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Nucleic Acids Research 2004 32(16):4852-4861; doi:10.1093/nar/gkh799
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Published online 14 September 2004

Nucleic Acids Research, Vol. 32 No. 16 © Oxford University Press 2004; all rights reserved

Determination and augmentation of RNA sequence specificity of the Nova K-homology domains

Kiran Musunuru1,2 and Robert B. Darnell1,3,*

1 Laboratory of Molecular Neuro-Oncology, 2 Laboratory of Molecular Biophysics and 3 Howard Hughes Medical Institute, The Rockefeller University, 1230 York Avenue, New York, NY 10021, USA

* To whom correspondence should be addressed. Tel: +1 212 327 7460; Fax: +1 212 327 7109; Email: darnelr{at}mail.rockefeller.edu

Received May 29, 2004; Revised July 16, 2004; Accepted August 10, 2004

The Nova onconeural antigens are implicated in the pathogenesis of paraneoplastic opsoclonus-myoclonus-ataxia (POMA). The Nova antigens are neuron-specific RNA-binding proteins harboring three repeats of the K-homology (KH) motif; they have been implicated in the regulation of alternative splicing of a host of genes involved in inhibitory synaptic transmission. Although the third Nova KH domain (KH3) has been extensively characterized using biochemical and crystallographic techniques, the roles of the KH1 and KH2 domains remain unclear. Furthermore, the specificity determinants that distinguish the Nova KH domains from those of the closely related hnRNP E and hnRNP K proteins are undefined. We demonstrate through the use of RNA selection and biochemical analysis that the sequence specificity of the Nova KH1/2 domains is similar to that of Nova KH3. We also show that the mutagenesis of a Nova KH domain to render it similar to the KH domains of the heterogeneous nuclear ribonucleoprotein E (hnRNP E) and hnRNP K allow it to recognize longer RNA sequences. These data yield important insights into KH domain function and suggest a strategy by which to engineer KH domains with novel sequence preferences.


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