René Olsthoorn
Universitair docent
- Naam
- Dr. R.R.C.L. Olsthoorn
- Telefoon
- +31 71 527 4773
- olsthoor@chem.leidenuniv.nl
- ORCID iD
- 0000-0003-0315-3005
Promovendi
Universitair docent
- Wiskunde en Natuurwetenschappen
- Leiden Institute of Chemistry
- LIC/Chemical Biology
- Strien J. van, Makurat D.M.M., Zeng Y., Olsthoorn R.R.C.L., Schneider G.F., Slutter B.A., MacKay J.A., Jiskoot W. & Kros A. (2024), Noncovalent conjugation of OVA323 to ELP micelles increases immune response, Biomacromolecules 25(2): 1027-1037.
- Dilweg I.W., Oskam M.G., Overbeek S. & Olsthoorn R.R.C.L. (2023), Investigating the correlation between Xrn1-resistant RNAs and frameshifter pseudoknots, RNA Biology 20(1): 409-418.
- Dilweg I.W., Peer J. & Olsthoorn R.R.C.L. (2023), Xrn1-resistant RNA motifs are disseminated throughout the RNA virome and are able to block scanning ribosomes, Scientific Reports 13(1): 15987.
- Strien J. van, Warmenhoven H., Logiantara A., Makurat D.M.M., Aglas L., Bethanis A., Leboux R.J.T., Rijt L. van, MacKay J. A., Schijndel J.W. van, Schneider G.F., Olsthoorn R.R.C.L., Jiskoot W., Ree R. van & Kros A. (2022), Bet v 1-displaying elastin-like polypeptide nanoparticles induce a strong humoral and weak CD4+ T-cell response against Bet v 1 in a murine immunogenicity model, Frontiers in immunology 13: 1006776.
- Olsthoorn R.C.L. (2022), Replication of alphaviruses requires a pseudoknot that involves the poly(A) tail, RNA 28(10): 1348-1358.
- Olsthoorn R.C.L., Owen C.A. & Livieratos I.C. (2022), Role of an RNA pseudoknot involving the polyA tail in replication of Pepino mosaic potexvirus and related plant viruses, Scientific Reports 12(1): 11532.
- Shen M.J., Olsthoorn R.C.L., Zeng Y., Bakkum T., Kros A. & Boyle A.L. (2021), Magnetic-activated cell sorting using coiled-coil peptides: an alternative strategy for isolating cells with high efficiency and specificity, ACS Applied Materials and Interfaces 13(10): 11621-11630.
- Dilweg I.W., Savina A., Köthe S., Goultiaev A.P., Bredenbeek P.J. & Olsthoorn R.C.L. (2021), All genera of Flaviviridae host a conserved Xrn1-resistant RNA motif, RNA Biology 18(12): 2321-2329.
- Chen S.C., Olsthoorn R.C.L. & Yu C.H. (2021), Structural phylogenetic analysis reveals lineage-specific RNA repetitive structural motifs in all coronaviruses and associated variations in SARS-CoV-2, Virus Evolution 7(1): veab021.
- Goultiaev A.P., Olsthoorn R.C.L., Spronken M. & Richard M. (2021), Structural Bioinformatics of Influenza Virus RNA Genomes: Virus Bioinformatics. In: Frishman D. & Marz M. (red.), Virus Bioinformatics. Boca Raton: Chapman and Hall/CRC.
- Zammit A., Helwerda L.S., Olsthoorn R.C.L., Verbeek F.J. & Goultiaev A.P. (2020), A database of flavivirus RNA structures with a search algorithm for pseudoknots and triple base interactions, Bioinformatics 37(7): 956-962.
- Dilweg I.W., Bouabda A., Dalebout T., Goultiaev A.P., Bredenbeek P.J. & Olsthoorn R.C.L. (2020), Xrn1-resistant RNA structures are well-conserved within the genus flavivirus, RNA Biology 18(5): 709-717.
- Dilweg I.W., Goultiaev A.P. & Olsthoorn R.C.L. (2019), Structural features of an Xrn1-resistant plant virus RNA, RNA Biology 16(6): 838-845.
- Chen S.C. & Olsthoorn R.C.L. (2019), Relevance of the iron-responsive element (IRE) pseudotriloop structure for IRP1/2 binding and validation of IRE-like structures using the yeast three-hybrid system, Gene 710: 399-405.
