A Comprehensive Guide on How to Calculate the Size of a DNA Band on a Gel

How do scientists determine the size of DNA bands on an agarose gel? In this guide, I will walk you through the step-by-step process of calculating the size in base pairs of a DNA band on an agarose gel. 

Blog Bonus: Free information sheet summarising the video and the steps - download.

 

Introduction

When working in a lab and running an agarose gel, you may need to determine the size of the DNA fragment, and this information may be crucial for various biological research applications. 

This approach is also described in the following video:

Setting Up the Experiment

Imagine you have loaded a DNA ladder with known sizes in one lane and your DNA sample with an unknown size in another lane of the gel and you get a result that looks like this when the gel has been run.

Before you can calculate the size of your DNA band, you must first label the gel and collect data to create a calibration curve.

Data Collection and Analysis

By measuring the distances the DNA bands in the ladder (see below) have moved and plotting the log values of their sizes against the distances travelled in millimetres (or you can do it in pixels), you can create a calibration curve. This curve will help you accurately determine the size of the DNA band in your unknown sample.

The image below shows the gel and the data table for the plot.

From the table, you plot the calibration curve.

Calculating the Size of the DNA Band

After plotting the calibration curve (above) and identifying the distance your unknown band has travelled, you can use the curve to determine the size of the DNA band in base pairs. By following a simple formula involving logarithms, you can convert the log value to the actual size in base pairs.

Conclusion

Calculating the size of a DNA band on an agarose gel requires careful data collection, analysis, and interpretation. By following the steps outlined in this guide, you can confidently determine the size of DNA fragments in your samples. 

If you would like to support my blogging efforts, then please feel free to buy me a coffee at https://www.buymeacoffee.com/drnickm

Blog Bonus: Free information sheet summarising the video and the steps - download.

Additional Resources

• 📗 - Maths and Chemistry Refresher for Life and Biomedical Scientists
• 📗 - Catchup Chemistry (affiliate link to the book)
• 📗 - Catchup Maths and Stats (affiliate link to the book)

New video posted: DNA Cloning - how to overcome some common problems

In this video, I examine the step-by-step process of cloning DNA into plasmids and address common challenges faced in the lab. I start by preparing the DNA and then move on to using restriction enzymes like EcoRI and HindIII. I explain the importance of choosing the correct enzyme pairs to prevent self-ligation and ensure the correct orientation of the insert. I also cover the blue-white selection method to verify successful cloning and discuss using different vectors for larger DNA segments. 

     

If you would like to support my blogging efforts, then please feel free to buy me a coffee at https://www.buymeacoffee.com/drnickm

Blog Bonus: Free information sheet summarising the video and defining the key terms - download.

 

Additional Reading

The video was produced with help from the following resources:

• 📗 - The Biosciences Glossary
• 📗 - Molecular Biology of the Cell (Alberts) - (affiliate link)
• 📗 - Molecular Cell Biology (Lodish) - (affiliate link)
• 📗 - Biochemistry (Stryer) - (affiliate link)

New video posted: DNA Cloning - how do we clone DNA in the lab?

In this video, I give a brief introduction to the subject of DNA cloning.

DNA cloning is an important lab skill that all life and biomedical science students should possess. In the video, I provide a summary of in vivo and in vitro cloning, along with the key steps, tools and methods you would use.

If you would like to support my blogging efforts, then please feel free to buy me a coffee at https://www.buymeacoffee.com/drnickm

Blog Bonus: Free information sheet summarising the video and defining the key terms - download.

 

Additional Reading

The video was produced with help from the following resources:

• 📗 - The Biosciences Glossary
• 📗 - Molecular Biology of the Cell (Alberts) - (affiliate link)
• 📗 - Molecular Cell Biology (Lodish) - (affiliate link)
• 📗 - Biochemistry (Stryer) - (affiliate link)

New video posted: Gene Regulation - how do cells control the expression of genes?

I have just posted a video that looks at the complex processes of gene regulation and protein production within cells. In the video, I explore six key stages where cells regulate protein synthesis, ensuring precise protein production according to cellular needs. These stages include:

1. Transcriptional Control: The initiation of RNA production and the involvement of transcription factors.
2. RNA Processing: The conversion of pre-messenger RNA to mature mRNA, including splicing and editing.
3. Transport and Localisation: The transportation of mRNA to the correct cellular locations for protein synthesis.
4. Translational Control: Regulation of mRNA translation within the cellular environment.
5. RNA Degradation: Mechanisms that determine the lifespan of mRNA molecules.
6. Protein Regulation: Various methods cells use to control protein activity, such as chemical modifications and localisation.

If you would like to support my blogging efforts, then please feel free to buy me a coffee at https://www.buymeacoffee.com/drnickm

Blog Bonus: Free information sheet summarising the video and defining the key terms - download.

