Week 3 – Description of PCR Process

Christopher Y -

Hello everyone,

I spent Monday to Wednesday at the senior trip and was unable to make much progress this week. However, over the weekend I was able to start some bioinformatics that I will use next week. Currently, my plan for week 4 is to analyze breast cancer data from cbioportal.org and examine my last restriction enzyme digest. I plan to start hands-on lab work in week 5 after an orientation on Monday.

The PCR process I used to clone the Cxcr3 mutant gene is shown in the image below (Fig. 1). As shown in the image, designing an early stop codon with the complementary nucleotide bases allowed the PCR to clone the gene shorter than it would be normally. As a result, the gene expression of the mutant would be lacking amino acids that the missing nucleotides encoded for.

Diagram showing primers used in PCR process to create shortened Cxcr3 mutant.
Fig. 1. Diagram showing primers used in PCR process to create shortened Cxcr3 mutant.1

1Figure 1 Created with BioRender.com

Thank you for reading my blog post. Once again, feel free to leave any comments. I look forward to updating this page as I start doing more intense work following this senior trip week.

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Comments:

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    camille_bennett
    Hi Christopher, fascinating work and great image to demonstrate. What would be the impact of lacking amino acids in the gene expression?
    March 4, 2025 at 9:50 am - Reply
    christopher_y
    Hello Ms. Bennett, thank you for the question! By creating a mutant lacking amino acids that make up the end of Cxcr3, I can test if the cancer cell migration is dependent on that c-terminal part.
    March 11, 2025 at 1:48 am - Reply
    William Schaffer
    Just curious, how many times did you clone your mutant gene using PCR? Great to utilize stop codon to set a limit for the copy.
    March 12, 2025 at 2:49 pm - Reply

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