- Goultiaev A.P., Richard M., Spronken M., Olsthoorn R.C.L. & Fouchier R.A.M. (2019), Conserved structural RNA domains in regions coding for cleavage site motifs in hemagglutinin genes of influenza viruses, Virus Evolution 5(2): vez034.
- MacFadden A., O’Donoghue Z., Silva P.A.G.C., Chapman E.G., Olsthoorn R.C.L., Sterken M.G., Pijlman G.P., Bredenbeek P.J. & Kieft J.S. (2018), Mechanism and structural diversity of exoribonuclease-resistant RNA structures in flaviviral RNAs, Nature Communications 9: 119.
- Arjmandi Tash H., Bellunato A., Wen C., Olsthoorn R.R.C.L., Scheicher R.H., Zhang S.L. & Schneider G.F. (2018), Zero-Depth Interfacial Nanopore Capillaries, Advanced Materials 30(9): 1703602.
- Yang J., Meng Z., Liu Q., Shimada Y., Olsthoorn R.R.C.L., Spaink H.P., Herrmann A. & Kros A. (2018), Performing DNA nanotechnology operations on a zebrafish, Chemical Science 9(36): 7271-7276.
- Yang J., Tu J., Lamers G.E.M., Olsthoorn R.R.C.L. & Kros A. (2017), Membrane Fusion Mediated Intracellular Delivery of Lipid Bilayer Coated Mesoporous Silica Nanoparticles, Advanced Healthcare Materials 6(20): 1700759.
- Spronken M.I., Sandt C.E. van de, Jongh E.P. de, Vuong O., Vliet S. van der, Bestebroer T.M., Olsthoorn R.C.L., Rimmelzwaan G.F., Fouchier R.A.M. & Goultiaev A.P. (2017), A compensatory mutagenesis study of a conserved hairpin in the M gene segment of influenza A virus shows its role in virus replication, RNA Biology 14(11): 1606-1616.
- Yang J., Shimada Y., Olsthoorn R.R.C.L., Snaar-Jagalska B.E., Spaink H.P. & Kros A. (2016), Application of Coiled Coil Peptides in Liposomal Anti-Cancer Drug Delivery Using a Zebrafish Xenograft Model, ACS Nano 10(8): 7428-7435.
- Goultiaev A.P., Spronken M.I., Richard M., Schrauwen E.J.A., Olsthoorn R.C.L. & Fouchier R.A.M. (2016), Subtype-specific structural constraints in the evolution of influenza A virus hemagglutinin genes, Scientific Reports 6: 38892.
- Yang J., Bahreman A., Daudey G.A., Bussmann J., Olsthoorn R.R.C.L. & Kros A. (2016), Drug delivery via cell membrane fusion using lipopeptide modified liposomes, ACS Central Science 2016(2): 621-630.
- Olsthoorn R.C.L. (2016), Mechanical unfolding kinetics of the SRV-1 gag-pro mRNA pseudoknot: possible implications for -1 ribosomal frameshifting stimulation, Scientific Reports 6: 39549.
- Yu C.H. & Olsthoorn R.R.C.L. (2015), Monitoring ribosomal frameshifting as a platform to screen anti-riboswitch drug candidates, Methods in Enzymology 550: 385-393.
- Olsthoorn R.R.C.L. (2014), G-quadruplexes within prion mRNA: the missing link in prion disease?, Nucleic Acids Research 42(14): 9327-9333.
- Gultyaev A.P., Olsthoorn R.C.L., Spronken M.I.J. & Fouchier R.A.M. (2014), Detection of structural constraints and conformational transitions in the influenza virus RNA genome using structure predictions and mutual information calculations. Ortuno F. & Rojas I. (red.), Proceedings IWBBIO 2014, International Work-Conference on Bioinformatics and Biomedical Engineering. IWBBIO 2014, International Work-Conference on Bioinformatics and Biomedical Engineering 7 april 2014 - 9 april 2014. Granada: Copicentro Granada S.L. 273-284.
- Clabbers M.T.B., Olsthoorn R.C.L. & Goultiaev A.P. (2014), Tospovirus ambisense genomic RNA segments use almost complete repertoire of stable tetraloops in the intergenic region, Bioinformatics 30(13): 1800-1804.
- Delft P. van, Witte W.E.A. de, Meeuwenoord N.J., Noort G.J. van der Heden van, Versluis F., Olsthoorn R.R.C.L., Overkleeft H.S., Marel G.A. van der & Filippov D.V. (2014), Design of a ribosyltriazole-annulated cyclooctyne for oligonucleotide labeling by strain-promoted alkyne-azide cycloaddition, European Journal of Organic Chemistry 2014(34): 7566-7571.
