PMID: 8609622Mar 29, 1996Paper

RNA hairpins with non-nucleotide spacers bind efficiently to the human U1A protein

Journal of Molecular Biology
D J Williams, Kathleen B Hall

Abstract

The N-terminal RNA binding domain (RBD1) of the human U1A protein binds to the ten nucleotide loop in stemloop II of of U1 snRNA, and to its own 3' UTR structure. The nucleotides critical for recognition by the U1A RBD are displayed in very different geometric contexts in these two targets, leading to the question of what common features of RNA structure allow the RBD to efficiently recognize these two RNAs. The experiments described here used RNA hairpins, in which the loop size was altered by deletion, insertion or substitution with non-nucleotide (ethylene glycol)n spacers, to determine what features of this RNA structure were critical for interaction with the RBD1. Substitution of the three nucleotides on the 3' side of the RNA hairpin loop by (ethylene glycol)6-18 spacers does not significantly perturb the affinity, energetics or electrostatics of this RNA: protein association. These results confirm the suggestion that these loop nucleotides provide a flexible tether to allow the other seven nucleotides to fit onto the binding surface of the RBD, and lead to the hypothesis that conformational flexibility and the possible end-to-end distance of seven loop nucleotides are critical features of this complex formation.

Citations

Aug 7, 2014·Chemical Communications : Chem Comm·Katarzyna Wawrzyniak-Turek, Claudia Höbartner
Jul 1, 1998·Annual Review of Biophysics and Biomolecular Structure·G Varani, K Nagai
Apr 12, 2001·The Journal of Biological Chemistry·P S KatsambaI A Laird-Offringa
Dec 28, 2007·Nucleic Acids Research·Nicholas J ReiterSamuel E Butcher
Jun 26, 2002·The Journal of Biological Chemistry·Phinikoula S KatsambaIte A Laird-Offringa
Aug 24, 2020·Spectrochimica Acta. Part A, Molecular and Biomolecular Spectroscopy·Mateen A KhanJaved M Khan
Sep 26, 2009·The Journal of Physical Chemistry. B·Binh Nguyen, W David Wilson
May 23, 2014·Biochemistry·Sandra G Williams, Kathleen B Hall
May 29, 2014·Biochemistry·Sandra G Williams, Kathleen B Hall
May 21, 2014·RNA·Kimberly J DelaneyKathleen B Hall
Jun 21, 2011·Biophysical Chemistry·Sandra G Williams, Kathleen B Hall

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