Download Using microsatellites as molecular markers

Simple-Sequence Length Polymorphisms
SSLPs
Short tandemly repeated DNA sequences that are present in
variable copy numbers at a given locus.
Scattered throughout genome.
Different people may have different numbers of these repeats at
different loci (think of different copy numbers as alleles).
Microsatellite Markers:
Tandem repeats of a 2 bp sequence such as CA.
Minisatellite Markers (aka Variable Number Tandem Repeats):
Tandem repeating units of 15-100 bp.
Using microsatellites as molecular markers
Use PCR primers that are complementary to single copy sequences flanking
microsatellites to amplify microsatellite-containing region.
Depending on number of microsatellite repeats, will get different lengths
PCR products (many different possible alleles, not just two)
VNTRs can be used to generate DNA fingerprints
Since some repeated sequences are present at multiple places in genome, a
single probe can detect multiple VNTRs on one genomic Southern blot.
3 separate
VNTR loci
DNA fingerprint = set of VNTR
fragments from an individual’s
genome.
Advantages of SSLPs compared to RFLPs
1. Unlike RFLPs, both microsatellites and minisatellites usually
have > 2 alleles.
By having more allele possibilities, each allele can be used
as a more specific tag.
2. In a population, heterozygosity for a particular RFLP may be
low, whereas heterozygosity for SSLP alleles tends to be
higher.
Need RFLP or SSLP differences in order to be useful for
mapping (or DNA fingerprinting).
Can detect SSLPs by PCR, therefore, need very little DNA for
diagnostic tests.
Because a single minisatellite probe can detect multiple VNTRs,
can simultaneously examine multiple VNTR loci at a time.
Linkage map of human X chromosome
SSLPs mapped to many
locations throughout genome
Fluorescent In Situ Hybridization (FISH)
Used for low
resolution mapping
i.e., determining
approximate locations
of genes or other
DNA sequences in
genome.
Can use RFLP or SSLP tests to determine genotype
of individual even before phenotype (e.g., disease) is
observed.
Ethical concerns:
What if disease-causing allele can be detected,
but no treatment is available?
Who gets the information?
Prenatal diagnosis for genetic diseases
Extract DNA from cells &
use for RFLP or SSLP
analysis.