Panning for anticancer aptamers

GAINESVILLE, Fla.—Although researchers are increasingly using aptamers as high-specificity molecular probes, they generally need purified targets to generate these modified nucleic acids. In the Proceedings of the National Academy of Sciences, however, researchers at the University of Florida describe a way to use key molecular differences between two cell types to effectively "pan" for tissue-specific aptamers without foreknowledge of the molecular targets.

The group mixed a library of random single-stranded DNA molecules with cultured leukemia cells, washed away unbound aptamers, and eluted the bound aptamers. They then incubated these oligonucleotides with a control cell line and collected the aptamers that did not bind these cells. The scientists PCR amplified this subset of aptamers and repeated the selection cycle several more times, monitoring cell-aptamer interaction with flow cytometry.

After 20 cycles of enrichment, the researchers sequenced the aptamers and found 10 sequences that exhibited binding constants in the nanomolar to picomolar range. Using confocal imaging, the researchers noted that many aptamers recognized different cell subpopulations within a single culture, suggesting that these cells might carry unique molecular signatures. They also noted that the aptamers could distinguish leukemia cells that had been added to healthy human bone marrow aspirates, offering hope of using the aptamers as diagnostic probes in clinical samples.