DNA Extraction Methods — MCQs
Best site for DNA extraction from a 2-month-old decomposed body?
What is the technique for accurate quantification of gene expression?
For DNA extraction from blood samples, the preferred anticoagulant is:
Which of the following is a primarily RNA based technique?
DNA amplification is done by all, except:
Best sample for DNA profiling in sexual assault after 72 hours?
DNA fingerprinting can be done with all, except:
Which of the following is the least suitable source for DNA extraction?
Radiation causes cell death by:
A child was born 8 months after the father's death. The grandparents filed a case claiming that the baby is not their son's, but DNA testing confirmed paternity. What is the child called?
DNA Extraction Methods Indian Medical PG Practice Questions and MCQs
Question 1: Best site for DNA extraction from a 2-month-old decomposed body?
- A. Muscle
- B. Bone
- C. Teeth (Correct Answer)
- D. Hair
Explanation: ***Teeth*** - Teeth, particularly the **pulp and dentin**, provide a highly protected environment for DNA, making them ideal for DNA extraction from **decomposed remains** due to their robust structure. - The hard enamel casing shields the internal DNA from environmental degradation and microbial contamination, allowing for excellent preservation over extended periods. - **Dental pulp** is consistently reliable and easily accessible, making teeth the **preferred first choice** in forensic DNA extraction from decomposed bodies. *Bone* - **Bone**, particularly the **petrous portion of the temporal bone** and long bones, is also an **excellent source** of DNA in decomposed remains and is widely used in forensic practice. - However, DNA extraction from bone requires more extensive processing (demineralization, grinding) compared to teeth, making it a **second-line choice** when teeth are available. - The petrous temporal bone is notably resistant to degradation, but teeth remain more practically accessible. *Muscle* - **Muscle tissue** contains significant DNA when fresh, but is highly susceptible to **autolysis and bacterial degradation** in a decomposed body. - As decomposition progresses over 2 months, muscle tissue breaks down rapidly, reducing both the quantity and quality of recoverable DNA significantly. *Hair* - **Hair shafts** primarily contain mitochondrial DNA (mtDNA) with minimal nuclear DNA, which limits their use for individual identification. - Hair roots (if present) contain nuclear DNA, but in decomposed remains, hair is often shed or degraded, making it an unreliable source compared to teeth.
Question 2: What is the technique for accurate quantification of gene expression?
- A. PCR
- B. Real-Time Reverse Transcriptase PCR (Correct Answer)
- C. Reverse Transcriptase PCR
- D. Northern blot
Explanation: ***Real-Time Reverse Transcriptase PCR*** - This technique allows for the **quantification of gene expression** by concurrently reverse-transcribing RNA to cDNA and amplifying it while monitoring the accumulation of DNA in real-time using fluorescent reporters. - The ** threshold cycle (Ct) value** is inversely proportional to the initial amount of target mRNA, enabling precise quantification. *Northern blot* - This method is used to detect **RNA sequences** and can provide semi-quantitative data about gene expression levels based on band intensity. - However, it is generally **less sensitive** and provides less precise quantification compared to real-time PCR. *PCR* - **Standard PCR** amplifies DNA, but it is not directly used for gene expression quantification as it starts with DNA templates. - While it can be used to detect the presence of a gene, it does not quantify its expression without further modifications or additional steps like reverse transcription and real-time monitoring. *Reverse Transcriptase PCR* - This technique involves **reverse transcribing RNA into cDNA** and then performing standard PCR to amplify the cDNA. - While it confirms the presence of mRNA and allows for cDNA amplification, it is a **qualitative or semi-quantitative** method for expression, as the endpoint detection does not accurately reflect initial mRNA concentration due to plateau effects.
Question 3: For DNA extraction from blood samples, the preferred anticoagulant is:
- A. EDTA (Correct Answer)
- B. Plain bulb
- C. Formalin
- D. None of the options
Explanation: ***EDTA*** - **EDTA** (ethylenediaminetetraacetic acid) acts as an anticoagulant by **chelating calcium ions**, which are essential for the coagulation cascade, making it ideal for DNA extraction. - Using an EDTA collection tube ensures that the blood sample remains in its liquid state, preventing clot formation which can trap DNA and make isolation difficult. *Plain bulb* - A plain bulb refers to a tube without any anticoagulant, allowing the blood to **clot naturally**. - While serum can be obtained from such a tube, the DNA would be entrapped within the clot, making its extraction **less efficient and potentially damaging**. *Formalin* - **Formalin** (a solution of formaldehyde) is a fixative used to preserve tissue morphology by **cross-linking proteins**. - While useful for histopathology, it **damages DNA** through chemical modifications and fragmentation, making it unsuitable for DNA isolation or genetic analysis. *None of the options* - This option is incorrect because **EDTA is a widely recognized and appropriate** anticoagulant for preserving DNA samples from blood for molecular studies.
