Related Experiment Video
Updated: Jun 23, 2026

Manipulation of Gene Function in Mexican Cavefish
Published on: April 22, 2019
Co-occupancy of two Pumilio molecules on a single hunchback NRE
Yogesh K Gupta1, Tammy H Lee, Thomas A Edwards
1Department of Structural and Chemical Biology, Mount Sinai School of Medicine, New York, New York 10029, USA.
Abstract:
Pumilio controls a number of processes in eukaryotes, including the translational repression of hunchback (hb) mRNA in early Drosophila embryos. The Pumilio Puf domain binds to a pair of 32 nucleotide (nt) Nanos response elements (NRE1 and NRE2) within the 3' untranslated region of hb mRNA. Despite the elucidation of structures of human Pumilio Puf domain in complex with hb RNA elements, the nature of hb mRNA recognition remains unclear. In particular, the site that mediates regulation in vivo is significantly larger than the 8-10-nt RNA elements bound to single Puf molecules in crystal structures. Here we present biophysical and biochemical data that partially resolve the paradox. We show that each NRE is composed of two binding sites (Box A and Box B) and that two Puf domains can co-occupy a single NRE. The Puf domains have a higher affinity for the 3' Box B site than the 5' Box A site; binding to the intact NRE appears to be cooperative (at least in some experiments). We suggest that the 2 Pumilio:1 NRE complex is the functional regulatory unit in vivo.
Related Concept Videos
¹H NMR: Pople Notation
A proton...
Interpreting ¹H NMR Signal Splitting: The (n + 1) Rule
Hybridization of Atomic Orbitals II
The Aufbau Principle and Hund's Rule
¹H NMR of Conformationally Flexible Molecules: Temporal Resolution
¹H NMR: Complex Splitting
Splitting diagrams or splitting tree diagrams are routinely used to depict such complex couplings. While drawing splitting diagrams, the splitting with the larger coupling constant is usually applied first.

