Sequence-specific binding of DNA and RNA to immobilized Nickel ions

Immobilization of divalent Nickel cations provides a tool for affinity purification of proteins containing hexahistidine tags. During experiments to generate single-stranded DNA aptamers to immobilized proteins we inadvertently identified DNA sequences with affinity for Nickel-nitrilotriacetic acid (Ni²⁺-NTA) magnetic beads. Analysis of these aptamers revealed that affinity for the Ni²⁺-NTA support requires only single-stranded sequences with multiple adenosine residues. Bound nucleic acids can be eluted with imidazole. A single-stranded dA₂₀ affinity tag (but not other homopolymer sequences) is sufficient for immobilization of double-stranded DNA PCR products on Ni²⁺-NTA magnetic beads. Addition of an rA₂₀ sequence to an RNA transcript allowed its affinity capture on Ni²⁺-NTA magnetic beads, suggesting an approach for purification of poly(A) mRNA.