12 research outputs found
Pinpointed Stimulation of EphA2 Receptors via DNA-Templated Oligovalence
DNA nanostructures enable the attachment of functional molecules to nearly any
unique location on their underlying structure. Due to their single-base-pair structural resolution,
several ligands can be spatially arranged and closely controlled according to the geometry of their
desired target, resulting in optimized binding and/or signaling interactions. Here, the efficacy of SWL,
an ephrin-mimicking peptide that binds specifically to EphrinA2 (EphA2) receptors, increased by
presenting up to three of these peptides on small DNA nanostructures in an oligovalent manner.
Ephrin signaling pathways play crucial roles in tumor development and progression. Moreover,
Eph receptors are potential targets in cancer diagnosis and treatment. Here, the quantitative impact
of SWL valency on binding, phosphorylation (key player for activation) and phenotype regulation in
EphA2-expressing prostate cancer cells was demonstrated. EphA2 phosphorylation was significantly
increased by DNA trimers carrying three SWL peptides compared to monovalent SWL. In comparison
to one of EphA2âs natural ligands ephrin-A1, which is known to bind promiscuously to multiple
receptors, pinpointed targeting of EphA2 by oligovalent DNA-SWL constructs showed enhanced
cell retraction. Overall, we show that DNA scaffolds can increase the potency of weak signaling
peptides through oligovalent presentation and serve as potential tools for examination of complex
signaling pathways
Pinpointed stimulation of EphA2 receptors via DNA-templated oligovalence
DNA nanostructures enable the attachment of functional molecules to nearly any unique location on their underlying structure. Due to their single-base-pair structural resolution, several ligands can be spatially arranged and closely controlled according to the geometry of their desired target, resulting in optimized binding and/or signaling interactions. Here, the efficacy of SWL, an ephrin-mimicking peptide that binds specifically to EphrinA2 (EphA2) receptors, increased by presenting up to three of these peptides on small DNA nanostructures in an oligovalent manner. Ephrin signaling pathways play crucial roles in tumor development and progression. Moreover, Eph receptors are potential targets in cancer diagnosis and treatment. Here, the quantitative impact of SWL valency on binding, phosphorylation (key player for activation) and phenotype regulation in EphA2-expressing prostate cancer cells was demonstrated. EphA2 phosphorylation was significantly increased by DNA trimers carrying three SWL peptides compared to monovalent SWL. In comparison to one of EphA2's natural ligands ephrin-A1, which is known to bind promiscuously to multiple receptors, pinpointed targeting of EphA2 by oligovalent DNA-SWL constructs showed enhanced cell retraction. Overall, we show that DNA scaffolds can increase the potency of weak signaling peptides through oligovalent presentation and serve as potential tools for examination of complex signaling pathways
Pinpointed Stimulation of EphA2 Receptors via DNA-Templated Oligovalence
DNA nanostructures enable the attachment of functional molecules to nearly any
unique location on their underlying structure. Due to their single-base-pair structural resolution,
several ligands can be spatially arranged and closely controlled according to the geometry of their
desired target, resulting in optimized binding and/or signaling interactions. Here, the efficacy of SWL,
an ephrin-mimicking peptide that binds specifically to EphrinA2 (EphA2) receptors, increased by
presenting up to three of these peptides on small DNA nanostructures in an oligovalent manner.
Ephrin signaling pathways play crucial roles in tumor development and progression. Moreover,
Eph receptors are potential targets in cancer diagnosis and treatment. Here, the quantitative impact
of SWL valency on binding, phosphorylation (key player for activation) and phenotype regulation in
EphA2-expressing prostate cancer cells was demonstrated. EphA2 phosphorylation was significantly
increased by DNA trimers carrying three SWL peptides compared to monovalent SWL. In comparison
to one of EphA2âs natural ligands ephrin-A1, which is known to bind promiscuously to multiple
receptors, pinpointed targeting of EphA2 by oligovalent DNA-SWL constructs showed enhanced
cell retraction. Overall, we show that DNA scaffolds can increase the potency of weak signaling
peptides through oligovalent presentation and serve as potential tools for examination of complex
signaling pathways
Measuring Influenza A Virus and Peptide Interaction Using Electrically Controllable DNA Nanolevers
Electrically controllable deoxyribonuclic acid (DNA) nanolevers are used to investigate the binding interaction between Influenza A/Aichi/2/1968 and the peptide called âPeBâ, which specifically binds the viral surface protein hemagglutinin. PeB is immobilized on gold electrodes of a âswitchSENSEâ biochip by conjugation to DNA-strands that are hybridized to complementary anchors. The surface-tethered DNA strand carries a fluorophore while the complementary strand is a multivalent arrangement carrying up to three PeB peptides. The nanolevers are kept upright (static) by applying a negative potential. Signal read-out for this static measurement mode is the change in fluorescence intensity due to changes in the local environment of the dye upon binding. Measurements of virus-peptide interaction show that the virus material specifically binds to the immobilized peptides and remains bound throughout the measurement time. Immobilized viruses are subsequently used as ligands to characterize oligovalent peptide binding to hemagglutinin, revealing rate constants of the interaction. Moreover, three Influenza A subtypes are compared in their binding behavior. Overall, this paper shows the ability to immobilize virus material on a sensor surface, which allows to target virus-proteins in their native environment. The âswitchSENSEâ method is therefore applicable to characterize virus-receptor interactions
Pinpointed Stimulation of EphA2 Receptors via DNA-Templated Oligovalence
DNA nanostructures enable the attachment of functional molecules to nearly any
unique location on their underlying structure. Due to their single-base-pair structural resolution,
several ligands can be spatially arranged and closely controlled according to the geometry of their
desired target, resulting in optimized binding and/or signaling interactions. Here, the efficacy of SWL,
an ephrin-mimicking peptide that binds specifically to EphrinA2 (EphA2) receptors, increased by
presenting up to three of these peptides on small DNA nanostructures in an oligovalent manner.
