A versatile strategy has been developed for selectively and sequentially isolating targets in a liquid-phase affinity separation environment. The strategy uses a recently developed approach for joiningtogether molecules in linkages that are defined by the complementary pairing of oligonucleotidesconjugated to the different molecules [Niemeyer, C. M., Sano, T., Smith, C. L., and Cantor, C. R.(1994)
Nucleic Acids Res. 22, 5530-9]. In the work presented here, streptavidin was noncovalentlycoupled with the temperature-responsive poly(
N-isopropylacrylamide) [poly(NIPAAM)] through thesequence-specific hybridization of oligonucleotides conjugated to the protein and polymer. A 20-meroligonucleotide was covalently linked through a heterobifunctional linker to a genetically engineeredstreptavidin variant that contained a unique cysteine residue at the solvent-accessible site Glu 116.The complementary DNA sequence was conjugated to the end of a linear ester-activated poly(NIPAAM).The two conjugates were allowed to self-assemble in solution via hybridization of their complementaryDNA sequences. The streptavidin-poly(NIPAAM) complex could be used to affinity-precipitateradiolabeled biotin or biotinylated alkaline phosphatase above 32
C through the thermally inducedphase separation activity of the poly(NIPAAM). The streptavidin-oligo species could then be reversiblyseparated from the precipitated polymer-oligo conjugate and recycled by lowering the salt concentration, which results in denaturation of the short double-stranded DNA connection. The use ofoligonucleotides to couple polymer to streptavidin allows for selective precipitation of different polymersand streptavidin complexes based on the sequence-specific hybridization of their oligonucleotideappendages.