DNA Methodologies

1
DNA Methodologies

• Sterilization
• Clean the workstation with alcohol and bleach.
• Autoclaving and ultraviolet light (UV radiation).
• Consumables and reagents.
• Equipment
• Pipettes- P20, P200, P1000
• Block heater
• Vortex
• Centrifuge
• PCR machine
• Electrophoresis box and power supply
• DNA sequencing machine
• Computer

2
Tissue Sample
DNA Extraction
DNA Quantitation
PCR mtDNA
PCR STRs
Genetic Analyzer- mtDNA sequencing and STR
analysis
Analysis of Results
Conclusion/s
3
DNA Protocol

• DNA Extraction
• FTA Card
• Chelex
• Spin columns
• Organic- simple and differential.
• DNA Quantitation
• Direct, non-blot
• Direct, slot-blot
• Real Time PCR
• PCR Amplification
• Polymerase Chain Reaction
• DNA Sequencing or Typing
• Analysis and Interpretation

4
Human Cell

• How do we get the nuclear and mitochondrial DNA
• out of the cell?

5
DNA Extraction Protocols 1

• FTA Card
• Pipette aliquot on card.
• WBCs lyse on paper and DNA is trapped.
• Use hole punch to remove paper for DNA analysis.
• Wash.
• Analysis.

6
(No Transcript)
7
FTA Protocol
8
DNA Extraction Protocols 2

• Chelex
• Incubate blood sample in 5 Chelex at 56C for 30
  min.
• Boil for 8 min.
• Centrifuge to remove inhibitors and cellular
  debris.

9
DNA Extraction Protocols 3

• Column Extraction
• Lyse cells and digest proteins.
• Physical, heat, detergent
• Proteinase K
• Bind DNA to silica membrane by centrifugation.
• Wash with 70 ethanol by centrifugation.
• Elute DNA with TAE (Tris-Acetate - EDTA) or water
  by centrifugation.

10
(No Transcript)
11
(No Transcript)
12
(No Transcript)
13
DNA Extraction Protocols 4

• Organic Extraction
• Lyse cells and digest proteins.
• Physical, heat, detergent
• Proteinase K
• Organic extraction.
• Phenol-chloroform
• Centrifuge to remove supernatant.
• Precipitate DNA.
• Ethanol or isopropanol
• Centrifugation to pellet DNA.
• Elute DNA with TAE or water.

14
Differential Extraction

• Technique used to separate sperm cells from
  non-sperm cells (epithelial cells).
• Vaginal swabs
• 1. Epithelial cells are lysed with a mild
  extraction buffer containing Sodium Dodecyl
  Sulfate (SDS).
• 2. Centrifugation to pellet sperm cells, DNA from
  epithelial cells is in the supernatant.
• 3. Lyse sperm cells using Dithiothreitol (DTT).

15
DNA Quantitation

• DNA Quantitation
• Direct, non-blot
• Direct, slot-blot
• Real Time PCR
• Why quantitate?
• U.S. FBI Standards require it!
• 1ng-2.5ng yields consistent typing results.
• 1 cell 6.1pg (164 cells needed for analysis)
• Too much DNA leads to artifacts and too much
  signal.
• Too little DNA leads to allelic dropout.

16
DNA Quantitation 1

• Direct, non-blot
• AluQuant (Promega Corp.)
• Human-specific probe that binds to Alu insertions
  (highly repetitious DNA).
• Luciferin-luciferase reaction and a luminometer
  to detect the amount of light.
• Emission is compared against standards.
• Yield Gel
• Standards of known concentration are compared
  against a sample.

17
DNA Quantitation 2

• Direct, slot-blot
• QuantiBlot (Applied Biosystems)
• Human-specific probe (D17Z1) binds to DNA.
• Chemiluminescence is used to determine the DNA
  concentration against a set of standards.

18
DNA Quantitation 3

• Real Time PCR
• Quantifiler (Applied Biosystems)
• Human genes are amplified.
• Gene number doubles after each cycle.
• Each cycle yields more fluorescence.
• Fluorescence is recorded and compared against
  standards to determine DNA concentration.

19
PCR Product Amount is Proportional to the Amount
of Input DNA Template
During the exponential expansion of the PCR the
amount of product produced is proportional to the
amount of template. Here we show the total
amount of product following 32 cycles.
2ng template
1ng template
0.5ng template
20
Develop a standard curve
(reagent blank)