Aptamers Targeting RNA Molecules

Abstract

Oligonucleotides complementary to RNA sequences interact poorly with folded target regions. In vitro selection of oligonucleotides carried out against RNA structures have led to aptamers that frequently differ from antisense sequences, but rather take advantage of non-double-stranded peculiarities of the target. Studies along this line provide information about tertiary RNA architectures as well as their interaction with ligand of interest. We describe here a genomic SELEX approach and its application to the recognition of stem-loop structures prone to the formation of kissing complexes. We also provide technical details for running a procedure termed 2D-SELEX that takes advantage of both in vitro selection and dynamic combinatorial chemistry. This allows selecting aptamer derivatives containing modified nucleotides that cannot be incorporated by polymerases. Last we present in vitro transcription conditions under which large amounts of RNA, suitable for NMR structural studies, can be obtained. These different aspects of the SELEX technology have been applied to the trans-activating responsive element of the human immunodeficiency virus type 1, which is crucial for the transcription of the retroviral genome.

Long noncoding RNAs: emerging players in thyroid cancer pathogenesis

“…They bind to their target lncRNAs specifically fitting to the 3-D structures of lncRNA. Aptamers suppress the interactions of lncRNAs and their critical components and certain distinct characteristics of lncRNAs show advantages over siRNAs (Watrin et al 2009). On the other hand, small molecules are synthesized to specifically bind to the RNA binding pockets of lncRNAs and compete with protein factors or intracellular small ligands for the binding of lncRNAs.…”

RNA modularity for synthetic biology

“…From a structural perspective, in vitro selection offers the possibility of creating new structural motifs, not selected for in natural systems, including novel long-range interactions (e.g. [65,77,90-91]). The possibility of selecting new RNA interactions and shapes significantly increases our ability to create more complex nano-structures and nano-machines.…”

Nucleic acid aptamers as antithrombotic agents: Opportunities in extracellular therapeutics

“…The methods include: convergent SELEX (initial rounds with a complex proteome and later rounds with a target protein); blending SELEX (library of oligonucleotides covalently bound to a ligand or protein target); mirror-image SELEX (selection of enantiomers of natural compounds); toggle SELEX (selection of several protein targets or targets of differing species through alternating rounds); cell-SELEX ( selection against a specific cell type); 2D-SELEX (recognition of stem-loop structures); genomic SELEX (employment of a library based on genomic sequences), and tailored SELEX (library without fixed sequences) (6)(7)(8).…”