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STR (Short Tandem Repeat) Markers – Detailed Notes


STR (Short Tandem Repeat) Markers – Detailed Notes


Introduction


STRs, also called microsatellites, are short sequences of 2–6 base pairs repeated in tandem at specific loci in the genome.
Examples: (CA)n, (GT)n, (TATC)n, where n is the number of repeats.
STRs are highly polymorphic, co-dominant, and widely used in forensic analysis, paternity testing, genetic mapping, and population genetics.
STRs occur throughout the genome, mostly in non-coding regions, but can occasionally be in coding sequences.


Structure of STR


Repeat motif: 2–6 bp (e.g., CA, GT, GATA)
Number of repeats: Varies among individuals → basis of polymorphism
Flanking regions: Conserved sequences on both sides of repeats → used to design PCR primers
Principle
STR polymorphism arises from variation in the number of repeat units at a specific locus among individuals.
PCR amplification using primers flanking STR → fragments of different lengths → fragment size indicates allele
Allelic differences allow distinction between individuals, detect heterozygosity, and perform genetic analysis.
Materials Required
Genomic DNA
STR-specific primers (flanking repeats)
PCR reagents: Taq polymerase, dNTPs, buffer, Mg²⁺
Thermal cycler
Gel electrophoresis system: Polyacrylamide gel or capillary electrophoresis
DNA stains: Ethidium bromide, SYBR Green, or fluorescent labeling


Procedure


Step 1: DNA Isolation

Extract high-quality genomic DNA from blood, saliva, hair, tissue, or forensic samples.

Step 2: PCR Amplification


Use specific primers flanking STR loci.
PCR cycles:
Denaturation: 94–95°C
Annealing: 50–60°C (primer-dependent)


Extension: 72°C


25–35 cycles typically yield sufficient product.


Step 3: Fragment Analysis


Separate PCR products based on size differences:
High-resolution polyacrylamide gel electrophoresis
Capillary electrophoresis with fluorescent labeling for precise sizing
Fragment length corresponds to number of repeat units (allele size).


Step 4: Data Analysis


Score alleles based on fragment size
Determine genotype (homozygous or heterozygous)
Use data for forensic identification, paternity testing, or population studies




Genomic DNA → PCR with primers flanking STR → Amplified fragments
      ↓
High-resolution gel or capillary electrophoresis
      ↓
Fragment size analysis → Determine alleles (repeat number)
      ↓
Genetic profiling / Fingerprinting
Characteristics of STR Markers
Highly polymorphic → variation in repeat number
Co-dominant → distinguish homozygotes from heterozygotes
PCR-based → requires very small DNA amounts
Locus-specific and reproducible
Present in both coding and non-coding regions


Merits


High polymorphism, ideal for individual identification
Co-dominant, can detect heterozygotes
PCR-based, works with degraded DNA
Small DNA quantity required, useful in forensic cases
Applicable in forensics, paternity testing, population genetics, and medical genetics


Limitations


PCR inhibitors may affect results in forensic samples
Allele drop-out possible with degraded DNA
High mutation rate can complicate evolutionary studies
Requires known STR loci and flanking sequences
Equipment like capillary electrophoresis is costly


Applications


Forensic DNA profiling (criminal identification)
Paternity and maternity testing
Population genetics (gene flow, diversity, inbreeding)
Genetic mapping and linkage analysis
Conservation biology (identifying individuals in wild populations)
Medical genetics: Detection of STR expansion disorders (e.g., Huntington’s disease, Fragile X syndrome)


Applications


Diversity
Genome-wide
MAS, Trait mapping
Forensic, Paternity, Mapping
Conclusion
STR markers are highly reliable, co-dominant, and polymorphic, making them ideal for forensic profiling, paternity testing, and genetic mapping.
They require small DNA amounts, are PCR-based, and provide high-resolution genotyping, though they need known flanking sequences and high-resolution analysis tools.






STR Markers – 50 MCQs with Answers


Basic Concepts


1. STR stands for:
A. Short Tandem Repeat
B. Single Tandem Repeat
C. Sequence Tagged Repeat
D. Short Transcribed Region
Answer: A


2. STRs are also called:
A. Microsatellites
B. Minisatellites
C. RFLPs
D. SCARs
Answer: A


3. STR repeat units are typically:
A. 1–2 bp
B. 2–6 bp
C. 10–20 bp
D. 50–100 bp
Answer: B


4. STRs are mostly located in:
A. Coding regions
B. Non-coding regions
C. Only exons
D. Only introns
Answer: B


5. STR markers are:
A. Dominant
B. Co-dominant
C. Multi-allelic
D. All of the above
Answer: B


Principle
6. STR polymorphism arises from:
A. Variation in repeat number
B. Restriction site changes
C. Point mutations in coding region
D. Protein modifications
Answer: A


7. STR analysis is based on:
A. Hybridization
B. PCR amplification using flanking primers
C. Southern blotting
D. Protein digestion
Answer: B


8. STR primers are designed:
A. Randomly
B. Flanking the repeat region
C. Inside the repeats
D. From coding sequences only
Answer: B


