Chapter 5 · Topic 5.1 · Prelims + Mains1 of 3
Biotechnology: Recombinant DNA, CRISPR and genomics
Key points
- rDNA tools: restriction enzymes (cut), ligase (join), vector (carry).
- First rDNA: Cohen and Boyer, 1972. Human insulin in E. coli: Eli Lilly, 1983.
- First gene therapy: ADA deficiency, 1990.
- CRISPR-Cas9: Nobel Chemistry 2020 (Charpentier, Doudna).
- SDN-1/2 edited plants exempted (30 March 2022). First edited rice: 4 May 2025.
- GenomeIndia: 10,000 genomes opened 9 January 2025 via IBDC.
5 PYQs 2013–2026
Prelims box: facts and traps
| Item | Fact |
|---|---|
| DRR Dhan 100 (Kamala) | from Samba Mahsuri |
| Pusa DST Rice 1 | from MTU 1010 |
| Claimed yield gain | 19% (potential) |
- Trap (Prelims 2026): GenomeIndia is not part of the Human Genome Project.
- Trap (Prelims 2014): budding and grafting do not make transgenic crops.
On this page (3 sections)
Genetic engineering and recombinant DNA
Genetic engineering changes the genetic material (DNA or RNA) of an organism directly, by taking a gene out of one organism and putting it into another. It is like copying one useful recipe from one cookbook into another. The key steps are (NCERT Biology, Class 12, Chapter 9):
- identify the DNA with the desirable gene,
- introduce it into the host,
- keep it there so that it is passed on to the next generations.
Three tools make it possible (NCERT Biology, Class 12, Chapter 9):
- Restriction enzymes, the ‘molecular scissors’, cut DNA at specific sequences. EcoRI, for example, comes from Escherichia coli RY 13.
- DNA ligase, the ‘glue’, joins the cut pieces.
- A vector, the ‘delivery van’, carries the new gene into the host cell. It is usually a plasmid (an autonomously replicating circular extra-chromosomal DNA of bacteria) or a bacteriophage (a virus that infects bacteria).
Stanley Cohen and Herbert Boyer made the first recombinant DNA in 1972 by linking an antibiotic resistance gene with a plasmid of Salmonella typhimurium.
DNA is the same chemical in every organism, so a gene can work in a very different host. Bt toxin genes from a bacterium work in cotton. In 1983 Eli Lilly put DNA for the A and B chains of human insulin into plasmids of E. coli to make human insulin (NCERT Biology, Class 12, Chapter 10). So recombinant DNA technology allows genes to be moved across different species of plants, from animals to plants, and from microorganisms to higher organisms (Prelims 2013: answer (d), 1, 2 and 3).
Recombinant DNA technology (Genetic Engineering) allows genes to be transferred 1. across different species of plants 2. from animals to plants 3. from microorganisms to higher organisms Select the correct answer using the codes given below.
- 1 only
- 2 and 3 only
- 1 and 3 only
- 1, 2 and 3
Show answer
Answer: (d) · UPSC official key
Gene therapy, or genetic medicine, puts a working gene into a patient’s cells to correct or make up for the faulty genes that cause disease. The first clinical gene therapy, in 1990, was for a 4-year-old girl with adenosine deaminase (ADA) deficiency, an immune disorder. A working ADA gene was put into her lymphocytes (white blood cells) using a retroviral vector (NCERT Biology, Class 12, Chapter 10). Carriers today include modified viruses (viral vectors) and nanoparticles, which are less likely to cause immune reactions than viral vectors (MedlinePlus Genetics, US National Library of Medicine). Gene therapy delivers or edits particular genes. It does not rewrite the whole genome, so UPSC rejected statement 3 (Prelims 2026: answer (c), 1 and 2 only, answer key provisional).
