How does EcoRI specifically act on DNA molecule ? Explain.

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Q. How does EcoRI specifically act on DNA molecule ? Explain.

CBSECBSE Class XII Board 2020Subjective· 2mImportance★★★★★

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Concept understanding — Restriction Enzyme Action

Imagine you have a long, tangled piece of string, and you need to cut it into smaller, specific pieces — not just anywhere, but exactly at the places where a certain pattern of letters appears. That is the core idea behind restriction enzyme action.

In the world of biology, the "string" is a DNA molecule — the long, thread-like chemical that carries the genetic instructions for every living thing. A restriction enzyme is a molecular "scissors" that cuts DNA, but it is incredibly precise. It does not chop randomly. Instead, it recognises a very specific, short sequence of DNA letters (usually 4 to 8 base pairs long) and cuts only at that exact spot.

Note

Think of it like a word processor's "Find and Replace" function, but instead of replacing text, the enzyme finds a specific word and cuts the page at that word.

This ability to cut DNA at precise locations is what makes restriction enzymes the fundamental tool of genetic engineering. Without them, scientists would have no way to isolate a specific gene from a long DNA strand.

How does the enzyme "know" where to cut?

The DNA molecule is made of two strands twisted together (the famous double helix). Each strand has a sequence of four chemical "letters": A, T, G, and C. A restriction enzyme scans along the DNA until it finds its target sequence — a short, palindromic pattern (meaning it reads the same forwards on one strand and backwards on the other). For example, the enzyme EcoRI recognises the sequence GAATTC.

When it finds this exact sequence, it binds to the DNA and makes a cut in both strands. The cut can be one of two types:

Sticky ends: The enzyme cuts the two DNA strands at different points, leaving short, single-stranded overhangs. These overhangs are like pieces of Velcro — they can easily stick to a complementary overhang from another DNA piece cut by the same enzyme. This is extremely useful for joining different DNA fragments together.
Blunt ends: The enzyme cuts both strands straight across at the same point, leaving no overhang. These are harder to join together later, but they are still useful.

Why does this matter?

Restriction enzymes are the reason we can manipulate DNA at all. They allow scientists to:

Cut out a specific gene from the DNA of one organism (say, the human insulin gene).
Cut open a carrier DNA (like a plasmid from a bacterium) at the same spot.
Insert the gene into the carrier, because the sticky ends match perfectly.
Splice the carrier back together using another enzyme (DNA ligase), creating a recombinant DNA molecule. …

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EcoRI is a restriction enzyme that cuts DNA at a specific palindromic sequence (GAATTC) by making staggered cuts, producing sticky ends that enable precise DNA recombination.

EcoRI is a type II restriction endonuclease isolated from the bacterium Escherichia coli (strain RY13). Its job is to protect the bacterium from invading viral DNA by chopping it up at precise locations. What makes EcoRI remarkable is its specificity — it does not cut DNA randomly but recognises a particular sequence of six base pairs.

The recognition site for EcoRI is 5'-GAATTC-3' on one strand, with the complementary strand reading 3'-CTTAAG-5'. This sequence is palindromic, meaning it reads the same forwards on one strand and backwards on the other — like the word "MALAYALAM". This symmetry is crucial for how the enzyme cuts.

When EcoRI binds to this sequence, it makes a staggered cut. It breaks the phosphodiester bond between the G and the first A on each strand, but at positions that are offset from each other. On the top strand (5' to 3'), it cuts after the G, leaving a 5' overhang of AATT. On the bottom strand, it cuts after the G on that strand as well, which corresponds to a position several bases away. The result is that each end of the cut DNA has a short, single-stranded overhang.

Note

These overhangs are called "sticky ends" because they can base-pair with complementary overhangs from another DNA fragment cut by the same enzyme. This property is the foundation of recombinant DNA technology.

The overhang sequence is always 5'-AATT-3'. Because these bases are unpaired, they can hydrogen-bond with a complementary overhang from any other DNA molecule that has been cut with EcoRI. This allows scientists to join DNA from different sources — for example, inserting a human gene into a bacterial plasmid — as long as both have been cut with the same restriction enzyme. …

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Same / Similar Concept — real previous-year questions on the same or a closely similar concept, not this exact question.

Showing the 12 most recent of 53 on this concept.

