VIRTUAL LABORATORY 1

Virtual Laboratory for Electrophoresis Using DNA

Please use the given URL below to watch the Virtual Laboratory

https://www.youtube.com/watch?v=FY5wv9ktEOc Virtual Laboratory for

Electrophoresis using DNA

Inclusive Date of Observation: August 3, 2023

Student: AJ Thone Olaño
Faculty: Prof. Genelita Garcia – Faculty of Science, Technology and Mathematics

Answer the following study questions concisely

Study Questions:
1. Give the basic principle of Electrophoresis? What is the technology for?
Electrophoresis is a widely used technique to separate and analyze DNA or RNA based
on their size, charge, or other properties.

2. Why is agarose gel used in electrophoresis?

Agarose gel forms a porous matrix when solidified, allowing for the migration of charged
biomolecules through the gel during electrophoresis. The size of the pores can be
adjusted by changing the agarose concentration, making it suitable for separating
molecules of different sizes.

3. Differentiate the use of agarose gel and polyacrylamide gel in electrophoresis?

Agarose gels provide larger pores, allowing the migration of larger DNA fragments,
making it cost-effective and straightforward to visualize with DNA-specific dyes. In
contrast, polyacrylamide gels have smaller pores, providing higher resolution for smaller
molecules like proteins, allowing for precise separation and analysis. The choice
between agarose and polyacrylamide gel electrophoresis depends on the size range of
the biomolecules being studied.

4. Why is glycerol added to the solutions before they are loaded into the wells?
 Glycerol is included in the buffer to ensure that the solution efficiently fills the wells of
the gel without dispersing or spreading.

5. What would happen if distilled water were substituted for buffer in either the chamber
solution or the gel solution?
Using distilled water instead of a proper buffer in gel electrophoresis would negatively
impact the stability, resolution, and reproducibility of the experiment. The buffer's role
in providing ions, maintaining the pH, and stabilizing the gel matrix is crucial for the
success and accuracy of gel electrophoresis.

6. Ethidium bromide is a potent mutagen and is currently banned in many research

laboratories, what is the alternative dye or stain that is being used today?
Alternatives to ethidium bromide include SYBR® Safe DNA Gel Stain, EvaGreen, GelRed,
and GelGreen, which are also DNA intercalating dyes with low toxicity and improved
safety profiles compared to ethidium bromide.

7. What is the Marker DNA in the activity? What is it for?

The activity includes a DNA standard marker with a known length. It is included to serve
as a reference for determining the lengths of DNA strands in the experimental sample.

8. Differentiate Northern Blotting, Southern Blotting and Western Blotting?

Northern blotting is employed for RNA analysis and gene expression studies. It involves
separating RNA molecules based on size using gel electrophoresis, transferring them to
a solid support, and then detecting specific RNA transcripts using complementary DNA
or RNA probes. Southern blotting, on the other hand, is used for DNA analysis. It
separates DNA fragments based on size using gel electrophoresis, transfers them to a
solid support, and detects specific DNA sequences using labeled DNA probes. Lastly,
Western blotting is utilized for protein analysis. It separates proteins based on size using
gel electrophoresis, transfers them to a solid support, and detects specific proteins using
labeled antibodies. Each technique provides valuable insights into RNA expression, DNA
sequences, and protein characteristics, contributing significantly to various research
fields and applications in molecular biology.

References: Place the references used below in answering the study questions
Cindy. (2020, September 29). Gel Electrophoresus Virtual Laboratory Short [Video]. YouTube.
https://www.youtube.com/watch?v=FY5wv9ktEOc

Ethidium bromide. Ethidium Bromide | Environmental Health and Safety. (n.d.).

https://ehs.research.uiowa.edu/ethidium-bromide

Lee, P. Y., Costumbrado, J., Hsu, C.-Y., & Kim, Y. H. (2012, April 20). Agarose gel electrophoresis for
 the separation of DNA fragments. Journal of visualized experiments : JoVE.
https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4846332/

Overview of electrophoresis: Thermo Fisher Scientific - US. Overview of Electrophoresis | Thermo Fisher
Scientific - US. (n.d.). https://www.thermofisher.com/ph/en/home/life-science/protein-
biology/protein-biology-learning-center/protein-biology-resource-library/pierce-protein-
methods/overview-electrophoresis.html

Smith, M. (2022, September 2). Electrophoresis. Genome.gov. Retrieved from

https://www.genome.gov/genetics-glossary/Electrophoresis