Combinatorial Design of a Nanobody that Specifically Targets Structured RNAs. Issue 11 (25th May 2018)

• Record Type: Journal Article
• Authors: Cawez, F.; Duray, E.; Hu, Y.; Vandenameele, J.; Romão, E.; Vincke, C.; Dumoulin, M.; Galleni, M.; Muyldermans, S.; Vandevenne, M.
• Is Part Of: Journal of molecular biology. Volume 430:Issue 11(2018)
• Page Start: 1652
• Page End: 1670
• Publication Date: 2018-05-25
• Subjects: stRNA structured RNA -- ncRNA non-coding RNA -- cAb camelid antibody fragment -- RBP RNA-binding protein; nanobody -- non-coding RNAs -- structured RNAs -- RNA/protein interactions -- antibody fragment engineering; Molecular biology -- Periodicals; Biology -- Periodicals; Biochemistry -- Periodicals; Bacteriology -- Periodicals; Molecular Biology -- Periodicals; Biochemistry -- Periodicals; Biologie moléculaire -- Périodiques; Biologie -- Périodiques; Biochimie -- Périodiques; Moleculaire biologie; Biochemistry; Biology; Molecular biology; Periodicals; 572.805
• DOI: 10.1016/j.jmb.2018.03.032
• Languages: English
• ISSNs: 0022-2836

Abstract

Abstract: Recent advances in transcriptome sequencing and analysis have revealed the complexity of the human genome. The majority (≈ 98%) of cellular transcripts is not translated into proteins and represents a vast, unchartered world of functional non-coding RNAs. Most of them adopt a well-defined three-dimensional structure to achieve their biological functions. However, only very few RNA structures are currently available which reflects the challenges associated with RNA crystallization. Nevertheless, these structures would represent a critical step in understanding functions of non-coding RNAs and their molecular mechanisms in the cell. The overall goal of this study is to develop an innovative and versatile tool to facilitate the functional study and crystallization of structured RNAs (stRNAs). In this work, we have engineered an antibody fragment from camelid heavy-chain antibody (nanobody) able to specifically bind with low nanomolar affinity to stRNA, while no binding could be detected for single-stranded DNA/RNA, double-stranded DNA/RNA or a negatively charged protein. However, this nanobody recognizes different and non-related stRNAs, this observation suggests that it binds to an epitope shared by these stRNAs. Finally, our data also show that the binding of the nanobody does not alter the secondary structure content of the stRNA as well as its unfolding/refolding processes during heat treatment. This work constitutes a successful proof of concept demonstrating that nanobodies can be engineered to recognize RNA-related epitopes. Graphical abstract: Unlabelled Image Highlights: Structured RNAs (stRNAs) are highly relevant in the cell biology and physiopathology. We designed a nanobody library optimized for nucleic acid binding. We screened this library against a stRNA and selected a high-affinity binder. This nanobody is specific for stRNAs and does not modify the fold of the later upon binding. Nanobodies can therefore be engineered against RNA epitopes.