Which of the following statements with regard to genetic medicine is/are correct ? 1. Genetic medicines correct/compensate for the faulty genes responsible for disease. 2. Engineered viruses and lipid nanoparticles are used as carriers of the genetic medicine. 3. Genetic medicines alter the entire DNA sequence. Select the answer using the code given below :
- 1 only
- 2 and 3 only
- 1 and 2 only
- 1, 2 and 3
Show answer
Answer: (c) · UPSC provisional key (final key awaited)
Gene editing and CRISPR
The 2020 Nobel Prize in Chemistry went to Emmanuelle Charpentier and Jennifer A. Doudna “for the development of a method for genome editing”. This is the CRISPR/Cas9 genetic scissors, which can change the code of life in a few weeks (nobelprize.org). Cas9 is the cutting part. Genome editing tools cut the DNA at a specific spot, after which scientists can remove, add or replace DNA, like using find-and-replace in a word processor (NHGRI). So Cas9 is a molecular scissors used in targeted gene editing (Prelims 2019: answer (a)).
What is Cas9 protein that is often mentioned in news?
- A molecular scissors used in targeted gene editing
- A biosensor used in the accurate detection of pathogens in patients
- A gene that makes plants pest-resistant
- A herbicidal substance synthesized in genetically modified crops
Show answer
Answer: (a) · UPSC official key
UPSC 2018 tested where such terms belong. Per the official key, CRISPR-Cas9 is not a particle physics term and Belle II is not an artificial intelligence term. Only the blockchain and cryptocurrency pair was correct (Prelims 2018: answer (b), 2 only).
Consider the following pairs : Terms sometimes seen in news Context/Topic 1. Belle II experiment Artificial Intelligence 2. Blockchain technology Digital/Cryptocurrency 3. CRISPR-Cas9 Particle Physics Which of the pairs given above is/are correctly matched ?
- 1 and 3 only
- 2 only
- 2 and 3 only
- 1, 2 and 3
Show answer
Answer: (b) · UPSC official key
Most ethical debate is about the human germline (egg, sperm and early embryo cells), because changes made there would pass down to future generations. As of 2014 about 40 countries discouraged or banned research on germline editing (NHGRI, What are the Ethical Concerns of Genome Editing?). UPSC 2020 treated all three as technically possible today: genetic changes can be made in the cells that produce eggs or sperm of a future parent, a person’s genome can be edited at the early embryo stage, and human induced pluripotent stem cells can be injected into a pig embryo (Prelims 2020: answer (d), 1, 2 and 3).
Consider the following statements : 1. Genetic changes can be introduced in the cells that produce eggs or sperms of a prospective parent. 2. A person’s genome can be edited before birth at the early embryonic stage. 3. Human induced pluripotent stem cells can be injected into the embryo of a pig. Which of the statements given above is/are correct ?
- 1 only
- 2 and 3 only
- 2 only
- 1, 2 and 3
Show answer
Answer: (d) · UPSC official key
India’s rules treat edits that add no foreign DNA differently. By an Office Memorandum of 30 March 2022, MoEFCC exempted genome-edited plants in the SDN-1 and SDN-2 categories, which are free of exogenously introduced (outside) DNA, from Rules 7-11 of the Rules 1989 (PIB, 19 Jul 2022). On 4 May 2025 ICAR announced India’s first two genome-edited rice varieties: DRR Dhan 100 (Kamala), from Samba Mahsuri, and Pusa DST Rice 1, from MTU 1010. Both were made with CRISPR-Cas without adding foreign DNA (PIB, 4 May 2025).
| Genome-edited rice (ICAR, May 2025) | Figure | Status |
|---|---|---|
| Yield increase | 19% | ICAR-reported potential, not a measured farm average |
| Cut in greenhouse gas emissions | 20% | ICAR-reported potential |
| Irrigation water saved | 7,500 million cubic metres | ICAR-reported potential |
Source: PIB, Ministry of Agriculture and Farmers Welfare, 4 May 2025 (PRID 2126802). These are benefits the varieties ‘offer’, as announced. They are not measured outcomes.
