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LAY OUT YARN PIECES ON YOUR DESK
DON’T STRETCH !
TRIM ALL YOUR YARN PIECES SO THEY ARE THE SAME LENGTH- 60 cm
Image from : http://thecreativeimperative.blogspot.com/2011/06/american-flag-wreath-sort-of.html
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RESTRICTION ENDONUCLEASES
Use the “restriction enzymes” provided to:
Cut one piece of yarn with EcoRI –Cuts at 15 cm AND 40 cm
Cut one piece of yarn with HindIII – Cuts at 7 cm AND 32 cm
Cut one piece of yarn with BOTH EcoRI AND HindIII
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SET UP YOUR DESKTOP AS A GEL
+
DNA
–
EcoRI +HindIIIEcoRI HindIII
Use sticky notes to LABEL THE + and – poles
Use sticky notes to LABEL your lanes
Load your “gel” withyour “DNA” that has been cut with“restriction enzymes”
Complete RFLP analysis and draw a picture of the results in your BILL
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2007-2008
More Basic Biotechnology ToolsSorting & Copying DNA
Modified from a slide show by Kim Foglia
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Engineered plasmids
Selectable marker antibiotic resistance gene on
plasmid ampicillin resistance
selecting for successful transformation successful uptake of
recombinant plasmid
plasmid
ampresistance
restriction sites
EcoRI
BamHI HindIII
• Building custom plasmids– restriction enzyme sites– antibiotic resistance genes as a selectable marker
ori
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Many uses of restriction enzymes…• Now that we can cut DNA with restriction
enzymes…– we can cut up DNA from different people… or
different organisms… and compare it
– why?• forensics• medical diagnostics• paternity• evolutionary relationships • and more…
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Comparing cut up DNA• How do we compare DNA fragments?– separate fragments by size
• How do we separate DNA fragments?– run it through a gelatin• agarose• made from algae
– gel electrophoresis
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Gel electrophoresis• A method of separating DNA in
a gelatin-like material using an electrical field– DNA is negatively charged– when it’s in an electrical field it
moves toward the positive side
+–
DNA
“swimming through Jello”
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• DNA moves in an electrical field…– so how does that help you compare DNA
fragments?• size of DNA fragment affects how far it travels– small pieces travel farther– large pieces travel slower & lag behind
Gel electrophoresis
+–
DNA
“swimming through Jello”
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Gel Electrophoresis
longer fragments
shorter fragments
powersource
completed gel
gel
DNA &restriction enzyme
wells
-
+
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Running a gel
1 2
cut DNA with restriction enzymes
fragments of DNAseparate out based on size
3
Stain DNA– ethidium bromide
binds to DNA– fluoresces under UV
light
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Uses: Evolutionary relationships• Comparing DNA samples from different
organisms to measure evolutionary relationships
–
+
DNA
1 32 4 5 1 2 3 4 5
turtle snake rat squirrel fruitfly
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Uses: Medical diagnostic• Comparing normal allele to disease allele
chromosome with disease-causing allele 2
chromosomewith normal allele 1 –
+
allele 1allele 2
DNA
Example: test for Huntington’s disease
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Uses: Forensics• Comparing DNA sample from crime scene
with suspects & victim
–
+
S1
DNA
S2 S3 Vsuspects crime
scene sample
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DNA fingerprints• Comparing blood
samples on defendant’s clothing to determine if it belongs to victim– DNA fingerprinting– comparing DNA banding
pattern between different individuals
– ~unique patterns
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Differences at the DNA level• Why is each person’s DNA pattern different?– sections of “junk” DNA• doesn’t code for proteins• made up of repeated patterns
– CAT, GCC, and others– each person may have different number of repeats
• many sites on our 23 chromosomes with different repeat patterns
GCTTGTAACGGCCTCATCATCATTCGCCGGCCTACGCTTCGAACATTGCCGGAGTAGTAGTAAGCGGCCGGATGCGAA
GCTTGTAACGGCATCATCATCATCATCATCCGGCCTACGCTTCGAACATTGCCGTAGTAGTAGTAGTAGTAGGCCGGATGCGAA
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Allele 1GCTTGTAACGGCCTCATCATCATTCGCCGGCCTACGCTTCGAACATTGCCGGAGTAGTAGTAAGCGGCCGGATGCGAA
repeats
DNA patterns for DNA fingerprintscut sitescut sites
GCTTGTAACG GCCTCATCATCATCGCCG GCCTACGCTTCGAACATTGCCG GAGTAGTAGTAGCGGCCG GATGCGAA
1 2 3
DNA – +allele 1
Cut the DNA
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Allele 1GCTTGTAACGGCCTCATCATCATTCGCCGGCCTACGCTTCGAACATTGCCGGAGTAGTAGTAAGCGGCCGGATGCGAA
Differences between peoplecut sitescut sites
DNA – +allele 1
Allele 2: more repeatsGCTTGTAACGGCCTCATCATCATCATCATCATCCGGCCTACCGAACATTGCCGGAGTAGTAGTAGTAGTAGTAGGCCGG
DNA fingerprint
allele 2
1 2 3
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RFLPs• Restriction Fragment Length Polymorphism– differences in DNA between individuals
change in DNA sequence affects restriction enzyme “cut” site
creates different fragment sizes & different band pattern
Alec Jeffries 1984
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RFLP / electrophoresis use in forensics• 1st case successfully using DNA evidence– 1987 rape case convicting Tommie Lee Andrews
“standard”
“standard”
“standard”
“standard”
semen sample from rapist
semen sample from rapist
blood sample from suspect
blood sample from suspect
How can you compare DNA fromblood & from semen?RBC?
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Electrophoresis use in forensics• Evidence from murder trial– Do you think suspect is guilty?
“standard”
blood sample 3 from crime scene
“standard”
blood sample 1 from crime scene
blood sample 2 from crime scene
blood sample from victim 2
blood sample from victim 1
blood sample from suspect OJ Simpson
N Brown
R Goldman
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Uses: Paternity • Who’s the father?
+
DNA
childMom F1 F2–