RNA pseudo-triloops: key structures in RNA-protein recognition and targets for potential drugs


RNA-protein interactions play a fundamental role in many cellular processes, including transcription, translation and splicing. Although the number of solved RNA-protein complexes has grown dramatically in the past decade, much remains to be learned regarding determinants of RNA recognition. The recent discovery of the pseudo-triloop as a potentially general RNA motif in protein binding offers new opportunities to further our knowledge about RNA recognition. Since this motif plays a key role in the life cycle of several pathogenic viruses and bacteria, it serves as an ideal target for drug development.
This proposal describes an approach towards the selection of small peptide binders directed against viral RNAs as well as the development of an in vivo system to study their potential anti-viral activity. Small peptides are able to bind to complex RNA structures with high specificity and affinity. A novel technique called "mRNA display" allows exploration of very large libraries of peptides for their ability to bind to an immobilized target. RNA transcripts corresponding to pseudo-triloop hairpins of human immunodeficiency, hepatitis B and C viruses will be used initially as targets for the selection of novel anti-viral drugs. A yeast three-hybrid system will be adapted to investigate RNA binding of these peptides in vivo. Combined expression of viral proteins and selected peptides in this system can be used as a fast and safe alternative to monitor potential anti-viral activity. Biochemical analysis of pseudo-triloop hairpins and their ligands, in combination with molecular modeling and NMR spectroscopy, should lead to further insight into protein-RNA interactions in general and the role of the pseudo-triloop motif in particular.

Keywords: RNA motif, in vitro selection, small peptides, RNA-protein interaction, anti-viral drugs



  • S.C. Chen(2010): Structural aspects of encapsidation signals in RNA viruses , LEIDEN  April 28, 2010

Chapter in book

  • C.W.A. Pleij, LB Kwang, R.C.L. Olsthoorn, MH de Smit, M Laurs(2007): New Messenger RNA Research Communications pp. 167 - 180
  • A.P. Gultyaev, R.C.L. Olsthoorn, C.W.A. Pleij, S.C. Cheng(2009): Viral Genomes: Diversity, Properties and parameters pp. 65 - 83

Scientific article

  • E Snijder, SHE van der Worm, R.C.L. Olsthoorn, E. van den Born, S.C. Chen, CWA Pleij(2007): New structure model for the packaging signal in the genome of group IIa coronaviruses. Journal of Virology pp. 6771 - 6774
  • R.C.L. Olsthoorn, HA Heus, A.P. Gultyaev(2007): An RNA conformational shift in recent H5N1 influenza A viruses Bioinformatics pp. 272 - 276
  • A Desprez, RCL Olsthoorn, S.C. Chen(2010): Structural homology between bamboo mosaic virus and its satellite RNAs in the 5'untranslated region Journal of General Virology pp. 782 - 787
  • RCL Olsthoorn, S.C. Chen(2010): In Vitro and In Vivo Studies of the RNA Conformational Switch in Alfalfa Mosaic Virus Journal of Virology pp. 1423 - 1429
  • S.C. Chen, RCL Olsthoorn(2010): Group-specific structural features of the 5'-proximal sequences of coronavirus genomic RNAs. Virology pp. 29 - 41
  • R. Van der werf, S.S. Wijmenga, H.A. Heus, R.C.L. Olsthoorn(2013): Structural and thermodynamic signatures that define pseudotriloop RNA hairpins RNA pp. 1833 - 1839


Project number


Main applicant

Dr. R.C.L. Olsthoorn

Affiliated with

Universiteit Leiden, Faculteit der Wiskunde en Natuurwetenschappen, Leiden Institute of Chemistry

Team members

Dr. S.C. Chen, Dr. S.C. Chen, Dhr. R. Reumerman, Drs. R.M. van der Werf


02/09/2004 to 26/05/2011