Chirality enriched carbon nanotubes with tunable wrapping <i>via</i> corona phase exchange purification (CPEP)

Nißler, Robert; Mann, Florian A.; Preiß, Helen; Selvaggio, Gabriele; Herrmann, Niklas; Kruss, Sebastian

doi:10.1039/c9nr03258d

Cited by 32 publications

(45 citation statements)

References 71 publications

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“…However, rational design methodologies for corona phase engineering would benefit from a systematic body of knowledge about how individual polymer properties, such as polymer length, sequence, and chemistry, relate to structural and kinetic properties of the resulting corona phase. As polymer corona cannot be directly visualized with atomic resolution in experiments, important characteristics of the corona phase, such as structural arrangement of polymers, corona thickness, dynamics of assembled polymers on different timescales, kinetic stability of polymer corona, and interactions with other molecules present in the suspension, have to be inferred from experiments with limited resolution [25][26][27][28][29] .…”

Section: Introductionmentioning

confidence: 99%

“…An alternative and a powerful way to characterize the corona phase includes computational modeling approaches, such as classical molecular dynamics (MD) simulations, which enable atomic resolution on the timescale of hundreds of nanoseconds 1,2,[29][30][31][32] . Yet, as reorganization of long polymers on SWNT surfaces occurs on a timescale of several nanoseconds, determining most probable equilibrium distributions of polymers in the corona phase necessitates enhanced sampling approaches, such as temperature replica exchange (T-REMD) MD simulations 33 .…”

Section: Introductionmentioning

confidence: 99%

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Binding Affinity and Conformational Preferences Influence Kinetic Stability of Short Oligonucleotides on Carbon Nanotubes

Alizadehmojarad

Zhou

Beyene

et al. 2020

Adv Materials Inter

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DNA-wrapped single walled carbon nanotubes (SWNTs) have found a widespread use in a variety of nanotechnology applications. Yet, the relationship between structural conformation, binding affinity and kinetic stability of these polymers on SWNTs remains poorly understood. Here, we used molecular dynamics (MD) simulations and experiments to explore this relationship for short oligonucleotides adsorbed on SWNTs. First, using classical MD simulations of oligonucleotide-(9,4)-SWNT hybrid complexes, we explored the relationship between ssDNA and ssRNA surface conformation and sequence chemistry. We screened the conformation of 36 sequences of short ssDNA and ssRNA polymers on (9,4) SWNT, where the contour lengths were selected so the polymers can, to a first approximation, wrap once around the SWNT circumference. From these screens, we identified structural motifs that we broadly classified into "rings" and "non-rings." Then, several sequences were selected for detailed investigations. We used temperature replica exchange MD calculations to compute two-dimensional free energy landscapes characterizing the conformations of select sequences. "Ring" conformations seemed to be driven primarily by sequence chemistry. Specifically, strong (n,n+2) nucleotide interactions and the ability of the polymer to form compact structures, as for example, through sharp bends in the nucleotide backbone, correlated with ring-forming propensity. However, ring-formation probability was found to be uncorrelated with free energy of oligonucleotide binding to SWNTs (∆Gbind). Conformational analyses of oligonucleotides, computed free energy of binding of oligonucleotides to SWNTs, and experimentally determined kinetic stability measurements show that ∆Gbind is the primary correlate for kinetic stability. The probability of the sequence to adopt a compact, ring-like conformation is shown to play a secondary role that still contributes measurably to kinetic stability. For example, sequences that form stable compact rings (C-rich sequences) could compensate for their relatively lower ∆Gbind and exhibit kinetic stability, while sequences with strong ∆Gbind (such as (TG)3(GT)3) were found to be kinetically stable despite their low ring formation propensity. We conclude that the stability of adsorbed oligonucleotides is primarily driven by its free energy of binding and that if ring-like structural motifs form, they would contribute positively to stability.

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Section: Introductionmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

Binding Affinity and Conformational Preferences Influence Kinetic Stability of Short Oligonucleotides on Carbon Nanotubes

Alizadehmojarad

Zhou

Beyene

et al. 2020

Adv Materials Inter

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“…The nanosensor stock concentration was determined by measuring the absorption spectrum in PBS (Supplementary Fig. 17) with a UV–vis–NIR spectrometer (JASCO V-670, Spectra Manager Software) and integrating the area below the (6,5) peak using the molar extinction coefficient at 991 nm and an estimated length of 200 nm 59 . NIR-fluorescence spectra (Supplementary Fig.…”

Section: Methodsmentioning

confidence: 99%

A fluorescent nanosensor paint reveals the heterogeneity of dopamine release from neurons at individual release sites

Elizarova

Chouaib

Shaib

et al. 2021

Preprint

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The neurotransmitter dopamine is released from discrete axonal structures called varicosities. Its release is essential in behaviour and is critically implicated in prevalent neuropsychiatric diseases. Existing dopamine detection methods are not able to detect and distinguish discrete dopamine release events from multiple varicosities. This prevents an understanding of how dopamine release is regulated across populations of discrete varicosities. Using a near infrared fluorescent (980 nm) dopamine nanosensor 'paint' (AndromeDA), we show that action potential-evoked dopamine release is highly heterogeneous across release sites and also requires molecular priming. Using AndromeDA, we visualize dopamine release at up to 100 dopaminergic varicosities simultaneously within a single imaging field with high temporal resolution (15 images/s). We find that 'hotspots' of dopamine release are highly heterogeneous and are detected at only ~17% of all varicosities. In neurons lacking Munc13 proteins, which prime synaptic vesicles, dopamine release is abolished during electrical stimulation, demonstrating that dopamine release requires vesicle priming. In summary, AndromeDA reveals the spatiotemporal organization of dopamine release.

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“…8,51 We used (GT) 15 -(6,5)-SWCNTs because they change their fluorescence in the presence of the neurotransmitter dopamine and are therefore powerful sensors. [52][53][54][55] Such sensors have been used to image dopamine release from cells with high spatiotemporal resolution. 56 As a second functional nanomaterial, we employed hemin-aptamer-functionalized SWCNTs, 57,58 which are known to decrease their fluorescence in the presence of H 2 O 2 .…”

Section: Programmed Release Of Functional Nanosensorsmentioning

confidence: 99%

Transport and programmed release of nanoscale cargo from cells by using NETosis

et al. 2020

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Chirality enriched carbon nanotubes with tunable wrapping via corona phase exchange purification (CPEP)

Abstract: A novel process (CPEP) for chirality enriched single-walled carbon nanotubes with tunable functionalization.

Cited by 32 publications

References 71 publications

Binding Affinity and Conformational Preferences Influence Kinetic Stability of Short Oligonucleotides on Carbon Nanotubes

Binding Affinity and Conformational Preferences Influence Kinetic Stability of Short Oligonucleotides on Carbon Nanotubes

A fluorescent nanosensor paint reveals the heterogeneity of dopamine release from neurons at individual release sites

Transport and programmed release of nanoscale cargo from cells by using NETosis

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