Ephrin signaling pathways play crucial roles in tumor development and progression. Moreover,
Eph receptors are potential targets in cancer diagnosis and treatment. Here, the quantitative impact
of SWL valency on binding, phosphorylation (key player for activation) and phenotype regulation in
EphA2-expressing prostate cancer cells was demonstrated. EphA2 phosphorylation was significantly
increased by DNA trimers carrying three SWL peptides compared to monovalent SWL. In comparison
to one of EphA2âs natural ligands ephrin-A1, which is known to bind promiscuously to multiple
receptors, pinpointed targeting of EphA2 by oligovalent DNA-SWL constructs showed enhanced
cell retraction. Overall, we show that DNA scaffolds can increase the potency of weak signaling
peptides through oligovalent presentation and serve as potential tools for examination of complex
signaling pathways
Prefusion-specific antibody- derived peptides trivalently presented on DNA- nanoscaffolds as an innovative strategy against RSV entr
Human respiratory syncytial virus (RSV) is the primary cause of acute lower
respiratory tract infections in children and the elderly worldwide, for which
neither a vaccine nor an effective therapy is approved. The entry of RSV into the
host cell is mediated by stepwise structural changes in the surface RSV fusion
(RSV-F) glycoprotein. Recent progress in structural and functional studies of
RSV-F glycoprotein revealed conformation-dependent neutralizing epitopes
which have become attractive targets for vaccine and therapeutic
development. As RSV-F is present on viral surface in a trimeric form, a
trivalent binding interaction between a candidate fusion inhibitor and the
respective epitopes on each of the three monomers is expected to prevent
viral infection at higher potency than a monovalent or bivalent inhibitor. Here
we demonstrate a novel RSV entry inhibitory approach by implementing a
trimeric DNA nanostructure as a template to display up to three linear peptide
moieties that simultaneously target an epitope on the surface of the prefusion
RSV-F protein. In order to design synthetic binding peptides that can be
coupled to the DNA nanostructure, the prefusion RSV-F-specific monoclonal
antibody (D25) was selected. Complementarity-determining region 3 (CDR3)
derived peptides underwent truncation and alanine-scanning mutagenesis
analysis, followed by systematic sequence modifications using non-canonical
amino acids. The most effective peptide candidate was used as a binding
moiety to functionalize the DNA nanostructure. The designed DNA-peptide
construct was able to block RSV infection on cells more efficiently than the
monomeric peptides, however a more moderate reduction of viral load was
observed in the lungs of infected mice upon intranasal application, likely due to
dissociation or absorption of the underlying DNA structure by cells in the lungs.Taken together, our results point towards the inhibitory potential of a novel
trimeric DNA-peptide based approach against RSV and open the possibility to
apply this platform to target other viral infections
Effect of staple age on DNA origami nanostructure assembly and stability
DNA origami nanostructures are widely employed in various areas of fundamental and applied research. Due to the tremendous success of the DNA origami technique in the academic field, considerable efforts currently aim at the translation of this technology from a laboratory setting to real-world applications, such as nanoelectronics, drug delivery, and biosensing. While many of these real-world applications rely on an intact DNA origami shape, they often also subject the DNA origami nanostructures to rather harsh and potentially damaging environmental and processing conditions. Furthermore, in the context of DNA origami mass production, the long-term storage of DNA origami nanostructures or their pre-assembled components also becomes an issue of high relevance, especially regarding the possible negative effects on DNA origami structural integrity. Thus, we investigated the effect of staple age on the self-assembly and stability of DNA origami nanostructures using atomic force microscopy. Different harsh processing conditions were simulated by applying different sample preparation protocols. Our results show that staple solutions may be stored at â20 âŠC for several years without impeding DNA origami self-assembly. Depending on DNA origami shape and superstructure, however, staple age may have negative effects on DNA origami stability under harsh treatment conditions. Mass spectrometry analysis of the aged staple mixtures revealed no signs of staple fragmentation. We, therefore, attribute the increased DNA origami sensitivity toward environmental conditions to an accumulation of damaged nucleobases, which undergo weaker base-pairing interactions and thus lead to reduced duplex stability
An Empirical Analysis of Traceability in the Monero Blockchain
Monero is a privacy-centric cryptocurrency that allows users to obscure their transactions by including chaff coins, called âmixins,â along with the actual coins they spend. In this paper, we empirically evaluate two weaknesses in Moneroâs mixin sampling strategy. First, about 62% of transaction inputs with one or more mixins are vulnerable to âchain-reactionâ analysis - that is, the real input can be deduced by elimination. Second, Monero mixins are sampled in such a way that they can be easily distinguished from the real coins by their age distribution; in short, the real input is usually the ânewestâ input. We estimate that this heuristic can be used to guess the real input with 80% accuracy over all transactions with 1 or more mixins. Next, we turn to the Monero ecosystem and study the importance of mining pools and the former anonymous marketplace AlphaBay on the transaction volume. We find that after removing mining pool activity, there remains a large amount of potentially privacy-sensitive transactions that are affected by these weaknesses. We propose and evaluate two countermeasures that can improve the privacy of future transactions