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AFLP (Amplified Fragment Length
Polymorphism), Alu PCR
Submitted to: Dr. Farkhanda Jabeen
Submitted by: Jannat Iftikhar
MS16-01
Semester 1st
1
Couse Title: Polymerase Chain Reaction; The Basis
Contents
AFLP
Introduction
Steps
Advantages
Applications
Alu PCR
Alu elements
Alu family
Alu sequence
Steps
Applications
2
3
AFLP
(Amplified Fragment
Length
Polymorphism)
Introduction
4
First described by Vos and Zabeau in 1993.
Involves the use of RFLP and PCR techniques.
Amplify the same gene from different individual
Powerful approach to detect polymorphism.
5
AFLP is a technique based on the principle of selectively
amplifying the subset of restriction fragments from a
complex mixture of DNA fragments obtained after the
digestion of genomic DNA with restriction endonucleases.
AFLP
Steps
6
1. Digestion
2. Adaptor ligation
3. Amplification
4. Electrophoresis
Digestion
• Different restriction endonucleases are used in digestion.
• One is four base cutter, MseI
• The other one is six base cutter, EcoRI
7
Adaptor ligation
• Two different adaptors (short double stranded DNA with
sticky ends) are ligated to the digested fragments.
• One adaptor will complement to MseI cut end and the
other will complement to the EcoRI cut end.
8
Amplification
• Selected fragments are amplified and separated by
polyacrylamide gel electrophoresis.
• By repeating this second amplification with other primer
pairs a different subset of the genome is amplified.
9
10
Electrophoresis
• Polyacrylamide gel is used for separating DNA bands.
• Normally, 30-100 DNA bands can be detected by AFLP on
polyacrylamide gel.
11
12
Advantages of AFLP
• No need for the known sequence in the genome
• High reproducibility
• Many loci are simultaneously analyzed
• By changing the selective nucleotide, different part of the
genome can be analyzed.
• Whole genome analysis is possible (theoretically).
13
The only disadvantage is that it is a complex procedure.
Applications
• The AFLP technology has the capability to detect various
polymorphisms in different genomic regions
simultaneously.
• AFLP has become widely used for the identification of
genetic variation in strains or closely related species of
plants, fungi, animals, and bacteria.
• The AFLP technology has been used in criminal and
paternity tests, also to determine slight differences within
populations, and in linkage studies to generate maps
for quantitative trait locus (QTL) analysis.
14
15
Alu PCR
Introduction
• Alu region discovered by Schmid and Deininger in 1975.
• Alu sequence on 16 no. chromosome of Human and
Primates
• Very conserved region
• Alu sequences are non-coding, repetitive, about
10,00,000 copies present
• Genotype +/+, +/-, -/-
16
Alu elements
• An Alu element is a short stretch of DNA originally
characterized by the action of the Arthrobacter
luteus (Alu) restriction endonuclease.
• Alu elements are the most abundant transposable
elements.
17
Alu family
• The Alu family is a family of repetitive elements in the
human genome. Modern Alu elements are about
300 base pairs long and are therefore classified as short
interspersed elements (SINEs) among the class of
repetitive DNA elements.
• Human-specific Alu insertion
• Approx. 1 million Alu copies per haploid genome
• 11% of the genome: role in genetic architecture and
genetic disorders
• Intron: Found in a non-coding region of your DNA
18
Alu sequence
• GGCCGGGCGCGGTGGCTCACGCCTGTAATCCCAGCA
CTTTGGGAGGCCGAGGCGGGCGGATCACGAGGTCA
GGAGATCGAGACCATCCCGGCTAAAACGCTGAAACCT
CGTCTCTACTAAAAATACAAAAAATTAGCCGGGCGTAG
TGGCGGGCGCCTGTAGTCCCAGCTACTTGGGAGGCT
GAGGCAGGAGAATGGCGTGAACCCGGGAGGCGGAG
CTTGCAGTGAGCCGAGATCCTGCCACTGCACTCCAG
CGTGGGCGACAGAGCGAGACTCCGTCTCAAAAAAAA
AAAAAAAAAAAAAAAAA
• 306 base pairs long: This sequence remains the same, no
matter where it is found in the genome
19
Steps
• DNA sample
• Add Primer of Alu segment
• Run PCR
• Result on Gel Eletrophoresis
20
21
22
Chromosome 16:
In metaphase
Applications
of Alu PCR
Paternity testing
Study population
genetics
Forensic purpose
References
• Nelson, D. L., Ledbetter, S. A., Corbo, L., Victoria, M. F.,
Ramírez-Solis, R., Webster, T. D., ... & Caskey, C. T.
(1989). Alu polymerase chain reaction: a method for rapid
isolation of human-specific sequences from complex DNA
sources. Proceedings of the National Academy of
Sciences, 86(17), 6686-6690.
