Division of Chemistry, Faculty of Science and Technology, Thammasat University , Pathumthani 12120, Thailand.
Division of Biochemistry, Department of Preclinical Science, Faculty of Medicine, Thammasat University , Pathumthani 12120, Thailand.
ACS Comb Sci. 2017 Oct 9;19(10):609-617. doi: 10.1021/acscombsci.6b00163. Epub 2017 Sep 5.
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 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.
截短可以通过限制非必需的片段来增强适体与靶标的亲和力，从而限制在结合过程中必须克服的分子自由度。本研究采用依赖竞争性抗体结合和互补寡核苷酸杂交的截短方案，以血小板衍生生长因子 BB（PDGF-BB）为模型靶标。基于免疫测定结果，将最初的长适体截短为多个长度为 36-40 个核苷酸（nt）的序列。这些序列在皮摩尔范围内显示出明显的 K 值，最佳情况是 36-nt 截短适体与全长适体的亲和力增加了 150 倍。观察到的结合能与分子动力学模拟计算的相对能很好地相关。发现截短适体对 PDGF-BB 刺激的成纤维细胞的作用与全长适体相当。
