Characterization of structural changes in aptamer films for controlled release nanodevices

Abstract

The dimension of the conformational changes of DNA-aptamers which can be used as stimulus-responsive gate-keepers in controlled delivery nanodevices has been determined by acoustic wave-based sensors upon molecular recognition of a small-sized target, adenosine-5'-monophosphate (AMP).

Antibiotic loaded nanocapsules functionalized with aptamer gates for targeted destruction of pathogens

“…The mechanism of gatekeeper function of aptamer hairpins were previously explained. 25,26 Fig. 1 The general scheme of aptamer-gated specific antibiotic delivery approach.…”

DNA Aptamers are Functional Molecular Recognition Sensors in Protic Ionic Liquids

“…Notably, it is known that the phosphate group of AMP is practically irrelevant for the recognition through an AMP aptamer as it is directed away from the DNA-binding pocket, [40] such that binding constants between the AMP aptamer and adenosine, AMP, ADP and ATP, respectively, have been found to be quite similar. [23] Indeed, the recognition of adenosine in the presence of 2 m of EAN using the same DNA aptamer beacon as in Figure 1 yielded a similar binding constant, K d , as AMP (285 mm for TBS and 634 mm for EAN; Figure S7 in the Supporting Information), dismissing in this way the hypothesis of a significant interaction of the ionic liquid with the target itself. Still the question remained as to how far interactions particularly occurring around the DNA aptamer binding pocket could be the responsible for modulating the molecular recognition capacity of DNA aptamer beacons in presence of ILs.…”

“…To verify this hypothesis, we determined the K d of the DNA aptamer beacon for the uncharged adenosine differing from AMP in the absence of the phosphate group, only. Notably, it is known that the phosphate group of AMP is practically irrelevant for the recognition through an AMP aptamer as it is directed away from the DNA‐binding pocket,40 such that binding constants between the AMP aptamer and adenosine, AMP, ADP and ATP, respectively, have been found to be quite similar 23. Indeed, the recognition of adenosine in the presence of 2 M of EAN using the same DNA aptamer beacon as in Figure 1 yielded a similar binding constant, K d , as AMP (285 μ M for TBS and 634 μ M for EAN; Figure S7 in the Supporting Information), dismissing in this way the hypothesis of a significant interaction of the ionic liquid with the target itself.…”

“…In fact, structural stability is to some extent unwanted for MBs as their function relies precisely on a reversibility of their structure depending on the presence of a target. This highly interesting feature has prompted DNA‐molecular beacons (DNA‐MBs) to be studied as “nanogates” in mesoporous devices 21–23. Since MB probes were developed,24 they have found applications in in vitro RNA and DNA monitoring, biosensors and biochips, nucleic‐acid amplification, enzymatic studies, as well as gene typing and mutation detection,25–29 mainly because their molecular interaction with targets can conveniently be measured by spectrofluorimetry.…”

Sensing Techniques Involving Thin Films for Studying Biomolecular Interactions and Membrane Fouling Phenomena

“…Layer-by-layer DNA fi lms [11], DNA hybridization [12], Holliday junctions [13], and aptamer-protein interactions [14] have been reported where the dissipation served as a major parameter for this fi lm characterization. Using a small molecule binding aptamer as a model system, Serrano Santos et al not only determined the interaction of adenosine-5´-monophosphate (AMP) with AMP-binding aptamer fi lms using QCM-D, but also succeeded in quantifying in situ and in real-time the structural changes that occur in this particular DNA aptamer when binding to AMP [15]. Th eir objective was to elucidate in how far aptamers or aptamer hairpins diff er in their conformational changes upon target binding, and in how far this feature could be used for stimuli-responsive nanoporous gating devices to be used in, for example, drug delivery.…”