The isolated 102 amino acid N-terminal RNA binding domain (RBD) of the
human U1A protein specifically interacts with a short RNA hairpin con
taining the U1 snRNA stem/loop II sequence. This recognition is nucleo
tide-specific, for substitutions of critical nucleotides in the RNA lo
op decrease binding affinity up to 10(6)-fold, as measured by nitrocel
lulose filter binding experiments. The magnitude of the loss of bindin
g free energy with single-nucleotide substitution in the conserved GCA
sequence suggests that the interaction between the RBD and RNA occurs
through a number of interdependent specific contacts in the complex.
C-13 and N-15 NMR experiments, using isotopically-labeled RNA together
with unlabeled protein, show that the chemical shifts of many protons
from the bound RNA are substantially different from those of the free
RNA, especially in the loop region of the hairpin. All these data sug
gest that there is a conformational change in the RNA upon formation o
f the RBD-RNA complex.