BME100 s2015:Group2 9amL4: Difference between revisions

From OpenWetWare
Jump to navigationJump to search
(5 intermediate revisions by 2 users not shown)
Line 43: Line 43:
| '''Tube Label''' || '''PCR Reaction Sample''' || '''Patient ID'''
| '''Tube Label''' || '''PCR Reaction Sample''' || '''Patient ID'''
|-
|-
| G# + || Positive control || none
| G2 + || Positive control || none
|-
|-
| G# - || Negative control || none
| G2 - || Negative control || none
|-
|-
| G# 1-1 || Patient 1, replicate 1 || 15062
| G2 1-1 || Patient 1, replicate 1 || 15062
|-
|-
| G# 1-2 || Patient 1, replicate 2 || 15062
| G2 1-2 || Patient 1, replicate 2 || 15062
|-
|-
| G# 1-3 || Patient 1, replicate 3 || 15062
| G2 1-3 || Patient 1, replicate 3 || 15062
|-
|-
| G# 2-1 || Patient 2, replicate 1 || 95748
| G2 2-1 || Patient 2, replicate 1 || 95748
|-
|-
| G# 2-2 || Patient 2, replicate 2 || 95748
| G2 2-2 || Patient 2, replicate 2 || 95748
|-
|-
| G# 2-3 || Patient 2, replicate 3 || 95748
| G2 2-3 || Patient 2, replicate 3 || 95748
|}
|}


Line 71: Line 71:
<!-- Include a description of the thermal cycling program below. You can use text, a screen capture, a camera snapshot of the computer screen, or a digital drawing (e.g., using shapes and text boxes in Microsoft Powerpoint) -->
<!-- Include a description of the thermal cycling program below. You can use text, a screen capture, a camera snapshot of the computer screen, or a digital drawing (e.g., using shapes and text boxes in Microsoft Powerpoint) -->


HEATED LID: 100°C
*HEATED LID: 100°C
*INITIAL STEP: 95°C for 2 minutes
*NUMBER OF CYCLES: 35
Denature at 95°C for 30 seconds, Anneal at 57°C for 30 seconds, and *Extend at 72°C for 30
seconds
*FINAL STEP: 72°C for 2 minutes
*FINAL HOLD: 4°C


INITIAL STEP: 95°C for 2 minutes


NUMBER OF CYCLES: 35


Denature at 95°C for 30 seconds, Anneal at 57°C for 30 seconds, and Extend at 72°C for 30
seconds


FINAL STEP: 72°C for 2 minutes


FINAL HOLD: 4°C
<br><br>


==Research and Development==


'''PCR - The Underlying Technology'''<br>
<!-- Add a write-up, essay-style, organized into paragraphs with descriptive headers, based on the questions and answers from the Research and Development exercise. BONUS points: Use a program like Powerpoint, Word, Illustrator, Microsoft Paint, etc. to illustrate how primers bind to the cancer DNA template, and how Taq polymerases amplify the DNA. Screen-captures from the PCR video/ tutorial might be useful. Be sure to '''credit the sources''' if you borrow images. You are not allowed to use images from current or past BME 100 students' reports on OpenWetWare. -->




Q1. What is the function of each component of a PCR reaction?
*Template DNA:
*Primers:
*Taq Polymerase:
*Deoxyribonucleotides (dNTP’s):


<br><br>


==Research and Development==
Q2. What happens to the components (listed above) during each step of thermal cycling?
*INITIAL STEP: 95°C for 3 minutes:
*Denature at 95°C for 30 seconds:
*Anneal at 57°C for 30 seconds:
*Extend at 72°C for 30 seconds:
*FINAL STEP: 72°C for 3 minutes:
*FINAL HOLD: 4°C:


'''PCR - The Underlying Technology'''<br>
<!-- Add a write-up, essay-style, organized into paragraphs with descriptive headers, based on the questions and answers from the Research and Development exercise. BONUS points: Use a program like Powerpoint, Word, Illustrator, Microsoft Paint, etc. to illustrate how primers bind to the cancer DNA template, and how Taq polymerases amplify the DNA. Screen-captures from the PCR video/ tutorial might be useful. Be sure to '''credit the sources''' if you borrow images. You are not allowed to use images from current or past BME 100 students' reports on OpenWetWare. -->


