Mechanism for Solid-Phase Nucleic Acid Deprotection and Cleavage

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In summary, the conversation discusses the task of solid-phase nucleic acid synthesis, specifically the deprotection and cleavage of a carrier with a 2'-O-TOM protected suitable phosphoramidite building block synt. dinucleotide of 5'-UG. The individual is having trouble understanding the task and is asking for guidance. They mention using the Tom method and question which base and protecting group should be used for the second nucleotide.
  • #1
physicisttobe
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Homework Statement
Deprotection and Delaware reaction
Relevant Equations
…
Hi everyone!

I can‘t solve this following task. Can you explain me how I have to draw the mechanism?

Task: Solid-phase nucleic acid synthesis: deprotection and cleavage of carrier with 2'-O-TOM protected suitable phosphoramidite building block synt. dinucleotide of 5'-UG.

I started with deprotection, but how should I continue? The task is a little bit strang. But I hope you understand it.
 

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  • #2
I agree that the task is very vague. Can you list out the steps in the phosphoramidite method?
 
  • #3
Yes, I can do it. But I think the task is about the cleavage and deprotection of a specific functional group. Therefore, I draw the cleavage mechanism. And how schould I draw the deprotection reaction?
I also used the Tom method here. But which base must I use for the second nucleotide? I simply wrote base-acyl because I did not know which base to use. I also dit not know which protecting group to use for the second nucleotide. Therefore, I wrote OPG. Which potecting group should I use for the second nucleotide ? Which would be appropriate?
 

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FAQ: Mechanism for Solid-Phase Nucleic Acid Deprotection and Cleavage

What is solid-phase nucleic acid deprotection and cleavage?

Solid-phase nucleic acid deprotection and cleavage refer to the processes involved in removing protective groups from synthetic nucleic acids and cleaving them from the solid support to which they are bound. These steps are essential in the synthesis of oligonucleotides, allowing the final product to be isolated and purified for further use.

Why are protective groups used in nucleic acid synthesis?

Protective groups are used in nucleic acid synthesis to prevent unwanted side reactions during the stepwise assembly of the oligonucleotide chain. They ensure that only the desired chemical reactions occur at specific sites, allowing for the correct sequence of nucleotides to be synthesized.

What are common methods for deprotection and cleavage?

Common methods for deprotection and cleavage include the use of chemical reagents such as ammonia or methylamine, which can remove protective groups and cleave the nucleic acid from the solid support. Other methods may involve the use of enzymatic reactions or photolabile groups that can be removed by light exposure.

What are the challenges associated with solid-phase nucleic acid deprotection and cleavage?

Challenges associated with these processes include ensuring complete removal of protective groups without damaging the nucleic acid, achieving efficient cleavage from the solid support, and minimizing the formation of side products. Additionally, optimizing reaction conditions to balance speed and yield can be difficult.

How is the efficiency of deprotection and cleavage assessed?

The efficiency of deprotection and cleavage can be assessed using various analytical techniques such as high-performance liquid chromatography (HPLC), mass spectrometry, and gel electrophoresis. These methods allow scientists to determine the purity and integrity of the synthesized nucleic acids and to identify any incomplete deprotection or cleavage products.

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