Methods for cell- and tissue-specific DNA aptamer selection

Aptamers are folded single-stranded DNA or RNA molecules with high affinity for target small molecules, proteins, cells, or tissues. Affinity arises from the three-dimensional structure of the aptamer. Many significant advancements in oligonucleotide selection strategies have been made since the first foundational reports of in vitro selection techniques over 30 years ago. Most notably, the last 15 years have seen major advancements in selection protocols for aptamers with affinity to unspecified targets in complex living mammalian contexts such as cultured cells or tissues and tumors in live animals. Chemically unmodified DNA aptamers have potential as low-cost, biodegradable drug delivery or diagnostic reagents offering highly specific interactions against targeted cell populations. Here, we provide routine protocols from our labs for design and implementation of aptamer selections against cells or tissues, including principles of library design, selection strategy, aptamer candidate identification, and complementary image- and qPCR-based techniques for validating aptamer specificity.