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Strawberry DNA
Plant Genomics
Genomics – The study of DNA
Plant chromosomal DNA
Chromosome number
Plant genes
Plant reproduction
Plant gene expression – the regulation
of genes
Why Plant Genomics
Agricultural applications – Production of
healthier crops- more nutritious( Genetic
engineering of crop plants
Production of crops with disease resistance
Pharmacology - What novel genes do plants
have to apply to human pharmacological
research? Many contain anti- cancer
compounds
Bioremediation – Plants removing pollutants
from the environment
Genomic DNA
30,000 genes
Satellite DNA – around the
centromeres
Telomeric DNA – repetitive copies of
TTAGGG
VNTR – variable number of tandem
repeats- variable per species
Retrotransposons – remains of ancient
retroviruses – are capable of
replicating and making enzymes capable
of jumping our of one position and
finding a new position in DNA
Genomic DNA
Sines- short interspersed
elements – 500 bp but are not
translated
Lines – long interspersed
elements – up to 7000 bases
some are transcribed and
translated
Transposons- move around in
the DNA
ALUs – a special type of DNA –
300 bp – accounts for 11 % of
the human genome
Contradictions to the Central Dogma
Retroviruses – Other RNA viruses
Transposons
Other elements in DNA - Alus
Prions ( proteins – Mad Cow)
Genes for t- RNA
Genes for Ribosomal RNAs
Spliceosomes and catalytic RNA’s
Enhancers and repressors
Promoters
Materials
Clean blue tube
Sharpie marker
Eppendorf holder( Microfuge
tubes)
Loading dye ( green and yellow
tube)
Tracking dye – white tube TD
Marker – white tube – M
Strawberry DNA- sample
from extraction
Extraction of DNA I
Homogenize strawberries
Filter the stawberry
homogenate
Place extract in Corning Tube
Add lysis mixture –
detergent containing lauryl
sulfate and salt, NaCl
Add papain mixture to
denature proteins( DNAses)
Mix by rocking and rolling
Extraction of DNA II
Heat at 55oC. This speeds up
degradation of proteins( 2
min)
Place in ice until cold
Add ice cold ethanol. Drip
slowly down the side of the
Corning tube making sure
that the alcohol forms a
layer on top of the juice.
This should form an
interface between the two
layers.
DNA Precipitate III
The DNA should precipitate
and form a mass of
slender,sticky strands
Remove the DNA from the
Corning tube, being careful
not to disturb the interface
The DNA should be placed in
a microcentrifuge tube,
Centrifuge for 2 minutes
Pellet and Supernatant
Spin the tube with the DNA
It forms a pellet on the side
of the microcentrifuge tube
Pour off the supernatant
which is alcohol
The DNA needs to be
resolubilized in Tris buffer
Mix the DNA from the pellet
with Tris
Tris and DNA
The DNA must be in solution
for electrophoresis.
Mix before using in the gel
Remove 25 ul of DNA and
place in a microcentrifuge
tube.
Add 3 ul of loading dye
Vortex to mix
Genomic DNA – Gel Lanes
Label on your index card
1-Tracking dye
2- Marker – Lambda phage HindII
3 -8- Strawberry DNA
samples( genomic DNA)
Name on Ziplock Snack Bag for Gel
Loading gels
Run DNA from
black to red
From the
cathode to the
anode
Remember
DNA has a
negative
charge
Reminders about loading gel
Aspirate to first stop
point
Deliver by dispensing into
the well to the second
stop point
Fill the well – being
careful not to overfill
Run the gel on a voltage of
80 volts
Staining
Stain with Methylene blue.
Fast Blast Stain. Gel should
stain for at least one hour
Destain with Distilled water
Place gel in ziplock bag with
water.
When gel is sufficeintly
destained - the stained gel can
be placed in a ziplock for
storage in the refrigerator
Gel Observation
Observe gel on light box
Measure the distance that each band in
the marker( standard) migrates
Measure any bands oar streaks of DNA
you observe.
Use the DNA graphing program to make
a semi-log graph to estimate the sizes
of your DNA
DNA gel