CRISPR-Cas9 Gene Editing: How It Works, Uses in Medicine and Agriculture, Genome-Edited Crops in India, Regulation and Ethical Questions (UPSC Notes + PYQs)

Where CRISPR came from

CRISPR stands for Clustered Regularly Interspaced Short Palindromic Repeats, odd repeating stretches of DNA first noticed in bacteria in 1987. Scientists later found that the spaces between the repeats held bits of viral DNA: bacteria keep a “memory” of past infections. When the same virus returns, the bacterium makes an RNA copy of the stored piece, which guides a Cas protein to cut the invading virus’s DNA. In 2012 Emmanuelle Charpentier and Jennifer Doudna showed this system could be programmed to cut any chosen DNA sequence in a test tube. In 2013 groups led by Feng Zhang and George Church used it in human and mouse cells. Charpentier and Doudna received the Nobel Prize in Chemistry in 2020.

How it works

The tool has two parts. A guide RNA of about 20 letters matches the target DNA sequence. The Cas9 enzyme binds the guide RNA, scans the DNA, and when it finds the match next to a short signal called a PAM, cuts both strands. The cell then repairs the cut. Its quick but error-prone repair often adds or deletes a few letters, disabling the gene, which is useful to switch off a harmful gene. If a DNA template is supplied, the cell can copy it in, correcting or inserting a sequence.

Newer versions avoid cutting both strands. Base editing (2016) changes a single DNA letter, such as C to T, and prime editing (2019) writes small edits using a “search and replace” approach, with fewer unwanted changes. Other Cas enzymes, such as Cas12 and Cas13, are used in cheap diagnostic tests; India’s FELUDA COVID-19 test, developed at CSIR-IGIB, used a Cas9 variant.

CRISPR vs older genetic engineering

Uses in medicine

• Sickle cell disease and beta-thalassaemia: Casgevy, which edits a patient’s own blood stem cells to switch on fetal haemoglobin, became the first approved CRISPR therapy, in the UK in November 2023 and the US in December 2023. India, with a large burden of sickle cell disease in tribal belts, launched the National Sickle Cell Anaemia Elimination Mission in 2023, and Indian labs are developing cheaper gene therapies.
• Cancer: edited immune cells (CAR-T) to attack tumours; India approved its own CAR-T therapy in 2023.
• Personalised editing: in 2025 doctors in the US treated an infant with a custom base-editing therapy for a rare liver disorder.
• Diagnostics and research models of disease.

The main hurdle is cost: approved therapies cost millions of dollars per patient abroad, far beyond most Indians.

Uses in agriculture

Editing can make crops tolerant of drought, salt and disease, or improve nutrition, without adding foreign genes. In May 2025, ICAR released India’s first two genome-edited rice varieties: DRR Dhan 100 (Kamala), based on Samba Mahsuri, which gives higher yield and matures about 20 days earlier, and Pusa DST Rice 1, based on MTU 1010, tolerant of salinity and alkalinity. Work is under way on mustard, banana, tomato and millets. Elsewhere, edited crops such as a high-GABA tomato in Japan and non-browning mushrooms in the US have reached markets.

Regulation in India

Genetically modified organisms are regulated under the Rules of 1989 made under the Environment (Protection) Act, with the Genetic Engineering Appraisal Committee (GEAC) approving release. In March 2022 the Environment Ministry exempted genome-edited plants of the SDN-1 and SDN-2 types, which carry no foreign DNA, from these rules; the Department of Biotechnology issued guidelines in May 2022 for their review by institutional biosafety committees. SDN-3 editing, which inserts larger foreign sequences, is still treated like GM. For human uses, ICMR’s National Guidelines for Gene Therapy Product Development and Clinical Trials (2019) apply, and editing of human embryos for reproduction is not allowed.

Ethics and risks

• Germline editing: in 2018 Chinese scientist He Jiankui announced the birth of twins whose embryos he had edited, causing global outrage; he was jailed. Edits to eggs, sperm or embryos pass to future generations, and most countries forbid it.
• Off-target effects: edits at the wrong place could cause harm, such as cancer.
• Equity: costly therapies could widen the gap between rich and poor.
• Designer babies and enhancement rather than cure.
• Biosecurity: misuse to create harmful organisms.
• Gene drives that spread edits through wild populations, proposed against malaria mosquitoes, could have unknown ecological effects.
• Patents and control by a few firms.

Way forward for India

Fund cheaper indigenous therapies for sickle cell disease and thalassaemia, build regulatory capacity with clear timelines, keep the distinction between edited and transgenic crops science-based while testing for safety, protect farmers’ access to seed, and keep a strict ban on heritable human editing while supporting research.

Gene editing and the bioeconomy

The BioE3 policy of 2024 (Biotechnology for Economy, Environment and Employment) lists precision biotherapeutics and climate-resilient agriculture among its focus areas, both of which rely on genome editing. India’s bioeconomy was estimated at about USD 165 billion in 2024, and the Government aims for USD 300 billion by 2030. Biofoundries and biomanufacturing hubs under BioE3 are meant to turn laboratory edits into products, from enzymes to cell therapies. Indian institutions active in genome editing include CSIR-IGIB in Delhi, which developed a smaller and more precise Cas9 variant from Francisella novicida, ICAR institutes for crops, and the National Institute of Plant Genome Research. A strong public research base keeps costs low and reduces dependence on foreign patents, many of which are still contested between US universities. For students, the practical point is simple: genome editing is now a tool of Indian public agriculture and medicine, not only a topic in foreign journals, and questions are likely to ask how it differs from older GM technology and how it is regulated.

PYQ trend

Prelims 2019 asked what Cas9 is. Expect questions on genome-edited crops and SDN categories, and Mains GS-III questions on biotechnology in health and farming.

CRISPR: UPSC angle

CRISPR UPSC PYQs (Prelims)

Questions UPSC has actually asked, from the official papers. Pick an option to check yourself.

Mains PYQs on this topic

No UPSC Mains question from 2023-2026 is directly on this topic. Older papers (2013-2022) will be added as the Mains bank grows.

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Image: Crisprbiotech, Wikimedia Commons, CC BY-SA 4.0