PCR Lab: Activity at A Glance

Discover the Microbes Within: The Wolbachia Project
PCR LAB
ACTIVITY AT A GLANCE
Goal:
To screen for Wolbachia pipientis symbiont DNA in the extracted
DNA from insects using one of the most widely used biotechnology
techniques in biological research, the Polymerase Chain Reaction
(PCR). PCR amplifies DNA millions of times in just a few hours, so
that the DNA becomes easy to detect and study in any fashion.
Learning Objectives:
Upon completion of this activity, students will:
1. Amplify DNA extracted from three morphospecies and three
controls using Polymerase Chain Reaction (PCR).
2. Understand the basic principles of PCR.
Prerequisite Skills:
• Prior practice with micropipettors.
• Familiarity with the roles and responsibilities of group work.
Teaching Time:
60 minutes
Timeline for Teaching Discover the Microbes Within: The Wolbachia Project
Order Check out

laboratory Insect
materials Field
Guides
Order
insects or At this
assign point, all
collection insects Activity 1: Activity Activity Activity Activity Activity 6:
should be Insect 2: DNA 3: DNA 4: Gel 5: Bioin- DNA
Reserve preserved Identifi- Extraction Amplifi- Electro- formatics Sequence
Computer in ethanol cation Lab Lab cation phoresis Alignments &
Lab & stored Lab Phylogenetics
in lab
freezer
8 weeks 3 days Monday Tuesday Wednesday Thursday Friday Monday
ahead ahead
1 PCR Lab
OVERVIEW
Most DNA analysis situations require fairly large amounts of DNA.

Usually the amount in a few cells is not enough to fully analyze. A
method called the polymerase chain reaction (PCR) has been
developed to amplify the amount of DNA in a sample. PCR is
essentially the microscope of the 21st century as it allows biologists
to study the DNA of microorganisms that we cannot see by either
eye or culture. It is revolutionizing research in microbial diversity,
genetic disease diagnosis, forensic medicine, and evolution. In this
portion of the lab series, you will use your samples from the DNA
Extraction Lab to decipher if Wolbachia symbionts are present
within your morphospecies. Your work could be new to science and
potentially lead to new discoveries on the presence and absence of
Wolbachia in insects. Contact Dr. Seth Bordenstein at The Marine
Biological Laboratory for – and + Nasonia insect controls and +
control DNA samples. As in the previous lab, students should work
in groups of two. Primers to specifically amplify a 438bp fragment
of the 16S ribosomal RNA gene (ubiquitous in all Wolbachia) are
WSPEC-F (5’-CATACCTATTCGAAGGGATAG-3’) and WSPEC-R (5’-
AGCTTCGAGTGAAACCAATTC-3’) are also provided by Dr.
Bordenstein (sbordenstein@mbl.edu).
MATERIALS (per group of two students)
 Thermalcycler  Gloves, two pair

 3 DNA Samples from  1 rack for holding PCR tubes
Morphospecies (USA Scientific 2396-5048)
 2 DNA Samples from + and –  1 tube of Wspec-F primer (5
Nasonia controls micromolar, 20µl)
 + DNA control  1 tube of Wspec-R primer (5
 Sharpie micromolar, 20µl)
 6 PCR Ready Bead Tubes  1 tube of d2H20 (200 µl)
 1 box of P200 pipet tips  1 waste cup for tips, tubes,
 1 box of P20 pipet tips etc.
 P200 and P20 pipettes  Saftey goggles
TEACHER PREPARTION
2 PCR Lab
Set up each activity station with its own set of materials as reflected
above.
ACTIVITY PROCEDURE
Review the basic principles of PCR with your class and instruct them
to revisit their hypothesis from the DNA Extraction Lab. Download
the lecture material on DNA-based technologies and PCR Basics. This
lecture describes how techniques such as PCR are changing the
landscape of biological research and where PCR has even been
mentioned in contemporary movies and TV shows today. This
lecture as well as others can be downloaded for free at
http://troi.cc.rochester.edu/~wolb/FIBR/workshops.html. As a
group, program the themalcycler to the settings listed on the
Student Sheet. Stress the importance of proper lab procedure in
obtaining accurate results. Students will work with their same
partners and follow the protocol outlined on the student sheet.
3 PCR Lab
Student Activity Sheet Name:__________
PCR Lab
Hypothesis: Based on extracted DNA from your sets of morphospecies

and the estimated global frequency of Wolbachia pipientis endosymbionts
(20%), formulate a hypothesis for your own specimens.
__________________________________________________________
__________________________________________________________
__________________________________________________________
__________________________________________________________
MATERIALS
 3 DNA Samples from  Gloves, 2 pair
Morphospecies  1 rack for holding PCR
 2 DNA Samples from + and tubes
– Nasonia controls  1 tube of Wspec-F primer (5
 + DNA control micromolar, 20µl)
 Sharpie  1 tube of Wspec-R primer
 6 PCR Ready Tubes (5 micromolar, 20µl)
 1 box of P200 pipet tips  1 tube of d2H20 (200 µl)
 1 box of P20 pipet tips  1 waste cup for tips, tubes
 P200 and P20 pipettes  Saftey goggles
INTRODUCTION
In this activity, you will:
1. Amplify DNA extracted from three morphospecies and three
controls using a procedure called Polymerase Chain Reaction (PCR).
2. Understand the basic principles of PCR.
PREPARATION
The thermalcycler should be programmed for the optimum settings:
1 cycle
2 min @ 95 C
38 Cycles
30 sec. @ 94 C
45 sec @ 55 C
90 sec @ 72 C
1 cycle
10 min. @72 C
4 PCR Lab
PROCEDURE:
1. Collect 6 PCR Ready tubes. Each of these already contains a

preformulated, pellet of “master mix”. This material contains
Taq polymerase, MgCl2, Buffer, and dNTPs.
Note that you will use 6 tubes because a previously purified sample of
Wolbachia DNA has been included as a procedural control.
Tube Tube Contents

# ( Voucher # )
1
2
3
4 - control
5 + control
6 Wolbachia DNA
2. In each tube, add the materials in the sequence below (total

volume of 25 µl). A new pipette tip should be used for each
step:
a. Add 19 µl of sterile distilled water to each tube
b. Add 2 µl of Primer W-spec forward to each tube
c. Add 2 µl of Primer W-spec reverse to each tube
d. Add 2 µl of DNA template from each sample to its
correlating tube. Be sure to change the pipette tips for
each DNA template!
3. Cap and gently tap the bottom of each tube to mix the
components. Place your six tubes with labels (initials and
number) into the thermalcycler. Once everyone has prepared
their samples, the thermalcycler can be turned on.
4. Clean up your lab station.
5 PCR Lab

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Discover the Microbes Within: The Wolbachia Project

Order Check out

Most DNA analysis situations require fairly large amounts of DNA.

MATERIALS (per group of two students)

 Thermalcycler  Gloves, two pair

Student Activity Sheet Name:__________

Hypothesis: Based on extracted DNA from your sets of morphospecies

1. Collect 6 PCR Ready tubes. Each of these already contains a

Tube Tube Contents

2. In each tube, add the materials in the sequence below (total

4. Clean up your lab station.

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