A DNA aptamer with high affinity and specificity for therapeutic anthracyclines

Wochner, Aniela; Menger, Marcus; Orgel, Dagmar; Cech, Birgit; Rimmele, Martina; Erdmann, Volker A.; Glökler, Jörn

doi:10.1016/j.ab.2007.09.007

Cited by 101 publications

(70 citation statements)

References 45 publications

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“…The control results agree with surface plasmon resonance findings in which nonspecific binding of daunomycin to control sequence DNA aptamers was not observed. 38 It should also be noted that the increase in SHG signal is not due to incoherent hyper-Rayleigh scattering of daunomycin nor daunomycin aggregates in the bulk solution. This is shown in Figure 2 where the SHG signal did not change, within experimental error, as the daunomycin concentration increased in the absence of DNA coated microparticles.…”

Section: ■ Results and Discussionmentioning

confidence: 96%

Binding of the Anti-Cancer Drug Daunomycin to DNA Probed by Second Harmonic Generation

et al. 2013

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Second harmonic generation (SHG) was used to selectively probe DNA−drug interactions without the need for chemical labels or invasive detection methods. In particular, the binding constant of the anticancer drug daunomycin to a recognition triplet sequence in a 33-mer of double stranded DNA was determined. The SHG method, which is interface selective, probed the binding of daunomycin to DNA that was tethered to the surface of colloidal microparticles suspended in aqueous solution. Probing biomolecule coated colloids is expected to yield larger SH signals and provides experimental flexibility as compared to experiments performed at planar interfaces. The change in SHG intensity as daunomycin was added to the microparticle solution was fit to a Langmuir binding model, which yielded an equilibrium constant of 2.3 (±0.7) × 10 5 M −1 ; the corresponding Gibbs free energy change at 20°C is −7.2 ± 0.2 kcal/mol. Control experiments established that daunomycin preferentially binds to DNA at the recognition sequence. The equilibrium was found to be unaffected by the presence of free DNA in solution, and hyper-Rayleigh scattering from bulk molecules did not change with increasing daunomycin concentration. The extracted equilibrium constants are in agreement with the range of reported values found in the literature. ■ INTRODUCTIONThis work presents a sensitive method for determining equilibrium binding constants for biomolecular interactions in a label free and noninvasive way. The experiments used second harmonic generation (SHG) to probe the binding of a drug to DNA tethered to the surface of colloidal microparticles suspended in aqueous solution. Biomolecule coatings on nano-and microparticle surfaces have opened up a broad field of self-assembling superstructured materials; 1−7 some biomolecule coated particles have found applications in drug delivery systems and in vivo detection schemes. 8,9 The present work also builds on interface specific nonlinear optical experiments that have measured the electronic and vibrational spectra of DNA covalently bound to planar fused quartz surfaces immersed in aqueous media, 10−13 and recent work that tracked in real time the cleavage of DNA by the restriction enzyme EcoR1 and the subsequent rehybridization of DNA attached to colloidal polymer microparticles without labeled reporter molecules or invasive detection methods. 14 Using SHG to study biomolecular reactions, with one of the reactants attached to a colloidal interface, can yield larger signals than analogous experiments performed at planar interfaces due to the larger number of molecules that can be accommodated in the laser focus. Additionally, the number of particles in solution can be changed without changing the density of the DNA that is attached to the individual particles, allowing for flexibility in experimental design.The class of anthracycline chemotherapeutic drugs has long been studied due to their potent anticancer properties. 15−20 Daunomycin (structure given in Figure 1a) is a member of this class ...

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Section: ■ Results and Discussionmentioning

confidence: 96%

Binding of the Anti-Cancer Drug Daunomycin to DNA Probed by Second Harmonic Generation

et al. 2013

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“…To demonstrate this ability, we first emplaced E-AB sensors for the detection of the cancer chemotherapeutic doxorubicin (DOX) (29,30) in the external jugular vein of anesthetized Sprague-Dawley rats (Fig. 1C).…”

Section: Resultsmentioning

confidence: 99%

Real-time measurement of small molecules directly in awake, ambulatory animals

Arroyo‐Currás

Somerson

Vieira

et al. 2017

Proc. Natl. Acad. Sci. U.S.A.

337

521

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The development of a technology capable of tracking the levels of drugs, metabolites, and biomarkers in the body continuously and in real time would advance our understanding of health and our ability to detect and treat disease. It would, for example, enable therapies guided by high-resolution, patient-specific pharmacokinetics (including feedback-controlled drug delivery), opening new dimensions in personalized medicine. In response, we demonstrate here the ability of electrochemical aptamer-based (E-AB) sensors to support continuous, real-time, multihour measurements when emplaced directly in the circulatory systems of living animals. Specifically, we have used E-AB sensors to perform the multihour, real-time measurement of four drugs in the bloodstream of even awake, ambulatory rats, achieving precise molecular measurements at clinically relevant detection limits and high (3 s) temporal resolution, attributes suggesting that the approach could provide an important window into the study of physiology and pharmacokinetics.aptamer | square-wave voltammetry | in vivo | E-DNA | precision medicine

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“…Encouraged by these successful test case design efforts, we next adapted our simple strategy to engineering cooperativity into two structurally more complex receptors. For the first, we employed a sequence based on the doxorubicin-binding aptamer of Wochner et al (36), which binds this important cancer chemotherapeutic with a dissociation constant of ∼200 nM. Of note, the 3D structure of this aptamer is not known, rendering this a significantly more challenging test of our design approach.…”

Section: Resultsmentioning

confidence: 99%

Intrinsic disorder as a generalizable strategy for the rational design of highly responsive, allosterically cooperative receptors

Simon

Vallée‐Bélisle

Ricci

et al. 2014

Proc. Natl. Acad. Sci. U.S.A.

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Control over the sensitivity with which biomolecular receptors respond to small changes in the concentration of their target ligand is critical for the proper function of many cellular processes. Such control could likewise be of utility in artificial biotechnologies, such as biosensors, genetic logic gates, and "smart" materials, in which highly responsive behavior is of value. In nature, the control of molecular responsiveness is often achieved using "Hilltype" cooperativity, a mechanism in which sequential binding events on a multivalent receptor are coupled such that the first enhances the affinity of the next, producing a steep, higher-order dependence on target concentration. Here, we use an intrinsicdisorder-based mechanism that can be implemented without requiring detailed structural knowledge to rationally introduce this potentially useful property into several normally noncooperative biomolecules. To do so, we fabricate a tandem repeat of the receptor that is destabilized (unfolded) via the introduction of a long, unstructured loop. The first binding event requires the energetically unfavorable closing of this loop, reducing its affinity relative to that of the second binding event, which, in contrast occurs at a preformed site. Using this approach, we have rationally introduced cooperativity into three unrelated DNA aptamers, achieving in the best of these a Hill coefficient experimentally indistinguishable from the theoretically expected maximum. The extent of cooperativity and thus the steepness of the binding transition are, moreover, well modeled as simple functions of the energetic cost of binding-induced folding, speaking to the quantitative nature of this design strategy. ultrasensitivity | intrinsically disordered proteins | biosensors | synthetic biology | ribozymes

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A DNA aptamer with high affinity and specificity for therapeutic anthracyclines

Cited by 101 publications

References 45 publications

Binding of the Anti-Cancer Drug Daunomycin to DNA Probed by Second Harmonic Generation

Binding of the Anti-Cancer Drug Daunomycin to DNA Probed by Second Harmonic Generation

Real-time measurement of small molecules directly in awake, ambulatory animals

Intrinsic disorder as a generalizable strategy for the rational design of highly responsive, allosterically cooperative receptors

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