Synthesis, characterization and in vitro activity of thrombin-binding DNA aptamers with triazole internucleotide linkages

Comparison of the ‘Chemical’ and ‘Structural’ Approaches to the Optimization of the Thrombin-Binding Aptamer

“…For K D determination see Figure S2. The obtained K D TBA value is higher than that determined previously by solution methods [12], [22], presumably due to the partial shielding of the aptamer binding sites upon aptamer immobilization on the biosensor surface).…”

“…A significant number of chemically modified TBA analogs have been reported in the last decade [10], [11], [12], [13], [14], [15]. The relative benefits of those modifications are difficult to determine based on published data because very few modified aptamers have been comprehensively investigated.…”

“…It has been shown that GQ formation is crucial for TBA binding with thrombin [10], [11], so modifications that decrease GQ thermostability (i.e. almost any substantial modification in the quadruplex core [11], [12], [13]) are undesirable. Loop modifications tend to have insignificant effects on quadruplex thermostability, but often impart increased nuclease resistance to the aptamer [11], [12], [13].…”

“…almost any substantial modification in the quadruplex core [11], [12], [13]) are undesirable. Loop modifications tend to have insignificant effects on quadruplex thermostability, but often impart increased nuclease resistance to the aptamer [11], [12], [13]. Unmodified loops are quickly degraded in blood, like all single stranded ON fragments.…”

“…Internucleotide modifications, including the thiophosphoryl modification and the triazole modification, are well known to protect oligonucleotides (ONs) from nuclease hydrolysis [11], [12], [16], [17]. The introduction of anomeric nucleoside moieties (alpha-nucleosides) has also been shown to impart increased enzymatic stability to ONs [18].…”