9. STR markers are highly:
A. Conserved
B. Polymorphic
C. Dominant only
D. Rare in the genome
Answer: B
10. STR polymorphism is detected by:
A. Protein gel
B. DNA fragment size differences
C. RNA expression
D. Restriction enzyme digestion
Answer: B
Technical Features
11. STR alleles are distinguished based on:
A. Sequence composition
B. Fragment size
C. Hybridization intensity
D. Protein mobility
Answer: B
12. STR markers are suitable for:
A. Forensics
B. Paternity testing
C. Genetic mapping
D. All of the above
Answer: D
13. STR is a:
A. Dominant marker
B. Co-dominant marker
Answer: B
14. STR PCR requires:
A. Primers flanking the repeat
B. Restriction enzymes
C. Random primers
D. Southern blot
Answer: A
15. STR is preferred over RAPD because:
A. Highly reproducible
B. Co-dominant
C. Locus-specific
D. All of the above
Answer: D
PCR and Detection
16. STR PCR uses:
A. Short primers flanking repeats
B. Random primers
C. Restriction enzymes
D. Protein primers
Answer: A
17. STR fragment separation is done by:
A. Agarose or polyacrylamide gel electrophoresis
B. SDS-PAGE
C. Native PAGE
D. RNA gel
Answer: A
18. STR detection can also use:
A. Fluorescent labeling in capillary electrophoresis
B. Radioactive labeling
C. Silver staining
D. All of the above
Answer: D
19. STR markers require DNA from:
A. Large quantities only
B. Very small quantities
C. RNA templates
D. Protein samples
Answer: B
20. STR marker data is interpreted as:
A. Presence/absence
B. Fragment length (allele size)
C. Protein intensity
D. RNA expression
Answer: B
Applications
21. STR markers are widely used in:
A. Forensic DNA profiling
B. Paternity testing
C. Population genetics
D. All of the above
Answer: D
22. STR markers are co-dominant, meaning they can:
A. Identify homozygotes only
B. Identify heterozygotes only
C. Identify both homozygotes and heterozygotes
D. Identify dominant alleles only
Answer: C
23. STRs are used in conservation biology to:
A. Identify individuals
B. Assess population diversity
C. Study gene flow
D. All of the above
Answer: D
24. STR markers are useful in medical genetics for:
A. STR expansion disorders (e.g., Huntington’s disease)
B. Protein synthesis disorders
C. RNA splicing defects
D. All of the above
Answer: A
25. STRs are polymorphic due to:
A. DNA replication slippage
B. Restriction enzyme mutations
C. Protein folding
D. RNA editing
Answer: A
Comparison with Other Markers
26. Compared to RAPD, STRs are:
A. Less reproducible
B. More reproducible
Answer: B
27. Compared to AFLP, STRs are:
A. Locus-specific
B. Dominant only
C. Random
Answer: A
28. Compared to SCAR markers, STRs are:
A. Short tandem repeats
B. Sequence-characterized amplified regions
C. Both are co-dominant
Answer: A
29. STR markers are co-dominant unlike:
A. RAPD
B. AFLP
C. SCAR (can be co-dominant)
D. All of the above
Answer: A
30. STR markers are used for:
A. Genome-wide screening
B. Individual identification
C. Forensic DNA profiling
D. Both B and C
Answer: D
Technical Knowledge
31. STR primers are usually:
A. 18–24 bp
B. 10-mer
C. 5-mer
D. 30-mer
Answer: A
32. STR loci are:
A. Highly conserved with low polymorphism
B. Highly polymorphic
Answer: B
33. STR alleles differ in:
A. Base sequence
B. Number of repeat units
C. Primer binding sites
D. Protein expression
Answer: B
34. STR markers are PCR-based because:
A. They amplify specific fragments
B. They digest DNA
C. They detect proteins
D. They detect RNA
Answer: A
35. STR markers require:
A. Large DNA amounts
B. Small DNA amounts
Answer: B
Applications in Forensics and Medicine
36. STR markers are ideal for forensic use because:
A. Highly polymorphic
B. Locus-specific
C. Co-dominant
D. All of the above
Answer: D
37. STR markers are useful in paternity testing because:
A. They detect specific alleles inherited from parents
B. They detect proteins
C. They analyze RNA
Answer: A
38. STR markers are used in population genetics to:
A. Estimate gene diversity
B. Detect migration
C. Study inbreeding
D. All of the above
Answer: D
39. STR markers are preferred over minisatellites because:
A. Easier PCR amplification
B. Small fragment sizes suitable for degraded DNA
C. Both A and B
D. Neither A nor B
Answer: C
40. STR allele sizes are measured in:
A. Base pairs
B. Amino acids
C. Nucleotides
D. Centimorgans
Answer: A
Miscellaneous
41. STR analysis is performed using:
A. Polyacrylamide gel
B. Capillary electrophoresis
C. Agarose gel (high-resolution)
D. All of the above
Answer: D
42. STR markers are highly polymorphic due to:
A. Mutation in flanking regions
B. Repeat number variation
C. RNA splicing
D. Protein folding
Answer: B
43. STR loci are abundant in:
A. Eukaryotic genomes
B. Prokaryotic genomes
C. Mitochondrial DNA only
Answer: A
44. STRs are used in forensic databases such as:
A. CODIS (USA)
B. STRBase
C. Both A and B
D. None of the above
Answer: C
45. STR markers are co-dominant, allowing:
A. Individual identification
B. Parentage verification
C. Both
Answer: C
Advanced Knowledge
46. STR alleles are often amplified using:
A. Fluorescently labeled primers for detection
B. Radioactive primers only
C. Protein labeling
Answer: A
47. STR markers are useful in disease studies for:
A. Detecting trinucleotide repeat disorders
B. Detecting point mutations only
Answer: A
48. STR markers are often multiplexed to:
A. Amplify multiple loci in one PCR
B. Amplify single locus only
Answer: A
49. STR polymorphism arises mainly due to:
A. Point mutations
B. Slippage during DNA replication
Answer: B
50. STR markers are a standard in:
A. Forensic identification
B. Paternity testing
C. Genetic mapping
D. All of the above
Answer: D

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