Biology · Biotechnology: Principles and Processes · NEET
Both exonuclease and endonuclease are nucleases (enzymes that cut DNA), but they cut in different places. Exonucleases remove nucleotides one by one from the ENDS of a DNA strand, while endonucleases make cuts at specific positions INSIDE (within) the DNA. Memory hook: "Exo = Exit (ends), Endo = Enter (inside)." Restriction endonucleases are the "molecular scissors" used in genetic engineering.
Exonuclease trims nucleotides from the DNA ends; endonuclease cuts at a specific site inside the DNA. Restriction endonuclease (the molecular scissors) belongs to the endonuclease type.
Your doubts, answered
Are exonuclease and endonuclease the same enzyme?
No. They are two kinds of the same larger class called nucleases. Both cut DNA, but the CUT SITE is different. Exonucleases work only at the ends of the DNA and take off nucleotides one at a time. Endonucleases cut at specific points inside the DNA molecule. So they are related (both nucleases) but not the same.
Which nuclease is used in recombinant DNA technology?
The ENDONUCLEASE, specifically the restriction endonuclease. It cuts DNA at a specific internal recognition sequence, which is exactly what genetic engineering needs to open a plasmid or cut out a gene. Exonuclease is NOT used to cut the gene, because it would just nibble away the ends. NEET loves this point.
Does endonuclease cut exactly in the middle of the DNA?
Not exactly. Endonuclease cuts at specific positions WITHIN the DNA (internal), not at the ends. But a restriction endonuclease cuts a little away from the centre of the palindromic recognition site, not precisely at the centre. NEET 2026 tested this: 'cuts only at the centre' is a FALSE statement.
Where does exonuclease remove nucleotides from?
From the ENDS of the DNA. Exonuclease removes nucleotides one by one from the free ends (either the 5' end or the 3' end). It cannot make an internal cut. Remember: Exo = ends.
Is restriction endonuclease an exonuclease?
No. A restriction endonuclease is a type of ENDOnuclease. The word 'endonuclease' is right in its name. It inspects the DNA, finds its specific recognition sequence, binds, and cuts each strand inside the double helix. It is the enzyme called 'molecular scissors'.
⚠️ The NEET trap ✗ Restriction endonucleases remove nucleotides from the ends of DNA fragments. ✓ Restriction ENDONUCLEASES make cuts at specific internal positions. Removing nucleotides from the ENDS is the job of EXONUCLEASES. 🧠 NCERT gives two properties side by side. NTA swaps them: they attach the 'removes nucleotides from ends' line to endonuclease. That line belongs to exonuclease. Exo = ends, Endo = inside.
Real NEET questions
NEET 2019
An enzyme catalysing the removal of nucleotides from ends of DNA is:
A · DNA ligase
B · Endonuclease
C · Exonuclease ✓
D · Protease
Solution: Nucleases are of two kinds. Exonucleases remove nucleotides from the ENDS of the DNA, whereas endonucleases make cuts at specific positions inside the DNA. DNA ligase joins ends and protease acts on proteins. So the enzyme removing nucleotides from DNA ends is the exonuclease. (NCERT Ch 9, p.166)
NEET 2019
Match the enzymes with their functions: (a) Restriction endonuclease (b) Restriction exonuclease (c) DNA ligase (d) Taq polymerase with (i) Joins DNA fragments (ii) Extends primers on genomic DNA template (iii) Cuts DNA at specific position (iv) Removes nucleotides from ends of DNA
A · a-iii, b-i, c-iv, d-ii
B · a-iii, b-iv, c-i, d-ii ✓
C · a-iv, b-iii, c-i, d-ii
D · a-ii, b-iv, c-i, d-iii
Solution: Endonuclease cuts DNA at a specific internal position (iii). Exonuclease removes nucleotides from the ends (iv). DNA ligase joins DNA fragments (i). Taq polymerase extends primers on the template during PCR (ii). Correct match: a-iii, b-iv, c-i, d-ii. (NCERT Ch 9, p.166)
NEET 2026
Which statements are NOT true regarding restriction endonucleases? A. They are called molecular scissors. B. They restrict growth of bacteriophages in E. coli. C. They cut DNA only at the centre of the palindromic sites. D. They remove nucleotides only from the ends of DNA fragments. E. They recognise specific palindromic base-pair sequences.
A · A and B only
B · A and E only
C · D and E only
D · C and D only ✓
Solution: C is false because restriction enzymes cut a little AWAY from the centre of the palindromic site, not exactly at the centre. D is false because removing nucleotides from ends is the property of EXONUCLEASES, not restriction endonucleases. A, B and E are all true. So C and D are the untrue statements. (NCERT Ch 9, p.167)
Solved Biotechnology: Principles and Processes NEET PYQs
Try the real previous-year questions from this chapter — each with the answer and a full solution.
What is the main difference between exonuclease and endonuclease?
Exonuclease removes nucleotides from the ENDS of DNA; endonuclease makes cuts at specific positions WITHIN (inside) the DNA. Both are nucleases.
Why are restriction endonucleases called molecular scissors?
Because they cut DNA at a specific internal recognition sequence, acting like scissors that snip the double helix at chosen points. They are essential tools in recombinant DNA technology.
Can exonuclease cut in the middle of a DNA strand?
No. Exonuclease can only act at the free ends of the DNA. Only endonucleases make internal cuts.
Which enzyme joins the cut DNA pieces?
DNA ligase. Nucleases cut DNA; ligase joins the ends together. Do not confuse ligase with nucleases in NEET matching questions.
Do endonucleases cut exactly at the centre of the palindrome?
No. Restriction endonucleases cut a little away from the centre of the palindromic recognition site, which is what creates sticky ends. NEET 2026 tested this exact point.
