23. Which one of the snRNAs given below base pairs with 5’splice Site of pre mRNA?
(1) U1               (2) U2
(3) U4               (4) U5

The snRNA that base pairs with the 5′ splice site of pre-mRNA is U1 snRNA (option 1).

Explanation:

• The 5′ splice site (5′ SS) is the exon-intron boundary at the start of an intron and is recognized early during spliceosome assembly.

• U1 snRNA, part of the U1 small nuclear ribonucleoprotein (snRNP), specifically base pairs with the conserved sequence at the 5′ splice site of pre-mRNA. This base pairing is critical for the initial recognition and definition of the splice site during the earliest step of splicing.

• Structural and biochemical studies have shown that the 5′ end of U1 snRNA contains a sequence complementary to the 5′ splice site, enabling direct RNA-RNA interaction. This interaction is stabilized by associated proteins such as U1-C but the specificity mainly arises from base pairing between U1 snRNA and the pre-mRNA 5′ splice site.

• Other snRNAs have different roles:

  • U2 snRNA base pairs with the branch point sequence, not the 5′ splice site.

  • U4 snRNA acts mainly as a chaperone, base pairing with U6 snRNA to regulate spliceosome activation.

  • U5 snRNA interacts with the 5′ exon near the splice site but does not base pair with the 5′ splice site itself; it helps align exons during splicing catalysis4.

Summary Table

Conclusion

The U1 snRNA is the key small nuclear RNA that base pairs with the 5′ splice site of pre-mRNA, playing a pivotal role in early spliceosome assembly and splice site recognition. This base pairing is essential for accurate splicing and proper gene expression.