genetics practical 1

Aim - To investigate human genetic variation and evidence for the Out-of-Africa (OOA) hypothesis using your own DNA.

marker 1 = Alu element is a:

  • Short Interspersed Nuclear Element (SINE)

  • About 300 bp long

  • Repetitive DNA sequence


Some people have the Alu sequence present at the CD4 locus and some do not.

Alu+

  • Alu insertion present

Alu−

  • Alu insertion absent

Results

Genotype

Chromosome 1

Chromosome 2

PCR Band(s) Seen on Gel

Interpretation

Al

Alu present

Alu present

661 bp only

Homozygous for Alu insertion

Alu⁻

Alu absent

Alu absent

438 bp only

Homozygous for Alu deletion

Al

Alu present

Alu absent

661 bp and 438 bp

Heterozygous


marker 2 - STR = Short Tandem Repeat

A short DNA sequence repeated multiple times.

Example: TTTTC TTTTC TTTTC TTTTC

why are STRs useful?

People inherit one allele from each parent.

Different numbers of repeats produce PCR products of different lengths.

This makes STRs useful for:

  • DNA profiling

  • Population genetics

  • Studying inheritance

Allele

Repeat Number

PCR Size

STR80

4 repeats

80 bp

STR85

5 repeats

85 bp

STR90

6 repeats

90 bp

STR100

8 repeats

100 bp

STR110

10 repeats

110 bp


method

  1. Collect a saliva sample (contains cheek cells). Cheek cells contain nuclei, which contain your DNA.

  2. Transfer a small amount of saliva into dilution buffer.

  3. Vortex (mix) for ~10 seconds to distribute cells evenly.

  4. Centrifuge for 10 seconds to collect contents at the bottom.

  5. Heat at 98°C for 2 minutes to lyse (break open) cells and release DNA.

  6. Centrifuge again briefly.


Prepare two PCR tubes:

Red tube

  • Contains primers for the Alu marker.

Blue tube

  • Contains primers for the STR marker.

Add a small amount of extracted DNA to both tubes.


The PCR machine amplifies the target DNA regions using repeated cycles of:

  1. Denaturation (~95°C) → DNA strands separate.

  2. Annealing → Primers bind to target sequences.

  3. Extension (72°C) → DNA polymerase synthesises new DNA.

Repeating these cycles produces millions of copies of the Alu and STR regions.

Alu Marker Results

Band Pattern

Genotype

661 bp

Alu⁺/Alu⁺

438 bp

Alu⁻/Alu⁻

661 bp + 438 bp

Alu⁺/Alu⁻

STR Marker Results

  • Band size indicates the number of STR repeats.

  • Larger band = more repeats.

  • One band = homozygous.

  • Two bands = heterozygous