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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1. What is a solid-phase nucleic acid deprotection and cleavage mechanism?

A solid-phase nucleic acid deprotection and cleavage mechanism is a process used in molecular biology to remove protecting groups from nucleic acids and cleave them from a solid support. This allows for the purification and isolation of the desired nucleic acid sequence.

2. How does the mechanism work?

The mechanism involves the use of chemical reagents that selectively remove the protecting groups from the nucleic acid while it is still attached to a solid support. This is typically achieved through a series of chemical reactions that target specific functional groups on the nucleic acid.

3. What are the benefits of using solid-phase nucleic acid deprotection and cleavage?

Using this mechanism allows for the purification and isolation of specific nucleic acid sequences, which is crucial in many molecular biology experiments. It also reduces the risk of contamination and simplifies the purification process by eliminating the need for multiple purification steps.

4. Are there any limitations to this mechanism?

One limitation of this mechanism is that it requires specialized equipment and reagents, which can be costly. It also requires careful optimization and can be time-consuming, especially for larger nucleic acid sequences.

5. What are some common applications of solid-phase nucleic acid deprotection and cleavage?

This mechanism is commonly used in DNA and RNA synthesis, as well as in the production of oligonucleotides for use in PCR, sequencing, and other molecular biology techniques. It is also used in the production of synthetic genes and in the development of gene therapies.

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