Question 4: Which of the following is a primarily RNA based technique?
- A. Western blotting
- B. Northern blotting (Correct Answer)
- C. Southern blotting
- D. Sanger's technique
Explanation: ***Northern blotting*** - **Northern blotting** is a molecular biology technique used to study **gene expression** by detecting specific **RNA molecules** (mRNA) in a sample. - It involves separating RNA fragments by **gel electrophoresis**, transferring them to a membrane, and then detecting specific sequences using **labeled probes**. *Western blotting* - **Western blotting** is a technique used to detect specific **proteins** in a sample. - It involves separating proteins by **gel electrophoresis**, transferring them to a membrane, and then detecting specific proteins using labeled **antibodies**. *Southern blotting* - **Southern blotting** is a molecular biology method used for the detection of **specific DNA sequences** in DNA samples. - It involves separating **DNA fragments** by **gel electrophoresis**, transferring them to a membrane, and then hybridizing with a labeled probe. *Sanger's technique* - **Sanger sequencing**, or the **dideoxy chain-termination method**, is a widely used method for **DNA sequencing**. - It uses **dideoxynucleotides** to terminate DNA synthesis at specific bases, allowing the determination of the **DNA sequence**.
Question 5: DNA amplification is done by all, except:
- A. DNA sequencing (Correct Answer)
- B. Loop-mediated isothermal amplification (LAMP)
- C. Ligase chain reaction
- D. Polymerase chain reaction
Explanation: ***DNA sequencing*** - **DNA sequencing** determines the **nucleotide base order** in a DNA molecule but does not increase the amount of DNA. - While requiring a DNA template, it is an **analytical technique** rather than an amplification method. *Loop-mediated isothermal amplification (LAMP)* - **LAMP** is an **isothermal DNA amplification** technique that amplifies target DNA sequences at a constant temperature (60-65°C). - It uses a DNA polymerase with strand displacement activity and 4-6 primers to produce large amounts of DNA rapidly. *Ligase chain reaction* - **LCR** is an amplification method that detects specific **DNA sequences** by ligating adjacent probes. - It amplifies the signal from a target DNA sequence rather than the DNA itself by creating many copies of joined probes. *Polymerase chain reaction* - **PCR** is a widely used technique for **amplifying** a specific segment of DNA to produce many copies. - It involves cycles of **denaturation**, **annealing**, and **extension** using a DNA polymerase.
Question 6: Best sample for DNA profiling in sexual assault after 72 hours?
- A. Victim's clothes (Correct Answer)
- B. Cervical swab
- C. Vaginal swab
- D. Fingernail scrapings
Explanation: ***Victim's clothes*** - After 72 hours, **spermatozoa** in or on the skin are often degraded, but foreign DNA (from the perpetrator's skin cells, semen, or other bodily fluids) can persist on clothing, especially in protected areas. - Clothing acts as a **storage medium for trace evidence**, and DNA can remain viable for profiling much longer than on mucous membranes due to drying and lack of enzymatic degradation. *Cervical swab* - **Spermatozoa** typically become undetectable in the cervix within 24-48 hours, though some studies show persistence up to 72 hours. - Beyond 72 hours, the likelihood of obtaining viable **perpetrator DNA** from a cervical swab significantly decreases due to degradation and cellular turnover. *Vaginal swab* - **Spermatozoa** found in the vagina are subject to enzymatic degradation and expulsion, with viability for DNA profiling decreasing significantly after 24-48 hours. - While trace DNA might still be present, the quantity and quality for profiling are usually much lower than on clothing after such an extended period. *Fingernail scrapings* - While fingernail scrapings can yield **perpetrator DNA** if there was physical struggle, this is highly dependent on the act of scraping the assailant's skin. - It is not a guaranteed source in every sexual assault and is less likely to contain strong DNA evidence after 72 hours compared to clothing, which captures shed cells and fluids passively.
Question 7: DNA fingerprinting can be done with all, except:
- A. Saliva
- B. WBC
- C. RBC (Correct Answer)
- D. Spermatozoa
Explanation: ***RBC*** - **Mature red blood cells** lack a nucleus and therefore do not contain **DNA**. - DNA fingerprinting relies on analyzing an individual's unique DNA sequence, which is not present in RBCs. *Saliva* - Saliva contains **epithelial cells** from the mouth, which have intact nuclei and thus sufficient DNA for analysis [2]. - It is a common and non-invasive source of DNA for forensic and genetic testing [2]. *WBC* - **White blood cells** (leukocytes) are nucleated cells that contain a full complement of DNA [2]. - They are an excellent source of DNA for genetic analysis, including DNA fingerprinting. *Spermatozoa* - **Sperm cells** are haploid and contain a nucleus with DNA, making them suitable for DNA fingerprinting [1]. - They are frequently used in forensic cases, particularly in sexual assault investigations [1].