CBSE 2026Set V11 markMCQ
$Q. Identify the incorrect statement.$
(a) First letter of the restriction enzyme is derived from genus of the bacterium
(b) Second and third letters of the restriction enzyme are derived from species of the bacterium
(c) The fourth letter of the restriction enzyme is derived from the strain of the bacterium
(d) The Roman letter after the strain indicate the Roman origin of bacterium from which the restriction enzyme is isolated
›Reveal solutionSolution

The Roman numeral after the strain shows the order of discovery of the enzyme, not any "Roman origin".

Restriction enzyme nomenclature (e.g. EcoRI): first letter = genus (E, Escherichia), next two letters = species (co, coli), fourth letter = strain (R, RY13), and the Roman numeral (I) denotes the order in which the enzyme was isolated from that strain of bacteria. Statement (d) is therefore incorrect — the Roma …
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CBSE 2026Set A1 markMCQ
$Q. Who of the following scientists observed that restriction endonuclease can cut DNA strands in a particular shape?$
(a) Herbert Boyer
(b) Stanley Cohen
(c) Watson
(d) Crick
›Reveal solutionSolution

Herbert Boyer worked out that a restriction endonuclease cuts DNA into a particular (sticky-ended) shape; the correct option is (a).

Restriction endonucleases recognise a specific palindromic sequence and cut the two DNA strands a little away from the centre, but between the same two bases on opposite strands. This staggered cut leaves single-stranded overhangs called 'sticky ends'. Herbert Boyer isolated the restricti …

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CBSE 2026Set A1 markMCQ
$Q. Cutting DNA at a specific site is made possible by which enzyme?$
(a) Restriction endonuclease
(b) Alkaline phosphatase
(c) DNA ligase
(d) Nuclease
›Reveal solutionSolution
Restriction endonuclease cuts DNA at specific sites; the correct option is (a).

Restriction endonucleases are the 'molecular scissors' of genetic engineering. Each enzyme inspects the length of a DNA sequence, binds to its specific recognition site (a palindromic sequence of 4–8 bp) and cuts the DNA at that site.

Alkaline phosphatase removes phosphate groups, it does not cut at a specific site. …
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CBSE 2026Set A1 markMCQ
$Q. What is essential for occurrence of the same kind of sticky ends' of DNA fragments?$
(a) To cut DNA by the same restriction endonuclease
(b) To cut DNA by different restriction endonucleases
(c) DNA amplification
(d) All of these
›Reveal solutionSolution

The same enzyme gives the same sticky ends; the correct option is (a).

A given restriction endonuclease always cuts at its own specific recognition sequence, producing single-stranded overhangs of a fixed sequence. If a vector DNA and a foreign (target) DNA are both cut with the SAME restriction endonuclease, they generate identical, complementary sticky ends. These matching ends can base-pair and then be sealed by DNA ligase to form r …

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CBSE 2026Set ZOOLOGY1 markMCQ
$Q. What is the function of endonuclease?$
(a) Joining of DNA fragments
(b) Carrying foreign DNA
(c) Cutting DNA
(d) Amplifying a specific DNA sequence
›Reveal solutionSolution

Endonuclease is a restriction enzyme that cuts DNA at a specific internal recognition sequence.

Restriction endonucleases are enzymes used in genetic engineering to cut DNA molecules. Unlike exonucleases, which remove nucleotides from the free ends of a DNA strand, endonucleases make cuts at specific points within the DNA molecule, recognising a particular sequence of base pairs known as the recognition sequence (e.g., EcoRI recognises GAATTC). Each restriction enzyme scans the DNA, …

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CBSE 2026Set ANNUAL1 markMCQ
$Q. What does the 'co' derives from the EcoRI?$
(a) Genus
(b) Phylum
(c) Order
(d) Species
›Reveal solutionSolution

Restriction enzyme names are built from genus + species + strain + order of discovery; in EcoRI, 'co' comes from the species epithet 'coli', not the genus.

Restriction endonucleases are named after the bacterium from which they were isolated: the first letter comes from the GENUS, the next two letters come from the SPECIES, followed by a letter/number for the strain, and a Roman numeral for the order in which the enzyme was isola …

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CBSE 2026Set ANNUAL1 mark
$Q. Fill in the blank: The cutting of DNA at specific locations became possible with the discovery of molecular scissors called as ______ enzyme.$
›Reveal solutionSolution

Restriction endonucleases are the 'molecular scissors' that cut DNA at specific recognition sequences, enabling genetic engineering.