 

Additional Reading

The video was produced with help from the following resources:

• 📗 - The Biosciences Glossary
• 📗 - Molecular Biology of the Cell (Alberts) - (affiliate link)
• 📗 - Molecular Cell Biology (Lodish) - (affiliate link)
• 📗 - Biochemistry (Stryer) - (affiliate link)

New video posted: Translation - making proteins from DNA - decoding mRNA to make the protein

This is the second of two videos on how cells make proteins using DNA. In the first video, I looked at the first step, which is making the messenger RNA (mRNA) a process called transcription - Transcription - making proteins from DNA - the mRNA.

In this video, I will guide you through the process of producing the protein from the mRNA, also known as translation. I will look at the coding problem (how many mRNA bases do you need to code from an amino acid), the number of reading frames in a DNA molecule, and how the cell produces protein from the mRNA.

  

If you would like to support my blogging efforts, then please feel free to buy me a coffee at https://www.buymeacoffee.com/drnickm

Blog Bonus: Free information sheet summarising the video and defining the key terms - download.

 

Additional Reading

The video was produced with help from the following resources:

• 📗 - The Biosciences Glossary
• 📗 - Molecular Biology of the Cell (Alberts) - (affiliate link)
• 📗 - Molecular Cell Biology (Lodish) - (affiliate link)
• 📗 - Biochemistry (Stryer) - (affiliate link)

New video posted: Transcription - making proteins from DNA - the mRNA

This is the first of two videos on how cells make proteins using DNA. The second video looks at how we go from messenger RNA (mRNA) to protein - Translation - making proteins from DNA - decoding mRNA to make the protein

In this video, I will guide you through the first steps in the process of producing RNA from DNA, also known as transcription. In the next video, we will take the next step and examine how we produce the protein from mRNA.

The video looks at the five steps of mRNA production:

• initiation — activators bind upstream, often thousands of bases upstream, of the gene. The activators assemble the required proteins (the mediator, chromatin remodelling complex, the RNA polymerase and transcription factors) at the TATA box, which is a DNA sequence close to the gene
• production — DNA is transcribed into the pre-messenger RNA
• five prime capping — the five prime end of the pre-messenger RNA is capped with some modified nucleotides
• splicing — introns are spliced out of the pre-messenger RNA to leave just the exons (exons provide the sequence for the protein)
• three prime polyadenylation — addition of a polyadenylated tail to the three prime end of the pre-messenger RNA to give the final mature messenger RNA molecule

The video not only looks at mRNA production but also introduces the idea of non-coding RNA (ncRNA), which are RNA molecules that do not encode proteins. ncRNAs are essential in regulating gene expression and various cellular processes. For example:

• transfer RNA (tRNA) — involved in protein synthesis
• ribosomal RNA (rRNA) — involved in protein synthesis
• microRNA (miRNA) — control gene expression
• small interfering RNA (siRNA) — control gene expression 
• long non-coding RNA (lncRNA) — diverse functions
• circular RNA (circRNA) — gene regulation
• Piwi-interacting RNA (piRNA) — genome protection
• enhancer RNAs (eRNAs) — modulate gene activity

Finally, I cover how to write out DNA sequences, the means of the terms sense and antisense strands, and what we mean by upstream and downstream when talking about DNA and RNA molecules.

If you would like to support my blogging efforts, then please feel free to buy me a coffee at https://www.buymeacoffee.com/drnickm

Blog Bonus: Free information sheet summarising the video and defining the key terms - download.

 

Additional Reading

The video was produced with help from the following resources:

• 📗 - The Biosciences Glossary
• 📗 - Molecular Biology of the Cell (Alberts) - (affiliate link)
• 📗 - Molecular Cell Biology (Lodish) - (affiliate link)
• 📗 - Biochemistry (Stryer) - (affiliate link)

New video posted: DNA Recombination and Holiday Junction: The Key to Genetic Variation

In this video, I explore DNA recombination, a process where DNA strands swap segments, usually between similar sequences on sister chromatids. This swapping creates brand-new genetic combinations. DNA recombination isn't just a biological curiosity; it's crucial for increasing genetic diversity and ensuring the stability of our genome.

If you would like to support my blogging efforts, then please feel free to buy me a coffee at https://www.buymeacoffee.com/drnickm

Blog Bonus: Free information sheet summarising the video and defining the key terms - download.

 

Additional Reading

The video was produced with help from the following resources:

• 📗 - The Biosciences Glossary
• 📗 - Molecular Biology of the Cell (Alberts) - (affiliate link)
• 📗 - Molecular Cell Biology (Lodish) - (affiliate link)
• 📗 - Biochemistry (Stryer) - (affiliate link)