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    DNA Aptamers are functional molecular recognition sensors in protic Ionic liquids
    (Wiley-V C H Verlag Gmbh, 2014) Machado, Isabel; Özalp, Veli Cengiz; Rezabal, Elixabete; Schaefer, Thomas
    The function and structural changes of an AMP molecular aptamer beacon and its molecular recognition capacity for its target, adenosine monophosphate (AMP), was systematically explored in solution with a protic ionic liquid, ethylammonium nitrate (EAN). It could be proven that up to 2 M of EAN in TBS buffer, the AMP molecular aptamer beacon was still capable of recognizing AMP while also maintaining its specificity. The specificity was proven by using the guanosine monophosphate (GMP) as target; GMP is structurally similar to AMP but was not recognized by the aptamer. We also found that in highly concentrated EAN solutions the overall amount of double stranded DNA formed, as well as its respective thermal stability, diminished gradually, but surprisingly the hybridization rate (k(h)) of single stranded DNA was significantly accelerated in the presence of EAN. The latter may have important implications in DNA technology for the design of biosensing and DNA-based nanodevices in nonconventional solvents, such as ionic liquids.
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    DNA-aptamer gating membranes
    (Royal Soc Chemistry, 2015) Schaefer, Thomas; Özalp, Veli Cengiz
    This report describes a membrane barrier whose permeability is modulated through the recognition of a small-molecule target, adenosine triphosphate (ATP), by a DNA-aptamer. The gating function of the DNA-aptamer in the stimulus-responsive membrane was shown to be specific, concentration dependent, and reversible.
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    In situ monitoring of DNA-aptavalve gating function on mesoporous silica nanoparticles
    (Wiley-V C H Verlag Gmbh, 2014) Özalp, Veli Cengiz; Pinto, Alessandro; Nikulina, Elizaveta; Chuvilin, Andrey; Schaefer, Thomas
    Mesoporous silica nanoparticles have proved to be efficient stimuli-responsive controlled release systems for drug delivery when functionalized with nanovalves. Nucleic acid aptamers have recently been adapted to function as novel nanovalves, so-called aptavalves, with molecular-recognition capabilities and target concentration-dependent actuation in nanopore-controlled drug delivery and membrane separation systems. The working mechanism of aptavales relies on their structural rearrangement triggered by a specific target molecule. As a consequence, a controlled and concentration-dependent release of payload occurs rendering this system particularly appealing for therapeutic applications. However, straightforward monitoring techniques are necessary in order to elucidate the function of aptavalves in situ and varying experimental conditions. Here, the structure-switching mechanical movements of an ATP-responsive aptavalve on the surface of mesoporous silica are characterized in real-time and in situ using circular dichroism (CD). The experimental data obtained on the aptavalve actuation are in excellent agreement with the payload release kinetics determined by fluorescence measurements. It is shown that CD serves as a reliable real-time analysis of the function of aptalvalves, and that the results obtained obey furthermore standard controlled release models. This allows in principle to pre-determine the release rate of the modified silica particles according to particular application requirements.