[Haribo]

Hi all,

currently I'm working on the synthesis of oligonucleotides (on resin). according to literature and procedures aqueous ammonium hydroxide is used to deprotect the protecting groups of the nucleobases and to cleave the oligonucleotide from the solid support. When observing the mechanism, it's OH- which attacks the carbonyl group of the solid support and the protecting groups, resulting in deprotection/ cleavage. The mechanisms don't mention anything about the role of NH4+ in the reaction. So why is aqueous ammonium hydroxide needed for this reaction and is NaOH for instance not a possible deprotection reagent?

[Arkcon]

Ease of removal basically.  The final step is often evaporating  off the ammonia.  You may also want a gentler base.  For example, oligoribonucleotide may be cleaved/deprotected with dimethylamine, either alone or mixed with ammonia.

[Haribo]

Ease of removal basically.  The final step is often evaporating  off the ammonia.  You may also want a gentler base.  For example, oligoribonucleotide may be cleaved/deprotected with dimethylamine, either alone or mixed with ammonia.

I don't think that  ammonia is only used because of the ease of evaporation. Other alternative deprotection conditions mostly contain a combination of hydroxide and ammonia ions. Furthermore the oligonucleotide is stable when treated with (20%) diethylamine or dimethylamine. only the backbone protecting is cleaved then, but the solid support and nucleobases stay intact.

[Haribo]

could it have something to do with the temperature? deprotection and cleavage is performed at high temperatures (50 Celsius)

[Babcock_Hall]

Which is the stronger base, NaOH or ammonium hydroxide?

[Haribo]

Which is the stronger base, NaOH or ammonium hydroxide?

NH4OH has a pKa of 9.3 and NaOH a pKa of 14.8 at 25C. This would mean that NaOH is a stronger base at r.t.

[Babcock_Hall]

Do you see any bonds in oligonucleotides that might be susceptible to alkaline hydrolysis?

[Haribo]

Do you see any bonds in oligonucleotides that might be susceptible to alkaline hydrolysis?

All the nucleobases have carbonyl protecting groups and the solid support is attached with an ester linkage, both are susceptible to alkaline hydrolysis.

[Arkcon]

What do you know about the reactivity of fully deprotected, cleaved oligonucelotides against base hydrolysis?

[Haribo]

What do you know about the reactivity of fully deprotected, cleaved oligonucelotides against base hydrolysis?

I've mentioned everything I know... 
I think that my oligonucleotide would degrade or that the N-glycosidic bond would cleave??

[Babcock_Hall]

I am not sure what the right answer is in this case, but the glycosidic bond is subject both to acid-promoted and base-promoted cleavage;
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2918718/