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Abstract

Natural DNA contains only four canonical nucleobases. It is a major drawback in limiting aptamer chemical functionalities, compared to antibody diverse functionalities composed of 20 amino acids. To combatting aptamer functionality deficiency issue, we developed the approach of Ligasecatalyzed OligOnucleotide PolymERization (LOOPER) to accommodate small molecule modifications on oligonucleotides. Each unique functionality was coupled to amine termini of a predetermined sub-library in ANNXX version (N=A/G/C/T, X=encoding A/G/C/T). Total hetero-functionalized library would be composed of 16 unique modifications (aliphatic, aromatic, acidic, basic and polar), which is comparable to 20 natural amino acid functionalities. Diverse functionalized modifications could be joined by T4 DNA ligase on a randomized template and submitted to Systematic Evolution of Ligands by Exponential enrichment (SELEX) to evolve aptamers. Efficiency and fidelity of LOOPER methodology were well-studied by gel electrophoresis and statistics analysis on Illumina sequencing results. After confirming the robustness of LOOPER, we further applied it into in vitro evolution against human alpha thrombin. After six rounds of SELEX, sequencing results revealed a densely functionalized aptamer, TBL1 with Kd of 1.6 nM. Binding affinities were triple checked through three different bioassays (SPR, MST and BLI) with dissociation constants of same magnitude. Our novel aptamer is not a G-quadruplex sequence but quite rich in carboxylic acid and aromatic modifications, which shared similarities with hirugen, a peptide inhibitor for thrombin. Post-SELEX analysis is done to get a better understanding of TBL1 stability, structure-function relationships and evolutionary changes

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