Aptamer selections often yield distinct subpopulations, each with unique phenotypes that can be leveraged for specialized applications. Although most selections aim to attain ever higher specificity, we sought to identify aptamers that recognize increasingly divergent primate lentiviral reverse transcriptases (RTs). We hypothesized that aptamer subpopulations in libraries pre-enriched against a single RT may exhibit broad-spectrum binding and inhibition, and we devised a multiplexed poly-target selection to elicit those phenotypes against a panel of primate lentiviral RTs. High-throughput sequencing and coenrichment/codepletion analysis of parallel and duplicate selection trajectories rapidly narrowed the list of candidate aptamers by orders of magnitude and identified dozens of priority candidates for further screening. Biochemical characterization validated a novel aptamer motif and several rare and unobserved variants of previously known motifs that inhibited recombinant RTs to varying degrees. These broad-spectrum aptamers also suppressed replication of viral constructs carrying phylogenetically diverse RTs. The poly-target selection and coenrichment/codepletion approach described herein is a generalizable strategy for identifying cross-reactivity among related targets from combinatorial libraries.

适体的选择通常产生不同的亚群，每个亚群具有独特的表型，可用于特殊应用。尽管大多数选择都旨在获得更高的特异性，但我们试图鉴定能够识别越来越多的灵长类慢病毒逆转录酶（RTs）的适体。我们假设针对单个RT预富集的文库中的适体亚群可能表现出广谱结合和抑制作用，并且我们设计了一个多重多靶点选择来针对一组灵长类慢病毒RT引发这些表型。平行和重复选择轨迹的高通量测序和共富集/密码分析快速缩小了候选适体的数量级，并确定了数十个优先候选者，以供进一步筛选。生化特性验证了新型适体基序和先前已知基序的几种罕见且未观察到的变体，这些变体在不同程度上抑制了重组RT。这些广谱适体还抑制了携带系统发育多样的逆转录酶的病毒构建体的复制。本文所述的多靶标选择和共富集/编码完成方法是用于从组合文库鉴定相关靶标之间的交叉反应性的通用策略。