<p>I am trying to design a plasmid for our knock in experiment and wanted to clarify some technical issues.</p>
<p>I wanted to know exactly which components must be included in the plasmid.</p>
<p>I know that I have to include the 5' homology arm , insertion gene sequence, marker sequence and 3' homology arm.
But, I would like to know for certain the following details:</p>
<ol>
<li>Should I take the whole sequence of the gene or do I need to remove the introns/UTR regions or any other unnecessary part of the sequence?</li>
<li>Which sequence should I choose for gene insertion , gene sequence or mRNA transcript sequence?</li>
<li>When designing plasmids, should I insert extra promoters and/or terminators with the insertion genes?</li>
</ol>
<p>Additionally, can you recommend an online tool to design HDR Plasmid?
I have already tried using Alt R HDR design tool and Benchling but our target genome is not available there.</p>

CC BY-SA 4.0
2022-07-30T12:32:54.453Z
Please clarify your specific problem or provide additional details to highlight exactly what you need. As it's currently written, it's hard to tell exactly what you're asking.
Community
CC BY-SA 4.0
2022-08-01T16:13:08.583Z
You would probably get better answers on the [Biology forum](https://biology.stackexchange.com/). It would also help to mention whether you are using a commercial backbone for the plasmid or designing the whole construct from scratch.
Cloudberry
CC BY-SA 4.0
2022-08-04T03:31:26.987Z
Thank you @Cloudberry for your suggesion.
Research HMBR
<gene><genetics><computational-biochemistry><design><crispr>
Which components must be included in the HDR plasmid?
# Which components must be included in the HDR plasmid?

(Asked by: username_0 on 2022-07-30)

I am trying to design a plasmid for our knock in experiment and wanted to clarify some technical issues.

I wanted to know exactly which components must be included in the plasmid.

I know that I have to include the 5' homology arm , insertion gene sequence, marker sequence and 3' homology arm.
But, I would like to know for certain the following details:

1. Should I take the whole sequence of the gene or do I need to remove the introns/UTR regions or any other unnecessary part of the sequence?
2. Which sequence should I choose for gene insertion , gene sequence or mRNA transcript sequence?
3. When designing plasmids, should I insert extra promoters and/or terminators with the insertion genes?

Additionally, can you recommend an online tool to design HDR Plasmid?
I have already tried using Alt R HDR design tool and Benchling but our target genome is not available there.

**Tags:** gene, genetics, computational-biochemistry, design, crispr
> **Comments:**
> **username_1**: Please clarify your specific problem or provide additional details to highlight exactly what you need. As it's currently written, it's hard to tell exactly what you're asking.  
> **username_2**: You would probably get better answers on the [Biology forum](https://biology.stackexchange.com/). It would also help to mention whether you are using a commercial backbone for the plasmid or designing the whole construct from scratch.  
> **username_0**: Thank you @Cloudberry for your suggesion.  

---

## 0 answers

