Reduction of Dihydrouridine using Sodium borohydride or potassium hydroxyde

[P. Lombard]

Hello everyone, 
I'm a master's student in Biology and I'm facing a problem understanding the difference between the 2 reactions. I'm not specialized in chemistry or organic chemistry and have the basic knowledge.
In an experiment one of my predecessors did, he used NaBH4 to react with Dihydrouridine (see file), and the modification occurs on the base (not the sugar), causing either a cycle opening or a reduction of the carbonyl group (I don't even know if both are correct, so do tell me about these reactions please). This was the positive control because once this step is done, he uses the newly-produced compound to react with NH2-Rhodamine (how can it attack the new compound ?).

What's more, the negative control is a reaction using KOH, so OH-, which seems to cause a cycle opening too... So, how can it be that these 2 reactions that are opening the cycles react in different ways when labelling with Rhodamine-NH2 ? 

Thanks in advance for every answer !!

[chenbeier]

Here a paper about it

https://journals.plos.org/plosbiology/article?id=10.1371/journal.pbio.3001720

Borhydride reduce the Uracil amid part. KOH do a hydrolysis of amid.

 

[exchemist]

34 minutes ago, P. Lombard said:

Hello everyone, 
I'm a master's student in Biology and I'm facing a problem understanding the difference between the 2 reactions. I'm not specialized in chemistry or organic chemistry and have the basic knowledge.
In an experiment one of my predecessors did, he used NaBH4 to react with Dihydrouridine (see file), and the modification occurs on the base (not the sugar), causing either a cycle opening or a reduction of the carbonyl group (I don't even know if both are correct, so do tell me about these reactions please). This was the positive control because once this step is done, he uses the newly-produced compound to react with NH2-Rhodamine (how can it attack the new compound ?).

What's more, the negative control is a reaction using KOH, so OH-, which seems to cause a cycle opening too... So, how can it be that these 2 reactions that are opening the cycles react in different ways when labelling with Rhodamine-NH2 ? 

Thanks in advance for every answer !!

From @chenbeier's link it looks as if NaBH4 reduces one of the carbonyls to a hydroxy group, i.e. form dihydro to tetrahydrouridine. So that does not open the ring. Hydrolysis of the amide with KOH will open the ring of course and, by the look of it, may evolve ammonia and CO2, destroying it completely. 

[chenbeier]

The aminale RCH(OH)NHR' is also not very stable according Erlenmeyer.

Edited May 3, 2023 by chenbeier