How to Design Tetra-ARMS Primers for Mutation Identification? | Lecture 451 | Dr. Muhammad Naveed

🎓 “Tetra-ARMS PCR: Practical Primer Design for Mutation Screening!
📚 Description:

In this lecture, you’ll learn exactly how to design Tetra-ARMS primers for accurate and cost-effective mutation identification. We start by explaining the basic principle of Tetra-ARMS PCR — how four primers (two outer and two allele-specific inner primers) allow you to distinguish wild-type, mutant, and heterozygous genotypes using simple PCR and agarose gel electrophoresis.

You’ll see how to prepare your target sequence, locate the mutation site, and design the outer primers that act as a control amplicon. Then we move step-by-step through designing the inner allele-specific primers, including how to place the SNP at the 3′ end, how and why to introduce a deliberate mismatch, and how to ensure clear size separation of the PCR products.

The lecture covers:

Understanding Tetra-ARMS PCR and how the four primers work

Preparing your reference sequence and marking the mutation

Designing outer primers with correct Tm, GC content, and product size

Designing allele-specific inner primers with high discrimination

Choosing the right mismatch type and position

Ensuring distinct amplicon sizes for clear gel interpretation

In-silico checking for Tm, hairpins, dimers, and product prediction

Example walkthrough with complete primer sets

PCR setup, annealing considerations, and primer concentration tips

Reading gel results for homozygous wild, homozygous mutant, and heterozygous samples

Common troubleshooting mistakes and how to fix them

Validation strategies and essential controls

By the end, you’ll be able to confidently design your own Tetra-ARMS primers for SNP detection and mutation screening, with a clear workflow you can apply to any gene or variant.

If you want a template, checklist, or help designing primers for your own SNP, just comment with your sequence and mutation position — I’ll guide you through it.
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About Prof. Dr. Muhammad Naveed
(World’s Top 2% Scientists)
Prof. Dr. Muhammad Naveed, from the University of Central Punjab, Lahore, Pakistan is a renowned researcher ranked among the world’s top 2% scientists by Stanford University and Elsevier. He earned his Ph.D. in Biotechnology (Genomics & Bioinformatics) from Quaid-i-Azam University, Islamabad, and completed his postdoctoral research in Bioinformatics at Jiangsu University, China, along with pre-doctoral research at the University of Ghent, Belgium. Recipient of HEC's Indigenous and IRSIP scholarships, he was named Best Ph.D. (IRSIP) Scholar of the Year in 2013 and honored as a Distinguished Alumnus by Quaid-i-Azam University in 2017. His research spans Bioinformatics, Molecular Biotechnology, Nano-informatics, vaccine development, and drug design against infectious diseases. He has supervised over 90 MSc, 80 MPhil, and 2 Ph.D. students, and has published 304 research articles with a cumulative impact factor of 4470.86, over 22,560 citations, H-Index 45, one book, six book chapters, and five patents. His excellence in research has earned him multiple accolades, including the Prof. A.R. Shakoori Gold Medal (2025) and the “Researcher of the Year” award from the University of Gujrat (2016) and the University of Central Punjab (2018, 2019, and 2021).

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