RNAi, genome mapping and GenomeIndia
RNA interference (RNAi) silences a specific mRNA. A matching double-stranded RNA molecule binds to it and stops it being turned into protein, like putting a gag on a messenger. RNAi happens in all eukaryotic organisms as a way of cell defence. NCERT’s example: genes of the nematode (roundworm) Meloidegyne incognitia were put into tobacco through Agrobacterium vectors. The plant made sense and anti-sense RNA, the parasite’s mRNA was silenced and it could not survive (NCERT Biology, Class 12, Chapter 10). UPSC’s answer: RNAi is used in gene silencing therapies, in therapies for cancer, and to produce crop plants resistant to viral pathogens, but not hormone replacement therapies (Prelims 2019: answer (a), 1, 2 and 4).
‘RNA interference (RNAi)’ technology has gained popularity in the last few years. Why? 1. It is used in developing gene silencing therapies. 2. It can be used in developing therapies for the treatment of cancer. 3. It can be used to develop hormone replacement therapies. 4. It can be used to produce crop plants that are resistant to viral pathogens. Select the correct answer using the code given below.
- 1, 2 and 4
- 2 and 3
- 1 and 3
- 1 and 4 only
Show answer
Answer: (a) · UPSC official key
Which techniques create transgenic crops? Gene silencing does (as in the nematode-resistant tobacco above). So does engineered cytoplasmic male sterility: GM mustard carries the barnase and barstar genes for male sterility, used to make hybrids (PIB, 7 Apr 2008). Budding and grafting only join existing plants and add no new genes (Prelims 2014: answer (b), 2 and 3 only).
Consider the following techniques/phenomena : 1. Budding and grafting in fruit plants 2. Cytoplasmic male sterility 3. Gene silencing Which of the above is/are used to create transgenic crops?
- 1 only
- 2 and 3 only
- 1 and 3 only
- None
Show answer
Answer: (b) · UPSC official key
Gene mapping means knowing where genes sit on chromosomes. It helps breeders trace the pedigree of livestock and develop disease-resistant animal breeds, but it cannot explain the causes of all human diseases (Prelims 2011: answer (c), 1 and 3 only). In crops, genome sequencing can find genetic markers for disease resistance and drought tolerance, cut the time needed to develop new varieties and decode host-pathogen relationships (Prelims 2017: answer (d), 1, 2 and 3).
At present, scientists can determine the arrangement or relative positions of genes or DNA sequences on a chromosome. How does this knowledge benefit us ? 1. It is possible to know the pedigree of livestock. 2. It is possible to understand the causes of all human diseases. 3. It is possible to develop disease-resistant animal breeds. Which of the statements given above is/are correct ?
- 1 and 2 only
- 2 only
- 1 and 3 only
- 1, 2 and 3
Show answer
Answer: (c) · UPSC official key
With reference to agriculture in India, how can the technique of ‘genome sequencing’ often seen in the news, be used in the immediate future ? 1. Genome sequencing can be used to identify genetic markers for disease resistance and drought tolerance in various crop plants. 2. This technique helps in reducing the time required to develop new varieties of crop plants. 3. It can be used to decipher the host-pathogen relationships in crops. Select the correct answer using the code given below :
- 1 only
- 2 and 3 only
- 1 and 3 only
- 1, 2 and 3
Show answer
Answer: (d) · UPSC official key
GenomeIndia is led by the Department of Biotechnology (DBT) and aims to create a full database of India’s genetic diversity. On 9 January 2025 its data set of 10,000 whole genome samples from diverse Indian populations was opened to researchers through the Indian Biological Data Centre (IBDC), giving a rich catalogue of genetic variations (PIB, 9 Jan 2025). It is a national project, not a part of the Human Genome Project. Its main aim is to build a catalogue of genetic diversity of the Indian population (Prelims 2026: answer (b), 2 and 3 only, answer key provisional).