• Cardelli, M. (2011). Alu PCR. PCR Protocols, 221-229
• Sambrook J, Fritsch EF, Maniatis T (1989). Molecular
Cloning: A. Laboratory Manual. Cold Spring Harbor
Laboratory Press, Cold Spring Harbor, New York
• https://en.wikipedia.org/wiki/Alu_element
• http://www.geneticorigins.org/pv92/aluframeset.htm
23
24

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Aflp (amplified fragment length polymorphism), alu

  • 1. AFLP (Amplified Fragment Length Polymorphism), Alu PCR Submitted to: Dr. Farkhanda Jabeen Submitted by: Jannat Iftikhar MS16-01 Semester 1st 1 Couse Title: Polymerase Chain Reaction; The Basis
  • 4. Introduction 4 First described by Vos and Zabeau in 1993. Involves the use of RFLP and PCR techniques. Amplify the same gene from different individual Powerful approach to detect polymorphism.
  • 5. 5 AFLP is a technique based on the principle of selectively amplifying the subset of restriction fragments from a complex mixture of DNA fragments obtained after the digestion of genomic DNA with restriction endonucleases. AFLP
  • 6. Steps 6 1. Digestion 2. Adaptor ligation 3. Amplification 4. Electrophoresis
  • 7. Digestion • Different restriction endonucleases are used in digestion. • One is four base cutter, MseI • The other one is six base cutter, EcoRI 7
  • 8. Adaptor ligation • Two different adaptors (short double stranded DNA with sticky ends) are ligated to the digested fragments. • One adaptor will complement to MseI cut end and the other will complement to the EcoRI cut end. 8
  • 9. Amplification • Selected fragments are amplified and separated by polyacrylamide gel electrophoresis. • By repeating this second amplification with other primer pairs a different subset of the genome is amplified. 9
  • 10. 10
  • 11. Electrophoresis • Polyacrylamide gel is used for separating DNA bands. • Normally, 30-100 DNA bands can be detected by AFLP on polyacrylamide gel. 11
  • 12. 12
  • 13. Advantages of AFLP • No need for the known sequence in the genome • High reproducibility • Many loci are simultaneously analyzed • By changing the selective nucleotide, different part of the genome can be analyzed. • Whole genome analysis is possible (theoretically). 13 The only disadvantage is that it is a complex procedure.
  • 14. Applications • The AFLP technology has the capability to detect various polymorphisms in different genomic regions simultaneously. • AFLP has become widely used for the identification of genetic variation in strains or closely related species of plants, fungi, animals, and bacteria. • The AFLP technology has been used in criminal and paternity tests, also to determine slight differences within populations, and in linkage studies to generate maps for quantitative trait locus (QTL) analysis. 14
  • 16. Introduction • Alu region discovered by Schmid and Deininger in 1975. • Alu sequence on 16 no. chromosome of Human and Primates • Very conserved region • Alu sequences are non-coding, repetitive, about 10,00,000 copies present • Genotype +/+, +/-, -/- 16
  • 17. Alu elements • An Alu element is a short stretch of DNA originally characterized by the action of the Arthrobacter luteus (Alu) restriction endonuclease. • Alu elements are the most abundant transposable elements. 17
  • 18. Alu family • The Alu family is a family of repetitive elements in the human genome. Modern Alu elements are about 300 base pairs long and are therefore classified as short interspersed elements (SINEs) among the class of repetitive DNA elements. • Human-specific Alu insertion • Approx. 1 million Alu copies per haploid genome • 11% of the genome: role in genetic architecture and genetic disorders • Intron: Found in a non-coding region of your DNA 18
  • 20. Steps • DNA sample • Add Primer of Alu segment • Run PCR • Result on Gel Eletrophoresis 20
  • 21. 21
  • 22. 22 Chromosome 16: In metaphase Applications of Alu PCR Paternity testing Study population genetics Forensic purpose
  • 23. References • Nelson, D. L., Ledbetter, S. A., Corbo, L., Victoria, M. F., Ramírez-Solis, R., Webster, T. D., ... & Caskey, C. T. (1989). Alu polymerase chain reaction: a method for rapid isolation of human-specific sequences from complex DNA sources. Proceedings of the National Academy of Sciences, 86(17), 6686-6690. • Cardelli, M. (2011). Alu PCR. PCR Protocols, 221-229 • Sambrook J, Fritsch EF, Maniatis T (1989). Molecular Cloning: A. Laboratory Manual. Cold Spring Harbor Laboratory Press, Cold Spring Harbor, New York • https://en.wikipedia.org/wiki/Alu_element • http://www.geneticorigins.org/pv92/aluframeset.htm 23
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