title: Selection of DNA aptamers with two modified bases.
abstract: The nucleobases comprising DNA and RNA aptamers provide considerably less chemical diversity than protein-based ligands, limiting their versatility. The introduction of novel functional groups at just one of the four bases in modified aptamers has recently led to dramatic improvement in the success rate of identifying nucleic acid ligands to protein targets. Here we explore the benefits of additional enhancement in physicochemical diversity by selecting modified DNA aptamers that contain amino-acid-like modifications on both pyrimidine bases. Using proprotein convertase subtilisin/kexin type 9 as a representative protein target, we identify specific pairwise combinations of modifications that result in higher affinity, metabolic stability, and inhibitory potency compared with aptamers with single modifications. Such doubly modified aptamers are also more likely to be encoded in shorter sequences and occupy nonoverlapping epitopes more frequently than aptamers with single modifications. These highly modified DNA aptamers have broad utility in research, diagnostic, and therapeutic applications.
authors.affiliation: SomaLogic, Inc., Boulder, CO 80301.
authors.forename: Bharat N
authors.initials: BN
authors.lastname: Gawande
authors.affiliation: SomaLogic, Inc., Boulder, CO 80301.
authors.forename: John C
authors.initials: JC
authors.lastname: Rohloff
authors.affiliation: SomaLogic, Inc., Boulder, CO 80301.
authors.forename: Jeffrey D
authors.initials: JD
authors.lastname: Carter
authors.affiliation: SomaLogic, Inc., Boulder, CO 80301.
authors.forename: Ira
authors.initials: I
authors.lastname: von Carlowitz
authors.affiliation: SomaLogic, Inc., Boulder, CO 80301.
authors.forename: Chi
authors.initials: C
authors.lastname: Zhang
authors.affiliation: SomaLogic, Inc., Boulder, CO 80301.
authors.forename: Daniel J
authors.initials: DJ
authors.lastname: Schneider
authors.affiliation: SomaLogic, Inc., Boulder, CO 80301 njanjic@somalogic.com.
authors.forename: Nebojsa
authors.initials: N
authors.lastname: Janjic
mesh_terms: D052157:Aptamers, Nucleotide; D045744:Cell Line, Tumor; D003851:Deoxyribonucleases / Q000378:metabolism; D015723:Gene Library; D006801:Humans; D008024:Ligands; D000091362:PCSK9 Inhibitors; D000071449:Proprotein Convertase 9 / Q000737:chemistry / Q000235:genetics; D052156:SELEX Aptamer Technique
chemical_list: D052157:Aptamers, Nucleotide; D008024:Ligands; D000091362:PCSK9 Inhibitors; D003851:Deoxyribonucleases; C472125:PCSK9 protein, human; D000071449:Proprotein Convertase 9
keywords: PCSK9; PSMA; SELEX; SOMAmer; modified aptamer