title: Probing the limits of aptamer affinity with a microfluidic SELEX platform.
abstract: Nucleic acid-based aptamers offer many potential advantages relative to antibodies and other protein-based affinity reagents, including facile chemical synthesis, reversible folding, improved thermal stability and lower cost. However, their selection requires significant time and resources and selections often fail to yield molecules with affinities sufficient for molecular diagnostics or therapeutics. Toward a selection technique that can efficiently and reproducibly generate high performance aptamers, we have developed a microfluidic selection process (M-SELEX) that can be used to obtain high affinity aptamers against diverse protein targets. Here, we isolated DNA aptamers against three protein targets with different isoelectric points (pI) using a common protocol. After only three rounds of selection, we discovered novel aptamer sequences that bind to platelet derived growth factor B (PDGF-BB; pI = 9.3) and thrombin (pI = 8.3) with respective dissociation constants (K(d)) of 0.028 nM and 0.33 nM, which are both superior to previously reported aptamers against these targets. In parallel, we discovered a new aptamer that binds to apolipoprotein E3 (ApoE; pI = 5.3) with a K(d) of 3.1 nM. Furthermore, we observe that the net protein charge may exert influence on the affinity of the selected aptamers. To further explore this relationship, we performed selections against PDGF-BB under different pH conditions using the same selection protocol, and report an inverse correlation between protein charge and aptamer K(d).
authors: Interdepartmental Program in Biomolecular Science and Engineering, University of California Santa Barbara, Santa Barbara, California, United States of America.
authors: Kareem M
authors: KM
authors: Ahmad
authors: Seung Soo
authors: SS
authors: Oh
authors: Seon
authors: S
authors: Kim
authors: Forrest M
authors: FM
authors: McClellen
authors: Yi
authors: Y
authors: Xiao
authors: H Tom
authors: HT
authors: Soh
mesh_terms: D000818:Animals; D052157:Aptamers, Nucleotide / Q000235:genetics / Q000378:metabolism*; D001483:Base Sequence; D000077214:Becaplermin; D046210:Microfluidic Analytical Techniques / Q000379:methods*; D011485:Protein Binding; D020574:Proto-Oncogene Proteins c-sis / Q000378:metabolism; D052156:SELEX Aptamer Technique / Q000295:instrumentation*
chemical_list: D052157:Aptamers, Nucleotide; D020574:Proto-Oncogene Proteins c-sis; D000077214:Becaplermin