What is the charge on oligonucleotide 5' pGpGpApCpT 3' at pH 7.00?

Question

What is the charge on the nucleotide 5'pGpGpApCpT 3' @ pH 7.00?

I thought adenine has 1 NH group and Guanine has NH and OH groups and cytosine and thymine has OH groups on it and phosphate at 5' end an OH at 3' end .so at pH 2.00-3.00 OH will give away an electron and becomes negatively charged.so is it +2+2-1-1-1 which is -1? please explain?

Does gp mean group? Also, atoms don't become negatively charged by giving away electrons. — canadianer, Dec 02 '14 at 04:55
@canadianer GGACT are the nucleotides and the p stands for the phosphate backbone I presume.. — The Last Word, Dec 02 '14 at 09:57
@TheLastWord No I was referring to something else that was present before the post was edited. — canadianer, Dec 02 '14 at 09:59

score 3 · Answer 1 · answered Dec 02 '14 at 16:10

I didn't quite understand where you're getting all your OH groups, maybe from the enol tuatomers of the nucleotides. I tried to look up the pKa's for the keto tautomers of the nucleotides on Wikipedia1,2,3,4. enter image description here

In general, if pH is below a functional group's pKa, that group will be protonated, and if pH is above pKa, it will be deprotonated, though this is an equilibrium.

If we assume pH of 7 and assume I have the pKas right ( these values are for the free nucleic acids, no deoxyribose attached ), then the primary amines on A, G, and C will be protonated NH3 groups with positive charges.The amides on G and T should remain deprotonated and uncharged.

So with the sequence GGACT, we have 4 primary amines, so 4 positive charges. However, we also have 5 phosphates, each carrying a negative charge, so +4 plus -5 is -1.

Of course all of this goes out the window once we bind that oligonucleotide to another oligonucleotide, I assume the hydrogen bonding will alter the pKas and charges. For all I know, simply attaching the nucleic acids to a deoxyribose and stacking them together changes the pKas.

I don't think the OH group on the 3' terminal deoxyribose would deprotonate, hydroxyl groups don't usually deprotonate at neutral pH unless something is pulling electrons away to stabilize the negative charge, such as the carbonyl in carboxylic acids. For example phenol has pKa of 9.99, while benzoic acid has pKa of 4.2. — user137, Dec 02 '14 at 20:22

score 0 · Answer 2 · answered Jun 21 '20 at 19:01

There is no positive charge on the bases at pH 7, but there are 4 phosphodiester bonds which have -1 charge on each phosphate so total -4 also the terminal Phosphate at 5' end is free so it has a charge of -2. Thus the overall charge of the oligonucleotide is -4-2=-6 (determined by number of phosphate groups)

score -1 · Answer 3 · answered Feb 26 '20 at 15:56

-1

There is no positive charge on the bases at pH 7, thus the overall charge of the oligonucleotide is -4 (determined by number of phosphate groups)... See details here: https://books.google.cz/books?id=v9HL5VyRmZcC&lpg=PA204&ots=DQYKZ9PxXg&dq=why%20amino%20group%20of%20nucleo%20bases%20protonated&pg=PA204#v=onepage&q=why%20amino%20group%20of%20nucleo%20bases%20protonated&f=false

answered Feb 26 '20 at 15:56

user57040

1

3

It's unclear which text you are referencing in the linked book. Can you quote the relevant portion? – acvill Feb 26 '20 at 16:54
Welcome to Biology.SE! Answers are much more likely to receive a favorable response if you include supporting references (primary literature is best) that other users can access — note the language this site uses is English. Without that support, your answer is indistinguishable from opinion. A good example of how to format references. ——— You may also want to take the [tour] and then consult the help pages for additional advice on [Answer] effectively on this site. Thank you! – tyersome Feb 26 '20 at 21:27

What is the charge on oligonucleotide 5' pGpGpApCpT 3' at pH 7.00?

3 Answers3