Which of the following statements with regard to GenomeIndia Project is/are correct ? 1. It is a part of the Human Genome Project. 2. The project is funded by the Department of Biotechnology (DBT), Government of India. 3. Its primary aim is to build a catalogue of genetic diversity of the Indian population. Select the answer using the code given below :
- 1 only
- 2 and 3 only
- 1 and 2 only
- 1, 2 and 3
Show answer
Answer: (b) · UPSC provisional key (final key awaited)
What UPSC asks: Prelims: scissors, glue and vector, Cas9 cuts DNA, RNAi silences mRNA. Mains: insulin from E. coli, gene therapy (ADA, 1990), CRISPR Nobel 2020, SDN-1/2 with no foreign DNA, gene maps for breeding, GenomeIndia 10,000 genomes.
Mains box: analysis and answer points
- Gene editing: promise, germline ethics, India's SDN rules.
- Genomics: GenomeIndia and precision medicine.
Practice
Practice MCQs (8)
In genome editing with CRISPR-Cas9, the term 'PAM' (protospacer adjacent motif) refers to
Answer (c) & explanation
The PAM is a short signature of two to six bases immediately next to the target sequence in the DNA; for the commonly used Cas9 of Streptococcus pyogenes it is NGG. Cas9 first scans the DNA for a PAM and only then checks whether the guide RNA matches the adjacent sequence. The PAM is present in the invading virus but absent beside the spacer in the bacterium's own CRISPR array, which is how the bacterium avoids cutting itself. Because a PAM must be present, not every sequence in a genome can be targeted.
Consider the following statements:
1. The abbreviation CRISPR stands for Clustered Regularly Interspaced Short Palindromic Repeats.
2. Arrays made of such repeats separated by spacer sequences occur in many bacteria and archaea.
3. Similar CRISPR arrays occur naturally in the chromosomes of human beings.
Which of the statements given above is/are correct?
Answer (b) & explanation
Statements 1 and 2 are correct. The name describes what was seen in the genome: short repeated sequences that read similarly in both directions, spaced at regular intervals by unique spacers. Such arrays are widespread among bacteria and archaea, where they serve as immune memory. Statement 3 is wrong: human chromosomes have no natural CRISPR arrays; in human cells the Cas protein and the guide RNA have to be introduced from outside.
With reference to the guide RNA used in CRISPR-Cas9 genome editing, consider the following statements:
1. In the natural bacterial system a small CRISPR RNA pairs with a second RNA molecule, and in the laboratory the two are usually fused into a single guide RNA.
2. The guide RNA selects the site to be cut by base-pairing with a stretch of about twenty nucleotides of the target DNA.
3. To direct the system to a different gene, the Cas9 protein has to be redesigned afresh each time.
Which of the statements given above is/are correct?
Answer (b) & explanation
Statements 1 and 2 are correct. In Streptococcus pyogenes the crRNA pairs with a tracrRNA, and the 2012 work that turned the system into a tool fused them into one single guide RNA. The guide carries about twenty nucleotides that base-pair with the chosen DNA sequence, which is what makes the cut site programmable. Statement 3 is wrong and is the heart of the CRISPR revolution: the protein stays the same and only the short RNA sequence is rewritten, which is far simpler than redesigning a protein for every new target.
With reference to the natural origin of CRISPR, consider the following statements:
1. CRISPR sequences were first noticed as unusual repeated stretches in bacterial genomes long before their function was understood.
2. The spacer sequences lying between the repeats are fragments of genetic material of viruses and plasmids that had attacked the cell earlier.
3. A bacterium that survives such an attack passes this acquired resistance on to its daughter cells.
Which of the statements given above are correct?
Answer (d) & explanation
All three are correct. Repeated stretches near the iap gene of a bacterium were reported in 1987, years before anyone knew what they did. In 2005 it was shown that the spacers between the repeats match sequences of bacteriophages and plasmids, and in 2007 an experiment on Streptococcus thermophilus proved that these spacers give the cell resistance to the matching phage. Because the array sits in the bacterial chromosome, the memory is copied at cell division, which makes CRISPR an inheritable form of adaptive immunity in prokaryotes.
