Skip to main content

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

Comments

Post a Comment

Popular Posts

••CLASSIFICATION OF ALGAE - FRITSCH

      MODULE -1       PHYCOLOGY  CLASSIFICATION OF ALGAE - FRITSCH  ❖F.E. Fritsch (1935, 1945) in his book“The Structure and  Reproduction of the Algae”proposed a system of classification of  algae. He treated algae giving rank of division and divided it into 11  classes. His classification of algae is mainly based upon characters of  pigments, flagella and reserve food material.     Classification of Fritsch was based on the following criteria o Pigmentation. o Types of flagella  o Assimilatory products  o Thallus structure  o Method of reproduction          Fritsch divided algae into the following 11 classes  1. Chlorophyceae  2. Xanthophyceae  3. Chrysophyceae  4. Bacillariophyceae  5. Cryptophyceae  6. Dinophyceae  7. Chloromonadineae  8. Euglenineae    9. Phaeophyceae  10. Rhodophyceae  11. Myxophyce...
Post a Comment
Read more

ANTIGEN

1. Definition of ANTIGEN An antigen is any substance which, when introduced into the body, induces an immune response and specifically reacts with antibodies or sensitized T-cells. 👉 Substances may be foreign or self, but immunogenic antigens are usually foreign molecules. 2. Immunogen vs Antigen Immunogen Substance that induces immune response Antigen Substance that reacts with immune products Hapten Antigenic but not immunogenic alone 👉 All immunogens are antigens, but all antigens are not immunogens. 3. Chemical Nature of Antigens Antigens may be: a) Proteins (Most potent) Enzymes Toxins Structural proteins b) Polysaccharides Bacterial capsules Cell wall components c) Glycoproteins Viral envelope proteins d) Lipids & Nucleic acids Weakly antigenic Become immunogenic when combined with proteins 4. Properties of Antigens An ideal antigen shows: Foreignness High molecular weight (>10,000 Da) Chemical complexity Stability Specificity Degradability (processing by APCs) 5. Types ...
Post a Comment
Read more

MHC MOLECULES NOTES AND MCQ

MHC MOLECULES  1. INTRODUCTION MHC (Major Histocompatibility Complex): A set of cell surface proteins essential for the adaptive immune system to recognize foreign molecules. Function: Presents antigenic peptides to T cells, initiating immune responses. Location: Found in all vertebrates; in humans, MHC is called HLA (Human Leukocyte Antigen). HLA Full Form: Human Leukocyte Antigen 2. Types of MHC Molecules MHC molecules are classified into two main classes and a third minor class: A. Class I MHC (MHC-I) Expression: On all nucleated cells (except RBCs) Function: Presents endogenous antigens (from inside the cell, e.g., viral proteins) to CD8+ cytotoxic T cells Structure: Heavy α chain (3 domains: α1, α2, α3) Light chain (β2-microglobulin) Peptide-binding groove formed by α1 and α2 Peptide length: Typically 8–10 amino acids Genes: HLA-A, HLA-B, HLA-C (highly polymorphic) B. Class II MHC (MHC-II) Expression: On antigen-presenting cells (APCs) like dendritic cells, macrophages, B cell...
Post a Comment
Read more

Southern Blotting

Southern Blotting  Introduction Southern blotting is a molecular biology technique used for the detection of specific DNA sequences in a complex mixture of DNA. It was developed by Edwin M. Southern in 1975. The method involves restriction digestion of DNA, separation by gel electrophoresis, transfer (blotting) onto a membrane, and hybridization with a labeled DNA probe. Principle of Southern Blotting The technique is based on the principle of complementary base pairing. A single-stranded labeled DNA probe hybridizes specifically with its complementary DNA sequence immobilized on a membrane. Detection of the label confirms the presence and size of the target DNA fragment. Steps Involved in Southern Blotting. 1. Isolation of DNA Genomic DNA is extracted from cells or tissues. DNA must be pure and intact to ensure accurate results. 2. Restriction Enzyme  Digestion DNA is digested using specific restriction endonucleases. Produces DNA fragments of varying lengths. Choice of enzym...
Post a Comment
Read more

Third Semester M.Sc. Degree Examination, December 2025BotanyBO 531: PLANT BREEDING, HORTICULTURE AND BIOSTATISTICS.

