期刊
ACS COMBINATORIAL SCIENCE
卷 19, 期 10, 页码 609-617出版社
AMER CHEMICAL SOC
DOI: 10.1021/acscombsci.6b00163
关键词
aptamers; PDGF-BB; ELISA; free energy calculation; fibroblast proliferation
资金
- Central Scientific Instrument Center (CSIC), Faculty of Science and Technology, Thammasat University
- Asean Economics Community (AEC) scholarship from Thammasat University
- Research Grant for New Researcher from Thailand Research Fund
- Thammasat University [TRG5880201]
- Thammasat University
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.
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