Q3. DNA is made up of four types of molecules called nucleotides, designated as A, T, C and G. Base-pairing, driven by hydrogen bonding, allows base pairs to stick together. Which base anneals to each base listed below?
*Adenine (A):
*Thymine (T):
*Cytosine (C):
*Guanine (G):




Q4. During which two steps of thermal cycling does base-pairing occur? ==Explain your answers.==


<br><br>
<br><br>

Revision as of 20:19, 31 March 2015

BME 100 Spring 2015 Home
People
Lab Write-Up 1 | Lab Write-Up 2 | Lab Write-Up 3
Lab Write-Up 4 | Lab Write-Up 5 | Lab Write-Up 6
Course Logistics For Instructors
Photos
Wiki Editing Help


OUR TEAM

Ryan Bridges
Role(s)
Name: Michael Bejarano
Role(s)
Name: Virginia Fernandez
Role(s)
Morgan Johnson
Role(s)

LAB 4 WRITE-UP

Protocol

Materials

  • Lab coat and disposable gloves
  • PCR reaction mix, 8 tubes, 50 μL each: Mix contains Taq DNA polymerase, MgCl2, and dNTP’s (http://www.promega.com/resources/protocols/product-information-sheets/g/gotaqcolorless-master-mix-m714-protocol/)
  • DNA/primer mix, 8 tubes, 50 μL each: Each mix contains a different template DNA. All tubes have the same forward primer and reverse primer
  • A strip of empty PCR tubes
  • Disposable pipette tips: only use each only once. Never re-use disposable pipette tips or samples will be cross-contaminated
  • Cup for discarded tips
  • Micropipettor
  • OpenPCR machine: shared by two groups

PCR Reaction Sample List

Tube Label PCR Reaction Sample Patient ID
G2 + Positive control none
G2 - Negative control none
G2 1-1 Patient 1, replicate 1 15062
G2 1-2 Patient 1, replicate 2 15062
G2 1-3 Patient 1, replicate 3 15062
G2 2-1 Patient 2, replicate 1 95748
G2 2-2 Patient 2, replicate 2 95748
G2 2-3 Patient 2, replicate 3 95748


DNA Sample Set-up Procedure

  1. Step 1
  2. Step 2
  3. Step 3...


OpenPCR program

  • HEATED LID: 100°C
  • INITIAL STEP: 95°C for 2 minutes
  • NUMBER OF CYCLES: 35

Denature at 95°C for 30 seconds, Anneal at 57°C for 30 seconds, and *Extend at 72°C for 30 seconds

  • FINAL STEP: 72°C for 2 minutes
  • FINAL HOLD: 4°C





Research and Development

PCR - The Underlying Technology


Q1. What is the function of each component of a PCR reaction?

  • Template DNA:
  • Primers:
  • Taq Polymerase:
  • Deoxyribonucleotides (dNTP’s):


Q2. What happens to the components (listed above) during each step of thermal cycling?

  • INITIAL STEP: 95°C for 3 minutes:
  • Denature at 95°C for 30 seconds:
  • Anneal at 57°C for 30 seconds:
  • Extend at 72°C for 30 seconds:
  • FINAL STEP: 72°C for 3 minutes:
  • FINAL HOLD: 4°C:


Q3. DNA is made up of four types of molecules called nucleotides, designated as A, T, C and G. Base-pairing, driven by hydrogen bonding, allows base pairs to stick together. Which base anneals to each base listed below?

  • Adenine (A):
  • Thymine (T):
  • Cytosine (C):
  • Guanine (G):


Q4. During which two steps of thermal cycling does base-pairing occur? ==Explain your answers.==




Retrieved from "https://openwetware.org/mediawiki/index.php?title=BME100_s2015:Group2_9amL4&oldid=876351"