SELMA: Selection with Modified Aptamers

Abstract

In vitro selection of nucleic acid aptamers, coined SELEX, has led to the discovery of novel therapeutics and aided in the structural and mechanistic understanding of many ligand-biomolecule interactions. A related method, selection with modified aptamers (SELMA), enables selection of DNA aptamers containing bases with a large modification that cannot undergo PCR. A key application of this method is the evolution of aptamers containing carbohydrate modifications. Carbohydrate-binding proteins normally require several copies of the carbohydrate moiety for strong recognition. Whereas it may be difficult to rationally design synthetic scaffolds that cluster glycans in the optimal spacing and orientation for target recognition, SELMA furnishes glycoaptamers with highly optimized glycan clustering, achieving low-nanomolar recognition. Although numerous applications can be envisioned, the protocols and discussions in this article describe procedures involved in applying SELMA to the discovery glycoDNAs that bind to the HIV broadly neutralizing antibody 2G12.

Keywords: HIV; SELEX; SELMA; in vitro aptamer selection; protein-carbohydrate interaction.

Figure 1

SELMA scheme and components. Library forms: (A) Purchased ssDNA library or ssPCR product library; (B) dsDNA library; (C) ssDNA library; (C′ ) ssDNA hairpin library; (D) dsDNA hairpin library; (E) glycosylated dsDNA hairpin library; (F) glycosylated ss/dsDNA hybrid library; (G) selected aptamer library; (H) PCR library.

Figure 2

Glycosylation of a library with a 25-nt random region and 15% A content. Lane 1: Low-molecular-weight ladder. Lane 2: dsDNA hairpin library Form D. Lane 3: Man₉-cyclohexylglycosylated dsDNA hairpin Form E. Separate bands can also be visualized when the library is glycosylated with the smaller glycan Man₄-cyclohexyl.