Third Semester M.Sc. Degree Examination, December 2025 Botany BO 531: PLANT BREEDING, HORTICULTURE AND BIOSTATISTICS (2024 Admission) Time: 3 Hours Max. Marks: 75 Answer these questions in one or two sentences.  Each question carries 1 mark. 1. Who introduced maize in India? 2.Name an organization in India for plant introduction. 3.  What is BSI? 4.What is Super Rice? 5.Define somaticplastic sterility? 6.What is a chemical mutagen? Give example. 7.What is Arboriculture? 8.What is MAP in Horticulture? 9.Define probability. 10. What is LSD in Biostatistics? (10 × 1 = 10 Marks) II.Answer the following questions in not more than 50 words . 11] Comment on Primary plant introduction.                OR 12. What are microcenters? Explain. 13.Explain zygotic sterility. How can we overcome this in plant breeding?                          OR 14 Describe a green house and its uses. ...
Post a Comment
Read more

Mapping of DNA

DNA MAPPING   1. Introduction DNA mapping refers to the process of determining the relative positions of genes or DNA sequences on a chromosome. It provides information about the organization, structure, and distance between genetic markers in a genome. DNA mapping is an essential step toward genome sequencing, gene identification, disease diagnosis, and genetic engineering. DNA maps serve as roadmaps that guide researchers to locate specific genes associated with traits or diseases. 2. Objectives of DNA Mapping To locate genes on chromosomes To determine the order of genes To estimate distances between genes or markers To study genome organization To assist in genome sequencing projects. 3. Principles of DNA Mapping DNA mapping is based on: Recombination frequency Physical distance between DNA fragments Hybridization of complementary DNA Restriction enzyme digestion Use of genetic markers The closer two genes are, the less frequently they recombine during meiosis. 4 . Types of DNA...
2 comments
Read more

Plaque Blotting Technique

Plaque Blotting Technique Introduction Plaque blotting is a molecular biology screening technique used to identify specific DNA or RNA sequences present in bacteriophage plaques formed on a bacterial lawn. It is especially useful in the screening of recombinant phage libraries such as λ (lambda) phage genomic or cDNA libraries. This technique combines: Plaque assay (to isolate individual phage clones) Blotting technique (to transfer nucleic acids onto a membrane) Hybridization (to detect specific sequences using labeled probes) Principle of Plaque Blotting The principle of plaque blotting is based on nucleic acid hybridization. Each plaque represents a clone of phage particles containing identical DNA. DNA from phage particles in plaques is: Released Denatured into single strands Transferred onto a nitrocellulose or nylon membrane The membrane is incubated with a labeled DNA/RNA probe complementary to the target sequence. Hybridization between probe and target DNA identifies positive p...
Post a Comment
Read more

PLANT INTROUCTION: TYPES AND PROCEDURE

PLANT INTROUCTION: TYPES AND PROCEDURE 1. Introduction Plant introduction is the transfer of plant species, varieties, or genotypes from one geographical area to another where they were not previously grown.  It is one of the oldest and most important methods of crop improvement and forms the basis of modern agriculture. Many important crops such as wheat, rice, maize, potato, cotton, sugarcane, and tobacco have been introduced from other countries. Definition : Plant introduction is the process of introducing plants or plant genetic material from their native or foreign regions into a new area for cultivation, evaluation, and utilization. 2. Objectives of Plant Introduction To increase crop productivity To introduce high-yielding varieties To obtain disease- and pest-resistant plants To introduce early maturing or drought-tolerant varieties To improve quality traits (oil content, protein, fiber, taste) To broaden the genetic base of crops To replace inferior local varieties To dev...
Post a Comment
Read more