DNA, genes and genetic engineering

The first principle

Every living cell stores its instructions in the same chemical, DNA, and reads them with the same code, so a gene taken from a bacterium is read correctly by a plant and a human gene is read correctly by a bacterium. That shared code is the whole basis of genetic engineering: if instructions are universal, they can be cut out, moved and copied, and a cell can be made to work as a factory for a product it never made before.

The core

What DNA is and how it is read

• DNA is a double helix of two complementary strands. Each strand is a chain of nucleotides, each carrying one of four bases, adenine (A), thymine (T), guanine (G) and cytosine (C), and the strands are held together because A pairs only with T and G only with C. James Watson and Francis Crick proposed the structure in 1953, relying on the X ray diffraction work of Rosalind Franklin and Maurice Wilkins, and the pairing rule means each strand is a template for the other, which is how DNA is copied before a cell divides.
• A gene is a stretch of DNA that codes for a product, usually a protein, along with the control sequences that decide when and how much of it is made. The human genome has about 3.1 billion base pairs but only about 20,000 protein coding genes, which occupy under 2 per cent of it; much of the rest regulates genes or has no known function.
• The central dogma, stated by Crick in 1958, is that information flows from DNA to RNA to protein. In transcription an enzyme, RNA polymerase, copies a gene into messenger RNA (mRNA); in translation the ribosome reads the mRNA three bases at a time, each triplet or codon calling for one of 20 amino acids, and links them into a protein. Retroviruses such as the human immunodeficiency virus (HIV) reverse the first step, using an enzyme called reverse transcriptase to write their RNA back into DNA.
• The genetic code is nearly universal and redundant. There are 64 codons for 20 amino acids and three stop signals, so several codons name the same amino acid, and the code is the same in almost all organisms, which is why a human insulin gene works inside a bacterium.

How a gene is moved: recombinant DNA

• Restriction enzymes are the scissors. Bacteria make them to cut the DNA of invading viruses at short, specific sequences, often palindromes such as GAATTC, which the enzyme EcoRI cuts; many leave short single stranded "sticky ends", so any two pieces cut by the same enzyme can pair up.
• DNA ligase is the glue and a vector is the vehicle. Ligase seals the joined pieces, and the vector, usually a plasmid (a small circle of bacterial DNA that copies itself) or a modified virus, carries the new gene into the host cell; for plants, the Ti plasmid of the soil bacterium Agrobacterium tumefaciens is the classic vector.
• Selection finds the few cells that took the gene. The vector carries a marker, such as a gene for resistance to an antibiotic, so only transformed cells survive on a plate containing it, and those cells are then grown in bulk.
• The host decides what can be made. The bacterium Escherichia coli is cheap and fast but cannot add the sugar chains many human proteins need, so yeast is used for products such as the hepatitis B vaccine and mammalian cell lines, chiefly Chinese hamster ovary cells, are used for monoclonal antibodies.

Dimensions

• Medical. Recombinant insulin, licensed in 1982 as the first drug made by genetic engineering, replaced insulin extracted from the pancreas of cattle and pigs, and the same route now makes growth hormone, clotting factors, erythropoietin, vaccines and monoclonal antibodies.
• Agricultural. Moving a gene into a crop gives traits that breeding cannot, such as the insect killing protein of Bacillus thuringiensis in cotton; the regulation and the debate belong to the GM crops note.
• Industrial and environmental. Engineered microbes make enzymes for detergents, textiles and biofuels and are being developed to break down pollutants, which is the basis of the Union government's biomanufacturing push covered in the bioeconomy note.
• Legal and forensic. DNA fingerprinting, developed by Alec Jeffreys in 1984, compares regions where the number of short repeats differs between people, and it is now routine in criminal cases and in settling parentage.
• Ethical and privacy. DNA reveals a person's ancestry, relatives and disease risks, so a sample taken for one purpose can expose far more, which is why a law on DNA databases has been debated for two decades.