- Olsthoorn R.R.C.L. (2014), A recombinant RNA bacteriophage system to identify functionally important nucleotides in a self-cleaving ribozyme, Virology Journal 11: 116.
- Yu C.H., Teulade-Fichou M.P. & Olsthoorn R.R.C.L. (2014), Stimulation of ribosomal frameshifting by RNA G-quadruplex structures, Nucleic Acids Research 42(3): 1887-1892.
- Osman T.A.M., Olsthoorn R.R.C.L. & Livieratos I.C. (2014), Role of the Pepino mosaic virus 3 '-untranslated region elements in negative-strand RNA synthesis in vitro, Virus Research 190: 110-117.
- Goultiaev A.P., Tsyganov-Bodounov A., Spronken M.I., Kooij S. van der, Fouchier R.A.M. & Olsthoorn R.C.L. (2014), RNA structural constraints in the evolution of the influenza A virus genome NP segment, RNA Biology 11(7): 942-952.
- Werf R. van der, Wijmenga S.S., Heus H.A. & Olsthoorn R.C.L. (2013), Structural and thermodynamic signatures that define pseudotriloop RNA hairpins, RNA 19(12): 1833-1839.
- Yu C.H., Luo J.H., Iwata-Reuyl D. & Olsthoorn R.R.C.L. (2013), Exploiting preQ(1) riboswitches to regulate ribosomal frameshifting, ACS Chemical Biology 8(4): 733-740.
- Osman T.A.M., Olsthoorn R.R.C.L. & Livieratos I.C. (2012), In vitro template-dependent synthesis of Pepino mosaic virus positive- and negative-strand RNA by its RNA-dependent RNA polymerase, Virus Research 167(2): 267-272.
- Skov J., Gaudin M., Podbevsek P., Olsthoorn R.C.L. & Petersen M. (2012), The subgenomic promoter of brome mosaic virus folds into a stem-loop structure capped by a pseudo-triloop that is structurally similar to the triloop of the genomic promoter, RNA 18(5): 992-1000.
- Goultiaev A.P., Olsthoorn R.C.L., Pleij C.W.A. & Westhof E. (2012), RNA Structure: Pseudoknots. In: , Encyclopedia of Life Sciences. Encyclopedia of Life Sciences (eLS): Wiley.
- Liu Z., Galli F., Waterreus W.J., Meulenbroek E.M., Koning R.I., Lamers G.E.M., Olsthoorn R.C.L., Pannu N.S., Oosterkamp T.H., Koster A.J., Dame R.T. & Abrahams J.P. (2012), Single-walled carbon nanotubes as scaffolds to concentrate DNA for the study of DNA-protein interactions, ChemPhysChem 13(6): 1569-1575.
- Olsthoorn R.C.L. & Duin J. van (2011), Levivirus. In: Tidona C. & Darai G. (red.), The Springer Index of Viruses. New York: Springer-Verlag. 799-804.
- Duin J. van & Olsthoorn R.C.L. (2011), Leviviridae. In: King A.M.Q., Lefkowitz E., Adams M.J. & Carstens E.B. (red.), Ninth Report of the International Committee on Taxonomy of Viruses: Elsevier. 1035–1043.
- Olsthoorn R.C.L. & Duin J. van (2011), Bacteriophages with ssRNA. In: , Encyclopedia of Life Sciences.
- Yu C.-H., Noteborn M.H.M., Pleij C.W.A. & Olsthoorn R.C.L. (2011), Stem-loop structures can effectively substitute for an RNA pseudoknot in-1 ribosomal frameshifting, Nucleic Acids Research 39(20): 8952-8959.
- Girard G.A.O., Goultiaev A.P. & Olsthoorn R.C.L. (2011), Upstream start codon in segment 4 of North American H2 avian influenza A viruses, Infection, Genetics and Evolution 11(2): 489-495.
- Chen S.-C. & Olsthoorn R.R.C.L. (2010), In vitro and in vivo studies of the RNA conformational switch in Alfalfa mosaic virus, Journal of Virology 84(3): 1423-1429.
- Liu Z., Jiang L., Galli F., Nederlof I., Olsthoorn R.C.L., Lamers G.E.M., Oosterkamp T.H. & Abrahams J.P. (2010), A graphene oxide center dot streptavidin complex for biorecognition - towards affinity purification, Advanced Functional Materials 20(17): 2857-2865.
