Truncation can enhance the affinity of aptamers for their targets by limiting nonessential segments and therefore limiting the molecular degrees of freedom that must be overcome in the binding process. This study demonstrated a truncation protocol relying on competitive antibody binding and the hybridization of complementary oligonucleotides, using platelet derived growth factor BB (PDGF-BB) as the model target. On the basis of the immunoassay results, an initial long aptamer was truncated to a number of sequences with lengths of 36–40 nucleotides (nt). These sequences showed apparent K_D values in the picomolar range, with the best case being a 36-nt truncated aptamer with a 150-fold increase in affinity over the full-length aptamer. The observed binding energies correlated well with relative energies calculated by molecular dynamics simulations. The effect of the truncated aptamer on PDGF-BB-stimulated fibroblasts was found to be equivalent to that of the full-length aptamer.

中文翻译：

---

寡核苷酸杂交结合竞争性抗体结合的高亲和力的截断的截断。

截短可通过限制非必需区段并因此限制在结合过程中必须克服的分子自由度来增强适体对其靶标的亲和力。这项研究证明了以血小板衍生的生长因子BB（PDGF-BB）为模型目标的截短方案依赖于竞争性抗体结合和互补寡核苷酸的杂交。根据免疫测定结果，将最初的长适体截短为许多长度为36–40个核苷酸（nt）的序列。这些序列显示出明显的K _D值在皮摩尔范围内，最好的情况是36 nt的截短适体，亲和力比全长适体增加150倍。观察到的结合能与通过分子动力学模拟计算出的相对能很好地相关。发现截短的适体对PDGF-BB刺激的成纤维细胞的作用与全长适体的作用相同。