The discovery of restriction enzymes (restriction endonucleases) - proteins that recognise and cut double-stranded DNA at specific, short palindromic base sequences - made it possible to precisely cut DNA at defined locations, which is the …

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CBSE 2026Set ANNUAL1 markMCQ
$Q. The first isolated restriction endonuclease is$
(a) EcoRI
(b) Hind II
(c) Hind I
(d) EcoRII
›Reveal solutionSolution

Hind II, isolated from Haemophilus influenzae, was the first restriction endonuclease to be isolated and characterised; it cuts DNA at a fixed distance from a specific recognition sequence.

Restriction endonucleases occur naturally in bacteria, where they protect the cell by cutting up foreign (bacteriophage) DNA at specific sequences. The first restriction endonuclease to be isolated and characterised was Hind II (in 1970), obtained from the bacterium Haemophilus influenzae. It was shown to always cut DNA molecules at a particular point by recognising a specific sequence of base pairs.

…

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CBSE 2026Set ANNUAL1 markMCQ
$Q. The stickness of the sticky ends of DNA facilitates the action which of the following enzyme?$
(a) Restriction enzyme
(b) DNA Ligase
(c) Chitinase
(d) Hind-II
›Reveal solutionSolution

DNA ligase joins the base-paired sticky ends of DNA fragments.

When a restriction endonuclease cuts DNA at a palindromic site, it often leaves short single-stranded overhangs called sticky (cohesive) ends. Because these ends are complementary, a vector and a foreign DNA fragment cut by the same enzyme have matching sticky ends that pair up by hydrogen bonding. However, the sugar-phosphate backbone still has nicks. The enzyme DNA ligase seals these nicks by forming phospho …

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CBSE 2026Set ANNUAL1 mark
$Q. State whether True or False: Each restriction endonuclease recognizes a specific palindromic nucleotide sequences in the DNA.$
›Reveal solutionSolution

True - each restriction endonuclease recognises a specific palindromic sequence.

Restriction endonucleases are the 'molecular scissors' of genetic engineering. Each type recognises a specific short sequence of DNA, usually 4-8 base pairs long, that is palindromic (reads the same 5' to 3' on both strands). The enzyme binds this recognition sequence and cuts the DNA at a de …

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CBSE 2025Set 57/6/11 markMCQ
$Q. The cloning site present in the tetracycline resistance gene of E. coli cloning vector pBR322 is : (A) EcoR I (B) Pvu II (C) Sal I (D) Pst I$
›Reveal solutionSolution

The cloning site present in the tetracycline resistance gene of the pBR322 vector is Sal I, which disrupts tetracycline resistance when a foreign DNA fragment is inserted there.

The pBR322 plasmid is one of the earliest and most carefully designed cloning vectors used in recombinant DNA technology. It was constructed by Bolivar and Rodriguez, and its name comes from the researchers' initials. What makes pBR322 so useful is that it carries two antibiotic resistance genes — one for ampicillin (ampR) and one for tetracycline (tetR) — and each of these genes contains unique restriction sites where foreign DNA can be inserted.

When you insert a piece of DNA into a restriction site that lies within an antibiotic resistance gene, that gene gets inactivated. This is called insertional inactivation. It becomes a powerful selection tool: if you grow transformed bacteria on a plate containing that antibiotic, only those cells that still have a functional resistance gene will survive. But if you insert your target DNA into that gene, the gene breaks, and the bacteria become sensitive to the antibiotic.

Now, the question asks specifically about the cloning site present in the tetracycline resistance gene of pBR322. The NCERT textbook clearly lists the restriction sites present in pBR322. For the tetracycline resistance gene, the unique restriction sites are BamH I, Sal I, and Pvu II. Among the options given, only Sal I falls within the tetR gene.

Note

EcoR I and Pst I are also present in pBR322, but they lie in the ampicillin resistance gene, not the tetracycline resistance gene. Pvu II is indeed in the tetR gene, but it is not listed among the options — only Sal I is. …

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CBSE 2025Set A1 mark
$Q. Answer in one word / sentence: What is restriction enzyme?$
›Reveal solutionSolution

Restriction enzymes are 'molecular scissors' that cut DNA molecules at specific, sequence-recognised sites.

Restriction enzymes (restriction endonucleases) are proteins, naturally produced by bacteria as a defence mechanism against invading (viral/foreign) DNA, that recognise a specific short palindromic nucleotide sequence in a DNA molecule and cut the DNA strand at or near that sequence, generating fragments with 'sticky' or 'blunt' ends. In biotechnology, they are essential tools of recombinant DNA technology, us …

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Q.How does EcoRI specifically act on DNA molecule ? Explain.

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