- Liu Z., Galli F., Janssen K.G.H., Jiang L., Linden H.J. van der, Geus D.C. de, Voskamp P., Kuil M.E., Olsthoorn R.C.L., Oosterkamp T.H., Hankemeier T. & Abrahams J.P. (2010), Stable single-walled carbon nanotube-streptavidin complex for biorecognition, The Journal of Physical Chemistry Part C 114(10): 4345-4352.
- Goultiaev A.P., Fouchier R.A.M. & Olsthoorn R.C.L. (2010), Influenza virus RNA structure: unique and common features, International Reviews of Immunology 29(6): 533-556.
- Yu C.-H., Noteborn M.H.M. & Olsthoorn R.C.L. (2010), Stimulation of ribosomal frameshifting by antisense LNA, Nucleic Acids Research 38(22): 8277-8283.
- Goultiaev A.P. & Olsthoorn R.C.L. (2010), A family of non-classical pseudoknots in influenza A and B viruses, RNA Biology 7(2): 125-129.
- Olsthoorn R.C.L., Reumerman R., Hilbers C.W., Pleij C.W.A. & Heus H.A. (2010), Functional analysis of the SRV-1 RNA frameshifting pseudoknot, Nucleic Acids Research 38(21): 7665-7672.
- Chen S.C., Desprez A. & Olsthoorn R.R.C.L. (2010), Structural homology between bamboo mosaic virus and its satellite RNAs in the 5'untranslated region, Journal of General Virology 91(3): 782-787.
- Chen S.C. & Olsthoorn R.R.C.L. (2010), Group-specific structural features of the 5 '-proximal sequences of coronavirus genomic RNAs, Virology 401(1): 29-41.
- Chen S.C., Goultiaev A.P., Pleij C.W.A. & Olsthoorn R.C.L. (2009), A Secondary Structure Model for the 3'-Untranslated Region of Ilarvirus RNAs. In: Feng Z. & Long M. (red.), Viral Genomes: Diversity, Properties and Parameters: Nova Science Publishers, Inc.. 65-83.
- Chen S.C., Born E. van den, Pleij C.W.A., Snijder E.J., Olsthoorn R.R.C.L. & Worm S.H.E. van den (2007), A new structure model for the packaging signal in the genome of group IIa Coronaviruses, Journal of Virology 81(12): 6771-6774.
- Rudinger-Thirion J., Olsthoorn R.R.C.L., Giegé R. & Barends S. (2006), Idiosyncratic behaviour of tRNA-like structures in translation of plant viral RNA genomes, Journal of Molecular Biology/JMB Online 355(5): 873-878.
- Livieratos I.C., Eliasco E., Muller G., Olsthoorn R.R.C.L., Salazar L.F., Pleij C.W.A. & Coutts R.H.A. (2004), Analysis of the RNA of Potato yellow vein virus: evidence for a tripartite genome and conserved T-terminal structures among members of the genus Crinivirus, Journal of General Virology 85(7): 2065-2075.
- Olsthoorn R.C.L., Laurs M., Sohet F., Hilbers C.W., Heus H.A. & Pleij C.W.A. (2004), Novel application of sRNA: stimulation of ribosomal frameshifting, RNA 10(11): 1702-1703.
- Olsthoorn R.C.L., Haasnoot P.C. & Bol J.F. (2004), Similarities and differences between the subgenomic and minusstrand promoters of an RNA plant virus, Journal of Virology 78(8): 4048-4053.
- Haasnoot P.C.J., Bol J.F. & Olsthoorn R.R.C.L. (2003), A plant virus replication system to assay the formation of RNA pseudotriloop motifs in RNA-protein interactions, Proceedings of the National Academy of Sciences 100(22): 12596-12600.
- Haasnoot P.C.J., Olsthoorn R.C.L. & Bol J.F. (2002), The Brome mosaic virus subgenomic promoter hairpin is structurally similar to the iron-responsive element and functionally equivalent to the minus-strand core promoter stem-loop C, RNA 8(1): 110-122.
- Meerten D. van, Groeneveld H., Miller D.M.J., Marechal G.B., Tsareva N.V., Olsthoorn R.R.C.L., Pena M. de la & Duin J. van (2002), In vivo generation of hybrids between different species of RNA phages, Journal of General Virology 83(5): 1223-1235.
