Diversity of Oligonucleotide Functions

Abstract

SELEX is a technology for the identification of high affinity oligonucleotide ligands. Large libraries of random sequence single-stranded oligonucleotides, whether RNA or DNA, can be thought of conformationally not as short strings but rather as sequence dependent folded structures with high degrees of molecular rigidity in solution. This conformational complexity means that such a library is a source of high affinity ligands for a surprising variety of molecular targets, including nucleic acid binding proteins such as polymerases and transcription factors, non-nucleic acid binding proteins such as cytokins and growth factors, as well as small organic molecules such as ATP and theophylline. The range of applications of this technology for new discovery extends from basic research reagents to the identification of novel diagnostic and therapeutic reagents. Examples of these applications are described along with a discussion of underlying principles and future developments expected to further the utility of SELEX.

In vitro selection of RNAs that bind to the human immunodeficiency virus type-1 gag polyprotein

“…The pol gene encodes enzymes such as protease, integrase, reverse transcriptase and RNAse H. Multimerization of gag-pol results in the incorporation of these enzymes into virions. Systematic evolution of ligands by exponential enrichment (SELEX) is an in vitro selection and evolution method that has been used to isolate nucleic acid polymers that bind to various molecules (12,13). The SELEX process and similar methods have been used previously to isolate RNA ligands that bind to the HIV-1 rev (14)(15)(16)(17), tat (18), reverse transcriptase (19,20) and integrase (21) proteins.…”

A DNA aptamer population specifically detects Leishmania infantum H2A antigen

“…11,12 Structural studies with aptamer-target complexes have demonstrated insights into molecular diversity associated with nucleic acid architecture and molecular recognition. 13 Aptamers frequently form complexes that have dissociation constants in the nanomolar range and can clearly distinguish between even closely related protein targets. 14,15 The procedure for obtaining aptamers requires the incubation of a target with a library of DNA sequences, typically ranging from 10 14 to 10 18 molecules in complexity.…”

Expression of small, therapeutic RNAs in human cell nuclei

“…Several types of RNA inhibitors are potential advantage over the use of other pol III protheoretically possible, including antisense RNA, catalytic moters (5S rRNA and tRNA classes), where insert RNA RNA (ribozymes), and high-affinity RNA ligands, termed must be expressed as a fusion with the RNA sequences 'aptamers' or 'decoys'. [1][2][3][4][5][6][7][8][9][10][11] encoding the intragenic promoters. This is of special conTo deliver successfully the RNA inhibitors to their cern in strategies using viral RNAs, which might have intended targets in the appropriate subcellular compartcytotoxic effects, for example Refs 17 and 18).…”