DNA Polymorphisms: DNA markers a useful tool in biotechnology

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DNA Polymorphisms DNA markers a useful tool in
biotechnology

• Any section of DNA that varies among individuals
  in a population, many forms.
• Examples include SNPs, RFLPs, STRPs, and AFLPs
• RFLPs include VNTRs and STRPs
• microsatellites (STRs) SSLPs STRPs SSRs
• Useful for finding, mapping genes involved in
  disease, and
• Individual identification, epidemiology,
  anthropology, population/ecology studies,
  taxonomy.

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SNPs
Single nucleotide polymorphisms regions of DNA
where one base pair is different. Occur evenly
spread over all the DNA. 1/ 1000-3000
bp Detected by sequencing. If SNP occurs in a
restriction enzyme site, it generates an
RFLP. Could be in coding or non-coding
regions. Over 300,000 human SNPs known and are
being mapped.
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SNP
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RFLPs
Restriction fragment length polymorphism. Mutation
at a restriction site prevents recognition
cutting. Results in one band of larger DNA
instead of 2 smaller ones.
scidiv.bcc.ctc.edu/.../lectures/
DNATechnology/image021.jpg
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Other RFLPs VNTRs and STRPsMinisatellites and
Microsatellites

• These are RFLPs because they are defined by or
  visible following restriction enzyme cuts.
• Variable Number Tandem Repeats
• Groups (10-100) of nucleotides repeated 2 100
  times (depending on individual and locus).
• Restriction sites on both sides of repeated DNA
• The more repeats, the longer the fragment.
• Simple Tandem Repeat Polymorphisms
• Shorter, 2-9 nucleotides repeated
• Small enough number for PCR amplification
• Also called STRs, SSLPs, etc.

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Use of VNTRs
Restriction sites are on either side fragment
length depends on number of repeats in between
sites.
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STRPs
Primers for both sides of repeated region allow
PCR amplification of DNA generates PCR products
that differ in length depending on number of
repeats. Becoming the standard method for DNA
testing in forensics labs. Cheaper, easier, more
sensitive.
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STRs in forensics

• Locus vWA
• 14 0.081
• 15 0.107
• 15.2 0.179
• 16 0.306
• 17 0.192
• 18 0.089
• 19 0.047

Alleles in different ethnic and racial groups
examined, used as database. Panel of 13
different STRs are used. Because the odds of a
particular combination of the 13 is product of
the frequencies, numbers like 1 in 10 billion can
be generated.
Band frequency
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THE 13 CODIS STRs
STR African-American U.S. Caucasian
D3S1358 0.102 0.078
vWA 0.058 0.065
FGA 0.035 0.036
TH01 0.102 0.094
TPOX 0.081 0.211
CSF1PO 0.070 0.122
D5S818 0.097 0.140
D13S317 0.131 0.074
D7S820 0.081 0.061
D8S1179 0.075 0.067
D21S11 0.033 0.045
D18S51 0.028 0.030
D16S539 0.066 0.103
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RAPD using PCR to find polymorphisms

• Random amplified polymorphic DNA
• Screen DNA from individuals by doing PCR with
  random short primers.
• By random chance, primers will amplify many
  different sections of DNA.
• Look for bands on gel that are not present in
  each individual tested.

avery.rutgers.edu/.../ archives/onions/rapd.html
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RAPD using PCR to find polymorphisms-2