- Verheije M.H., Olsthoorn R.R.C.L., Kroese M.V., Rottier P.J.M. & Meulenberg J.J.M. (2002), Kissing interaction between 3 ' noncoding and coding sequences is essential for porcine arterivirus RNA replication, Journal of Virology 76(3): 1521-1526.
- Olsthoorn R.R.C.L., Bruyere A., Dzianott A. & Bujarski J.J. (2002), RNA recombination in brome mosaic virus: effects of strand-specific stem-loop inserts, Journal of Virology 76(24): 12654-12662.
- Olsthoorn R.R.C.L. & Bol J.F. (2002), Role of an essential triloop hairpin and flanking structures in the 3' untranslated region of Alfalfa mosaic virus RNA in in vitro transcription, Journal of Virology 76(17): 8747-8756.
- Verhaert R.M.D., Beekwilder J., Olsthoorn R.R.C.L., Duin J. van & Quax W.J. (2002), Phage display selects for amylases with improved low pH starch-binding, Journal of Biotechnology 96(1): 103-118.
- Aparicio F., Sanchez-Navarro J.A., Olsthoorn R.R.C.L., Pallas V. & Bol J.F. (2001), Recognition of cis-acting sequences in RNA 3 of Prunus necrotic ringspot virus by the replicase of Alfalfa mosaic virus, Journal of General Virology 82(4): 947-951.
- Olsthoorn R.C.L. & Bol J.F. (2001), Sequence comparison and secondary structure analysis of the 3' noncoding region of flavivirus genomes reveals multiple pseudoknots, RNA 7(10): 1370-1377.
- Neeleman L., Olsthoorn R.C.L., Linthorst H.J.M. & Bol J.F. (2001), Translation of a nonpolyadenylated viral RNA is enhanced by binding of viral coat protein or polyadenylation of the RNA, Proceedings of the National Academy of Sciences 98(25): 14286-14291.
- Meerten D. van, Olsthoorn R.R.C.L., Duin J. van & Verhaert R.M.D. (2001), Peptide display on live MS2 phage: restrictions at the RNA genome level, Journal of General Virology 82(7): 1797-1805.
- Haasnoot P.C.J., Brederode F.T., Olsthoorn R.C.L. & Bol J.F. (2000), A conserved hairpin structure in Alfamovirus and Bromovirus subgenomic promoters is required for efficient RNA synthesis in vitro, RNA 6(5): 708-716.
- Olsthoorn R.R.C.L., Mertens S., Brederode F.T. & Bol J.F. (1999), A conformational switch at the 3' end of a plant virus RNA regulates viral replication, The EMBO Journal 18(17): 4856-4864.
- Olsthoorn R.C.L. & Duin J. van (1998), Sense and nonsense DNA, Trends in Biochemical Sciences 23(4): 125.
- Klovins J., Duin J. van & Olsthoorn R.R.C.L. (1997), Rescue of the RNA phage genome from RNase III cleavage, Nucleic Acids Research 25(21): 4201-4208.
- Olsthoorn R.R.C.L. & Duin J. van (1996), Random removal of inserts from an RNA genome: selection against single-stranded RNA, Journal of Virology 70(2): 729-736.
- Olsthoorn R.R.C.L. & Duin J. van (1996), Evolutionary reconstruction of a hairpin deleted from the genome of an RNA virus, Proceedings of the National Academy of Sciences 93(22): 12256-12261.
- Olsthoorn R.R.C.L., Garde G., Dayhuff T., Atkins J.F. & Duin J. van (1995), Nucleotide sequence of a single-stranded RNA phage from Pseudomonas aeruginosa: kinship to coliphages and conservation of regulatory RNA structures, Virology 206(1): 611-625.
- Olsthoorn R.R.C.L., Zoog S. & Duin J. van (1995), Coevolution of RNA helix stability and Shine-Dalgarno complementarity in a translational start region, Molecular Microbiology 15(2): 333-339.
- Olsthoorn R.R.C.L., Licis N. & Duin J. van (1994), Leeway and constraints in the forced evolution of a regulatory RNA helix, The EMBO Journal 13(11): 2660-2668.
- Backendorf C.M.P., Olsthoorn R.R.C.L. & Putte P. van de (1989), Superhelical stress restrained in plasmid DNA during repair synthesis initiated by the UvrA, B and C proteins in vitro, Nucleic Acids Research 17(24): 10337-10351.