Body: <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>
  
Comments.ContentLicense: CC BY-SA 4.0
Comments.CreationDate: 2022-07-30T12:32:54.453Z
Comments.Text: 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.
Comments.UserDisplayName: Community
Comments.ContentLicense: CC BY-SA 4.0
Comments.CreationDate: 2022-08-01T16:13:08.583Z
Comments.Text: 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.
Comments.UserDisplayName: Cloudberry
Comments.ContentLicense: CC BY-SA 4.0
Comments.CreationDate: 2022-08-04T03:31:26.987Z
Comments.Text: Thank you @Cloudberry for your suggesion.
Comments.UserDisplayName: Research HMBR
Tags: <gene><genetics><computational-biochemistry><design><crispr>
Title: Which components must be included in the HDR plasmid?
ThreadText: # 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 @username_2 for your suggesion.  
  
  ---
  
  ## 0 answers
  
  