Which one of the following statements about the CRISPR-Cas9 system is not correct?
Answer (d) & explanation
Cas9 has no sequence specificity of its own. It becomes a precise tool only when loaded with a guide RNA, which pairs with the chosen DNA sequence; this is why the system is called RNA-guided. The other three statements are correct: the system is borrowed from a bacterial defence mechanism, the break is sealed by the cell's own repair pathways, and a new target needs only a new guide sequence.
Consider the following pairs: Scientist — Contribution to CRISPR research
1. Francisco Mojica — Proposed that the spacer sequences in bacterial arrays come from viruses
2. Rodolfo Barrangou and colleagues — Showed by experiment in a yoghurt bacterium that CRISPR gives resistance to a virus
3. Emmanuelle Charpentier and Jennifer Doudna — First demonstrated that zinc finger nucleases can cut chosen sites in DNA
How many of the pairs given above are correctly matched?
Answer (b) & explanation
Pairs 1 and 2 are correctly matched. Mojica's comparison of spacer sequences with databases in 2005 suggested that they come from phages and plasmids, and the 2007 experiment on Streptococcus thermophilus, a bacterium used in dairy cultures, confirmed that spacers give phage resistance. Pair 3 is wrong: Charpentier and Doudna, with colleagues, showed in 2012 that the CRISPR-Cas9 complex with a single guide RNA can be programmed to cut DNA; zinc finger nucleases are an older, separate technology.
With reference to the working of a CRISPR-Cas system in a bacterium, consider the following statements:
1. In the first stage, a piece of the invading genetic material is captured and inserted as a new spacer into the CRISPR array.
2. In the second stage, the array is transcribed and the long transcript is processed into small CRISPR RNAs.
3. In the final stage, the Cas protein guided by such an RNA destroys only the RNA of the invader and never its DNA.
Which of the statements given above is/are correct?
Answer (b) & explanation
Statements 1 and 2 are correct. The system works in three steps: adaptation, in which a fragment of the invader is added to the array as a new spacer; expression, in which the array is transcribed and cut into small crRNAs; and interference, in which the Cas protein loaded with a crRNA destroys the matching invader. Statement 3 is wrong: in the widely used type II system the target destroyed is the invader's DNA. Only some systems, such as those built around Cas13, act on RNA.
Which one of the following statements regarding the production of recombinant proteins is not correct?
Answer (c) & explanation
Option (c) is the incorrect statement. Bacteria lack the splicing machinery to remove introns, so if a eukaryotic gene with its introns were put into them, the protein would come out wrong. Scientists therefore use complementary DNA (cDNA), made from mature mRNA by reverse transcriptase, which has no introns. The other statements are correct: calcium chloride and heat shock make bacteria competent, disarmed retroviruses are used as animal-cell vectors, and recombinant proteins are made at scale in bioreactors followed by downstream processing.
0 / 0 correct
Prelims PYQs on this topic (3)
Recombinant DNA technology (Genetic Engineering) allows genes to be transferred
- 1. across different species of plants
- 2. from animals to plants
- 3. from microorganisms to higher organisms
Select the correct answer using the codes given below.
Answer (d) & explanation
All three are correct (d). Because the genetic code is universal, a gene from one organism can work in another. Recombinant DNA technology therefore allows transfer across plant species (1), from animals to plants, as in trials with a fish antifreeze gene in tomato (2), and from microbes to higher organisms, as with the Bt gene in cotton and the human insulin gene in bacteria in reverse (3). So options (a), (b) and (c) leave out real possibilities.
Notice the tools: restriction enzymes cut DNA, ligase joins it, and plasmids or Agrobacterium carry it. Newer CRISPR-Cas9 editing (Nobel 2020) changes a plant's own genes; India exempted such SDN-1 and SDN-2 edits from GM rules in 2022. Trap: the universality of the code makes all three transfers possible.
Answer as per the official UPSC answer key.
