DNA Fingerprinting – In Person

Scroll below for In Person Lab unit

Read along in your lab handout with the information in this webpage.  Fill in and answer all questions accordingly in the handout.  This handout will be collected and graded later.

Lab handout for DNA Fingerprinting – In-Person

Important Background Information to review:

An Introduction to the Human Genome – Basic Structure and Variation in Human DNA (5:32)

Restriction Enzymes and how they are used with DNA – show how DNA with Restriction Enzymes/Endonucleases and how strands can be put back together with DNA Ligase (another enzyme). Click on the Transcript tab if needed.

Polymerase Chain Reaction (PCR) 3D Animation Cold Springs Harbor  – click on video – used to make larger samples of DNA from an initial small sample of DNA. Click on the Transcript tab if needed.

PCR Animation  – a nice simple step by step animation to show how PCR works.

DNA Fingerprinting using PCR to isolate and amplify Short Tandem Repeats (STR) in small DNA samples, then what they look like separated by DNA Electrophoresis. (4:09)

DNA Gel with labeled known DNA fragment sizes/DNA Ladder/Marker DNA (lane 1). This also shows the different banding pattern results (different sized fragments) produced when using different restriction enzymes on the same DNA.

DNA Electrophoresis Equipment:

How DNA Electrophoresis works – the electrophoretic process.

Activity 1; Practice Pipetting – short videoclips

• How to adjust the volume on your micropipetter
• How to use a micropipetter

Activity 2: Restriction Digestion of DNA – view the background Information animations above. The DNA Kit used this semester provides DNA that is already pre-digested, but it is still important to understand how restriction enzymes work and their importance in DNA electrophoresis.

Activity 3 & 4: Preparation of the 0.8% Agarose Gel and Electrophoresis Unit and Preparing the DNA Samples and Loading the Gel

Videos that show how to make gels, loads, run and stain the DNA gels as we will do in lab this week:

• Casting an Agarose Gel – we will actually use a casting stand instead of tape to seal the gel tray.
• Loading an Agarose Gel – tips for loading gels and what not to do.
• DNA Electrophoresis Procedure  – loading and running an agarose gel (as you will do in lab with the same equipment).
• Staining Agarose Gels with Fast Blast Blue – In our teaching labs, we will use a non-toxic Fast Blast Blue stain that will bind to the DNA in the gels allowing us to visualize the bands of DNA.  This video does not have any volume, but provides captions.

In Activity Three, calculate and record the amount of agarose needed to make the indicated 0.8% agarose gel.

Activity 5: Analyzing the DNA Patterns

• In our lab we will look at the pattern and location of the Crime Scene DNA on the gel and look to see which of the suspects match the same pattern for all the bands.
• Sketch and label the lanes/samples in your stained DNA gel.  Include this sketch in your lab handout.  Answer all the end of lab Discussion Questions #1-5 in your lab handout based upon your stained gel. 
• We can look more closely at the size of sample DNA bands/fragments by comparing the distance traveled in the gel to the known base pair size of the fragments found in a known DNA Standards/Marker DNA. We are not using a DNA Standard/Marker DNA in our DNA gel in this week. If we did, you’d be able to estimate the size of each DNA band found in each of the samples. Below is an example of a commonly used DNA Standard. This standard contains bands (segments of DNA) that range in size from 564 to 23,130 base pair units.

Lambda HindIII DNA size Marker/standard*

* depending on how long a gel is run, you may or may not see all the bands separate.

  Who Stole the Crown Jewels?:

Activity to be run during the down time of lab. This is a paper simulation that clearly demonstrates how restriction enzymes work and how DNA fragments separate out during DNA electrophoresis. (Carry out this simulations and add completed pages 4, 5 & 6 to your DNA lab handout. A paper copy of these pages will be provided in lab for you to complete) 

• From this handout you will need to “add” the restriction enzyme to cut the long DNA sequences for each of the DNA samples on page 5.  This Restriction enzyme will find sequences CCGG and cut between the C and G as shown in the example.
• Then count and label the # of base pairs (bp) in each of the new DNA fragments.
• Sketch where these fragment will end up on the DNA gel diagram (page 4) comparing to the known bp units listed on the right of the paper gel. Ignore the 12 bp fragment on the diagram. This is just to show location.
• Examine your completed paper gel and answer question #6 at the end of your DNA Lab Unit Handout.
• Be sure to include the completed pages 4, 5 & 6 with your DNA Unit handouts. You will need to refer to these completed pages to support your answers to #6. You will not get credit for #6 if these completed pages are not provided and legible.

* If you find you need a paper copy of the whole activity, we can print a few copies per lab section. 

Basic DNA Structure – good basic information that you will learn more in depth in lecture.

The Human Genome Project 

Molecular Visualization of DNA  – do not worry if you have not covered all of these topics in lecture yet.  The animation will be helpful when you do review this material.

0-1:48 = DNA Structure — Also seen in the Mitosis and Meiosis lab (this part is important for lab this week)

The rest of this video with be taught later in lecture and be more applicable in the Transformation lab.

1:48-2:53 = DNA Replication –Can you relate this to DNA synthesis? = S phase that you leaned about in the Mitosis and Meiosis in lecture

2:53-4:48 = Transcription – (you will learn about this and Translation later in lecture)

4:48-6:57 = Translation –

6:58-7:47 = Hemoglobin and Sickle Cell Anemia  -not narrated

Group Work Peer Evaluation form   – each student should complete their own peer review and submit it on Moodle by the same due date as the Modern Molecular Techniques Assignment above. Late Peer Reviews will not be graded. You must indicate your own contributes on the peer review form to receive credit.

Interesting Molecular Biology courses and opportunities at NCSU

Opportunities for students:

• Minor in Biotechnology at NCSU(opens in new window)     
• BIT Program and Courses in Biotech (BIT Spring 2027 & Fall 2026(opens in new window)
• BTEC Undergraduate Programs – Biomanufacturing on a larger scale at on Centennial Campus. Click on link to find information on the Undergraduate Minor and Certiciate programs.
• NCSU Professional Sciences Master’s Degree(opens in new window)  (MMB Program – Master’s of Microbial Biotechnology).

Important Technologies in Molecular Biology

How DNA Electrophoresis is used in forensics – Nice new webpage – topics include: Can DNA Demand a Verdict? How can DNA be used to identify an individual? Forensic DNA Analysis.  Is DNA Analysis alone enough to acquit or convict?  

DNA Profiling: Tracing Killers and Solving Mysteries Using Genetic Clues – nice article with overview of the development of DNA fingerprinting technologies linked to real cases.

DNA Profiling: Tracing Killers and Solving Mysteries Using Genetic Clues

Early ideas and Development of PCR – A Not So Simple Idea

All About PCR – A good website with animations and interesting examples

Genome Editing with CRISPR-Cas9 a new and powerful technology with many applications.

Gene Editing Tool CRISPER Wins the Chemistry Nobel (2020)

NYT News Article about CRISPER used to create a personalized treatment to heal a baby with a fatal genetic condition.

ELISA Anitbody tests – animation that shows the different steps involved in ELISA testing for the presence of antibodies.

Gene Transformation – inserting new genes/transformation -former BIO 183 lab unit

Bioprocessing – Protein Production and Purification on an Industrial Scale

Careers in Biotech – nice website.  Careers at the Bench and Beyond

Short Reads:

The History of Genetic Fingerprinting

NCSU Researchers Irish Potato Famine Pathogen Stoked Outbreaks on 6 Continents – using a more specialized electrophoretic genotyping

DNA “Fingerprint” Can Aid Food Safety – NCSU researcher