Question 8: Which of the following is the least suitable source for DNA extraction?
- A. CSF (Correct Answer)
- B. Hair roots
- C. Semen
- D. Buccal mucosa
Explanation: ***CSF*** - **Cerebrospinal fluid (CSF)** contains a relatively **low number of cells**, making it a poor source for DNA extraction compared to other bodily fluids due to the scarcity of nuclear DNA. - While DNA can be extracted from CSF for specific diagnostic purposes (e.g., detection of pathogens), it is generally **not the preferred source** for DNA profiling or genetic studies due to the limited yield and potential for degradation. *Hair roots* - **Hair roots** (specifically the follicular tag) contain a significant number of **nucleated cells**, making them an excellent source for DNA extraction. - The DNA extracted from hair roots is often robust and sufficient for **forensic analysis** and genetic testing. *Semen* - **Semen** contains a high concentration of **sperm cells**, which are rich in nuclear DNA, making it a very good source for DNA extraction. - It is frequently used in **forensic investigations** and paternity testing due to its high DNA content. *Buccal mucosa* - **Buccal cells** scraped from the inside of the cheek provide a non-invasive and **abundant source of nucleated cells** for DNA extraction. - This method is widely used for genetic testing, **ancestry tracing**, and clinical diagnostics because of its ease of collection and high DNA yield.
Question 9: Radiation causes cell death by:
- A. Charring of nucleoproteins
- B. Ionization (Correct Answer)
- C. Disruption of cytosol
- D. Destroying their mitochondria
Explanation: ***Ionization*** - Radiation, particularly **ionizing radiation**, causes cell death by directly or indirectly damaging cellular components through the process of **ionization**. [1] - This involves the removal of electrons from atoms or molecules, leading to the formation of highly reactive **free radicals** (especially hydroxyl radicals from water radiolysis) that can damage DNA, proteins, and lipids. [1] - The most critical lethal lesion is **DNA double-strand breaks**, which are difficult to repair and trigger apoptosis or mitotic catastrophe. [1] *Charring of nucleoproteins* - **Charring** typically refers to the combustion or burning of organic matter, which is not the mechanism of cell death caused by therapeutic radiation doses. - While radiation can cause protein denaturation, it does not lead to the macroscopic charring of nucleoproteins within cells. *Disruption of cytosol* - While severe radiation damage can impact the entire cell, direct and selective **disruption of the cytosol** is not the primary or most impactful mechanism of radiation-induced cell death. - The critical targets for radiation-induced cell death are primarily the **nucleus** and its DNA, not the cytoplasm. [2] *Destroying their mitochondria* - Although radiation can induce **mitochondrial dysfunction** and contribute to cell death through apoptosis, it is not the initial or primary mechanism of cell destruction. - The most critical and direct damage leading to cell death is inflicted upon the **DNA** in the nucleus, particularly causing double-strand breaks. [1] **References:** [1] Cross SS. Underwood's Pathology: A Clinical Approach. 6th ed. (Basic Pathology) introduces the student to key general principles of pathology, both as a medical science and as a clinical activity with a vital role in patient care. Part 2 (Disease Mechanisms) provides fundamental knowledge about the cellular and molecular processes involved in diseases, providing the rationale for their treatment. Part 3 (Systematic Pathology) deals in detail with specific diseases, with emphasis on the clinically important aspects., pp. 100-102. [2] Kumar V, Abbas AK, et al.. Robbins and Cotran Pathologic Basis of Disease. 9th ed. Central Nervous System Synapse, pp. 438-439.
Question 10: A child was born 8 months after the father's death. The grandparents filed a case claiming that the baby is not their son's, but DNA testing confirmed paternity. What is the child called?
- A. Suppositious child
- B. Fabricated child
- C. Posthumous child (Correct Answer)
- D. Illegitimate child
Explanation: ***Posthumous child*** - A **posthumous child** is one born after the death of its father. - In most legal systems, such a child is considered an heir and has rights equivalent to those born before the father's death, especially after paternity is confirmed. *Suppositious child* - A **suppositious child** is one who is falsely substituted for another, typically with the intent to defraud or claim an inheritance under false pretenses. - This term does not apply here as paternity was confirmed by DNA testing, indicating the child is genuinely linked to the deceased father. *Fabricated child* - The term **fabricated child** implies the child does not exist or was created through fraudulent means, often in the context of false claims or elaborate schemes. - In this scenario, the child is real and paternity has been verified, making "fabricated" an inaccurate description. *Illegitimate child* - An **illegitimate child** is historically defined as one born outside of marriage between its biological parents. - While the father died before the child's birth, the question does not provide information about the parents' marital status, and the term primarily refers to marital legality rather than the circumstances of the father's death.
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