DNA Polymorphisms: DNA markers
a useful tool in biotechnology
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• 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.
SNPs
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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
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 STRPs
Minisatellites and Microsatellites
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• 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.
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
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Locus vWA
14
0.081
15
0.107
15.2
0.179
16
0.306
17
0.192
18
0.089
19
0.047
Band
frequency
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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.
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THE 13 CODIS STRs
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
STR
http://expertpages.com/news/dna.htm
RAPD: using PCR to find polymorphisms
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• “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
RAPD: using PCR to find polymorphisms-2
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