In practice

• The polymerase chain reaction (PCR), invented by Kary Mullis in 1983 (Nobel Prize in Chemistry, 1993), copies a chosen stretch of DNA in a machine. Heating to about 95 °C separates the strands, cooling to about 50 to 65 °C lets two short primers bind on either side of the target, and at 72 °C a heat stable DNA polymerase taken from the hot spring bacterium Thermus aquaticus builds new strands; since each cycle doubles the target, n cycles give up to 2ⁿ copies, so 30 cycles give about a billion. Reverse transcription PCR first turns RNA into DNA, which is why it detected the RNA virus of Covid, and real time PCR measures the product as it builds up.
• Gel electrophoresis sorts the products. DNA carries a negative charge, so in an electric field it moves through a gel towards the positive electrode, and shorter pieces move faster, giving the band patterns used in fingerprinting and diagnosis.
• India's institutions. The Department of Biotechnology (DBT), formed in 1986, funds research and, with its company the Biotechnology Industry Research Assistance Council (BIRAC), supports start ups; the Centre for DNA Fingerprinting and Diagnostics (CDFD) at Hyderabad, under DBT, does forensic DNA work and grew from the work of Lalji Singh at the Centre for Cellular and Molecular Biology.
• Industry. Shantha Biotechnics launched Shanvac B in 1997, India's first recombinant hepatitis B vaccine, which cut the price sharply, and Indian firms such as Biocon now make recombinant insulin and biosimilars, copies of biological drugs whose patents have expired.
• Regulation. All work with genetically engineered organisms falls under the Rules of 1989 made under the Environment (Protection) Act 1986, which set up a ladder of committees: an Institutional Biosafety Committee (IBSC) in every laboratory, the Review Committee on Genetic Manipulation (RCGM) under DBT, and the Genetic Engineering Appraisal Committee (GEAC) under the Ministry of Environment, Forest and Climate Change for release into the environment. The DNA Technology (Use and Application) Regulation Bill 2019, meant to regulate forensic DNA profiling and set up DNA data banks, was withdrawn from the Lok Sabha in July 2023.

Issues and way forward

• Biosafety rests on old rules. The 1989 Rules were written before gene editing, synthetic biology and cheap DNA synthesis, so regulators fit new methods into old categories by office memorandum; a single modern biosafety law with an independent regulator was proposed in the Biotechnology Regulatory Authority of India Bill 2013, which lapsed in 2014, and the need remains.
• Scale up is the weak link. Indian laboratories can make a recombinant protein in a flask, but turning it into a product needs pilot plants, good manufacturing practice and trained process engineers, which is why the bioeconomy push funds shared biomanufacturing facilities rather than only grants.
• Forensic DNA has no law. Without a statute, collection, storage and deletion of DNA profiles depend on police practice, so a law with clear rules on consent, deletion of profiles and independent oversight, the concerns the Parliamentary Standing Committee on Science and Technology raised in its 2021 report on the Bill, is still needed.
• Dual use. The same tools that make a vaccine can make a pathogen more dangerous, and India, a party to the Biological Weapons Convention, needs screening of orders for synthetic DNA and oversight of high risk experiments.
• Biosimilar approval. Because a biological drug cannot be copied exactly, a biosimilar needs comparison studies, and India's Guidelines on Similar Biologics, first issued in 2012 and revised in 2016, need regular updating so that cheap copies remain safe and are trusted abroad.

Common confusions

• Gene and genome. A gene is one unit of instruction, while the genome is the complete DNA of an organism, genes and everything between them.
• Transcription and translation. Transcription copies DNA into RNA in the nucleus, while translation reads that RNA on the ribosome to make a protein.
• Recombinant DNA and gene editing. Recombinant DNA moves a gene from one organism into another, while gene editing changes a gene in place, often without adding anything foreign; the gene editing note explains the difference.
• PCR and sequencing. PCR makes many copies of a known stretch of DNA, while sequencing reads the order of bases in it; sequencing often uses PCR first to get enough material.
• Biosimilar and generic. A generic is an exact chemical copy of a small molecule drug, while a biosimilar is a close but never identical copy of a protein drug made in living cells.

For the exam

• Keyword bank: double helix, complementary base pairing, central dogma, transcription and translation, genetic code, restriction enzyme, sticky ends, plasmid vector, recombinant protein, polymerase chain reaction, reverse transcription PCR, gel electrophoresis, DNA fingerprinting, biosimilar, biosafety committees.
• Previous year questions: Practise the previous year questions on this topic →
• Use in an answer:
  • Introduction with data: The human genome holds about 3.1 billion base pairs, yet only about 20,000 genes, under 2 per cent of it, code for proteins, and moving even one of them into a microbe can turn it into a factory for a medicine.
  • Introduction with a source: Crick's central dogma of 1958, that information flows from DNA to RNA to protein, explains why a human gene placed in a bacterium makes human insulin.
  • Conclusion: Genetic engineering has already made insulin, vaccines and biosimilars cheap in India; the next gain lies in a modern biosafety law and shared facilities that carry laboratory successes to scale.
  • Conclusion: Because DNA is both a tool and a record of identity, India needs to pair its push in biotechnology with a law that protects genetic privacy.