Which of the following statements with regard to GenomeIndia Project is/are correct ?
- 1. It is a part of the Human Genome Project.
- 2. The project is funded by the Department of Biotechnology (DBT), Government of India.
- 3. Its primary aim is to build a catalogue of genetic diversity of the Indian population.
Select the answer using the code given below :
Answer (b) & explanation
Statements 2 and 3 are correct (b). Statement 2 is right: GenomeIndia (2020) is funded by the Department of Biotechnology. Statement 3 is right: it sequenced 10,000 genomes from many Indian communities to build a catalogue of the country's genetic variation, and the data was released in 2025. Statement 1 is wrong: the international Human Genome Project was a separate effort that ended in 2003. So options (a), (c) and (d) fail.
Notice the uses: finding gene variants behind diseases common in India, such as sickle cell and thalassaemia, and building personalised medicine. The data is stored at the Indian Biological Data Centre in Faridabad. A larger follow-up aims to sequence one million genomes.
Answer as per the official UPSC answer key.
Mycorrhizal biotechnology has been used in rehabilitating degraded sites because mycorrhiza enables the plants to
- 1. resist drought and increase absorptive area
- 2. tolerate extremes of pH
- 3. resist disease infestation
Select the correct answer using the codes given below.
Answer (d) & explanation
All three are correct (d). Mycorrhiza is a partnership between a fungus and plant roots. The fungal threads extend the absorbing area of roots far into the soil, helping the plant take up water and resist drought (1). They help plants tolerate extremes of pH, salinity and heavy metals in poor soils (2). They also protect roots against soil pathogens by forming a barrier and competing with them (3). This is why mycorrhizal inoculants are used to rehabilitate degraded sites such as mine spoils. So (a), (b) and (c) leave out real benefits.
Notice the main benefit: mycorrhiza greatly improves phosphorus uptake. About 80% of land plants form such partnerships. TERI in India developed mycorrhizal biofertilisers for wasteland reclamation. Trap: all three effects are documented.
Answer as per the official UPSC answer key.
Mains PYQs on this topic (2)
- UPSC Mains 2026 · GS Paper III · Q5Explain by giving two examples, how biotechnology has helped the Indian farmers in processing their perishable crops.How to approach: Intro: scale of post-harvest loss. Body: example 1 and example 2 in depth, with one or two shorter mentions. Conclusion: scale through FPOs and food parks.
- UPSC Mains 2025 · GS Paper III · Q6How can India achieve energy independence through clean technology by 2047 ? How can biotechnology can play a crucial role in this endeavour ?How to approach: Intro: goal and import bill. Body: (1) Clean technology path; (2) Role of biotechnology. Conclusion: combine solar, wind, nuclear and bio-energy with domestic s…
Write an answer
In 150 words, explain the significance of Biotechnology with one recent example.
Flashcards (11)
Which enzymes are called molecular
scissors? Restriction enzymes (e.g. EcoRI).
Who made the first recombinant DNA, and
when? Cohen and Boyer, 1972.
First clinical gene therapy was for?
ADA deficiency (1990).
What is Cas9?
A protein that cuts DNA: molecular scissors for gene editing.
Who won the 2020 Chemistry Nobel for
CRISPR? Emmanuelle Charpentier and Jennifer Doudna.
Which genome edits did India exempt in
2022? SDN-1 and SDN-2, free of foreign DNA.
Name India's first genome-edited rice
varieties. DRR Dhan 100 (Kamala) and Pusa DST Rice 1.
What does RNAi do?
Silences a specific mRNA.
GenomeIndia data released in Jan 2025?
10,000 whole genome samples via IBDC.
Which department leads GenomeIndia?
Department of Biotechnology (DBT).
Genes in GM mustard DMH-11?
Barnase and barstar (male sterility system).
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Next topic · 5.2 →Biotechnology: Cloning, tissue culture and GM cropsSyllabus: GS-III · Awareness in the fields of IT, Space, Computers, robotics, nano-technology, bio-…