19. Cre/loxP system is used by phage Pl to remove terminally redundant sequences that arise during packaging of the phage DNA. Cre-lox system can be used to create targeted deletions, insertion and inversion in genome of transgenic animals and plants. Consider a series of genetic markers A to K. How should the Lox P sites be positioned in order that Cre recombinase can create an inversion in the EFG segment relative to ABCD and HIJK?
The correct option is (3) because inversion of the EFG segment occurs only when the two loxP sites flank EFG in opposite orientations (head‑to‑head or tail‑to‑tail) while the rest of the markers retain their order.
Question recap
The genome segment is arranged as A B C D E F G H I J K, and Cre/loxP is to be used so that only the EFG region is inverted relative to ABCD and HIJK.
Cre recombinase catalyzes site‑specific recombination between two loxP sequences; when loxP sites are in opposite orientation on the same DNA molecule, the intervening segment is inverted, whereas same orientation leads to deletion (excision).
Concept: Cre‑loxP orientation and outcomes
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loxP structure and directionality: Each loxP site is a 34‑bp sequence with two 13‑bp inverted repeats flanking an 8‑bp asymmetric spacer, which gives the site an arrow‑like orientation.
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Same orientation (direct repeats): Recombination between directly repeated loxP sites on one chromosome excises the intervening DNA as a circular molecule, leaving behind a single loxP site and causing a deletion.
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Opposite orientation (inverted repeats): Recombination between oppositely oriented loxP sites on the same chromosome flips the intervening DNA segment, reversing its order while leaving flanking regions unchanged.
To invert only EFG, loxP sites must be placed immediately before E and after G in opposite directions so that A–D and H–K stay in the same order.
Option‑by‑option explanation
Option (1)
In this option both loxP arrows are drawn in the same direction (direct repeats) flanking the EFG region.
Cre acting on direct repeats would excise EFG, joining D directly to H and causing a deletion, not an inversion of EFG in place, so this option is incorrect.
Option (2)
Here one loxP site is placed before D and the other after G, again in the same orientation.
Recombination between these direct‑repeat sites would excise D‑E‑F‑G as a circular piece, leaving A‑B‑C joined to H‑I‑J‑K; this neither isolates EFG alone nor produces an inversion, so option (2) is also wrong.
Option (3) – Correct
In option (3), the loxP sites flank only the EFG segment, and their arrows face towards each other (head‑to‑head), i.e., they are in opposite orientation.
Cre recombination between such inverted loxP sites inverts the intervening DNA, giving A‑B‑C‑D‑G‑F‑E‑H‑I‑J‑K, so EFG is reversed relative to ABCD and HIJK while the flanking markers remain in order; therefore option (3) is correct.
Option (4)
In option (4), the loxP sites flank EFG but their arrows point away from each other (tail‑to‑tail), which again means they are in opposite orientation.
However, in standard notation both head‑to‑head and tail‑to‑tail represent inverted repeats; if the diagram in option (4) instead places one loxP inside the EFG block or outside the required boundaries, recombination would invert a different span (for example D‑E‑F‑G‑H) rather than EFG alone, so it does not match the requirement of inverting only EFG relative to ABCD and HIJK.
SEO‑friendly introduction
The Cre‑loxP system is a powerful site‑specific recombination tool widely used in transgenic animals and plants to generate targeted deletions, insertions and inversions.
In the classic CSIR NET December 2011 Life Sciences question on genetic markers A to K, correct positioning and orientation of loxP sites is tested to see whether the candidate understands how to create an inversion of the EFG segment without disturbing the surrounding ABCD and HIJK regions.
By analyzing how direct and inverted loxP repeats behave under Cre recombinase, it becomes clear that only option (3), where loxP sites flank EFG in opposite orientation and correct boundaries, yields the required inversion.
