by iamcharity at 1:56 PM on February 9

Off the top of my head, I can think of "single stranded RNA vs double stranded RNA vs single stranded DNA vs double stranded DNA vs hybrid paired DNA-RNA" as possibilities for "physical identities". Do any of these ring a bell?

Actually, sample 3 can totally make sense... but that might give the answer away.
posted by Mercaptan at 1:59 PM on February 9

So I might guess that it's asking you to deduce if these samples are double stranded DNA, single stranded DNA, RNA or a DNA/RNA duplex.
posted by Cold Lurkey at 2:00 PM on February 9 [3 favorites]

That does sound really familiar. I suppose I could have been expecting something more complicated.
posted by iamcharity at 2:01 PM on February 9

It could be more complicated, what's the class? There's a big difference in the depth of answer for this question depending on whether this is Biology 101 or a graduate level structural biology course.
posted by Mercaptan at 2:02 PM on February 9

my answer to sample 2 was looking something like I would start by rerunning the sample. If that did not resolve the unequal proportions, I would then investigate for mutations like insertions or deletions. I hadn't considered that it would be ssDNA
posted by iamcharity at 2:02 PM on February 9

It is a grad level forensic genetic class online.
posted by iamcharity at 2:03 PM on February 9

Even though it is grad level, it is my first genetics class. anything prior to this was personal curiosity
posted by iamcharity at 2:04 PM on February 9

Oh! Then I think the options of the basic types of double stranded or single stranded or hybrid DNA or RNA are what you're looking for. I doubt you'd be getting into more detail like A-, B- or Z-form DNA or the pitch and rise of bases.
posted by Mercaptan at 2:07 PM on February 9

hmm... yeah she has only covered the basics. Perhaps, she finds it entertaining to see what we come up with. I know I would. Thank you all! or y'all if you prefer
posted by iamcharity at 2:11 PM on February 9

In this sort of situation, I recommending asking the instructor for help/clarification.
posted by leahwrenn at 2:19 PM on February 9