Role of pH controlled DNA secondary structures in the reversible dispersion/precipitation and separation of metallic and semiconducting single-walled carbon nanotubes

Dispersion of arc-discharged single-walled carbon nanotubes using the natural α-amino acid derivative N-dodecanoyl leucinate

The natural α-amino acid derivate N-dodecanoyl leucinate was synthesized via Schotten–Baumann reaction and alkali treatment, and was applied to the dispersion of arc-discharged single-walled carbon nanotubes (SWNTs). Optical absorption and Raman scattering spectra as well as AFM observation confirmed the effective individualization and selective dispersion of SWNTs. Moreover, charge transfer from N-dodecanoyl leucinate to SWNTs was evidenced by FT-IR and Raman scattering spectroscopic analyses. We believe that the formation of a charge transfer complex between dispersants and SWNTs is responsible for the effective individualization of SWNTs, and that the charge transfer from dispersants to SWNTs (or from SWNTs to dispersants) is crucial for selective dispersion of semiconducting (or metallic) SWNTs.

The synthesized natural α-amino acid derivative N-dodecanoyl leucinate demonstrates an effective and selective dispersion towards arc-discharged SWNTs.

Carbon Nanotubes and Short Cytosine-Rich Telomeric DNA Oligomeres as Platforms for Controlled Release of Doxorubicin-A Molecular Dynamics Study

This work deals with molecular dynamics analysis of properties of systems composed of carbon nanotubes and short telomeric DNA strands able to fold into i-motif structures at slightly acidic pH conditions. The studies are focused on possible application of such constructs as pH-controlled drug delivery and release systems. We study two different approaches. The first assumes that folding/unfolding property of these DNA strands might realize a gate closing/opening mechanism with carbon nanotube as a container for drug molecules. The second approach assumes that these DNA strands can modulate the drug intercalating property as a function of pH. As a model drug molecule we used doxorubicin. We found that the first approach is impossible to realize because doxorubicin is not effectively locked in the nanotube interior by DNA oligonuceotides. The second approach is more promising though direct drug release was not observed in unbiased molecular dynamics simulations. However, by applying detailed analysis of pair interaction energies, mobilities and potential of mean force we can show that doxorubicin can be released when the DNA strands fold into i-motifs. Carbon nanotube in that latter case acts mainly as a carrier for active phase which is composed of DNA fragments able to fold into noncanonical tetraplexes (i-motif).

Molecular Dynamics Study of the Interaction of Carbon Nanotubes With Telomeric DNA Fragment Containing Noncanonical G-quadruplex and i-Motif Forms

This work deals with molecular dynamics simulations of systems composed of telomeric dsDNA fragments, iG, and functionalized carbon nanotubes, fCNT. The iG contains 90 nucleotides in total and in its middle part the noncanonical i-motif and G-quadruplex are formed. Two chiralities of the fCNT were used, i.e., (10,0) and (20,0) and these nanotubes were either on-tip functionalized by guanine containing functional groups or left without functionalization. We proposed a dedicated computational procedure, based on the replica exchange concept, for finding a thermodynamically optimal conformation of iG and fCNT without destroying the very fragile noncanonical parts of the iG. We found that iG forms a V-shape spatial structure with the noncanonical fragments located at the edge and the remaining dsDNA strands forming the arms of V letter. The optimal configuration of iG in reference to fCNT strongly depends on the on-tip functionalization of the fCNT. The carbon nanotube without functionalization moves freely between the dsDNA arms, while the presence of guanine residues leads to immobilization of the fCNT and preferential location of the nanotube tip near the junction between the dsDNA duplex and i-motif and G-quadruplex. We also studied how the presence of fCNT affects the stability of the i-motif at the neutral pH when the cytosine pairs are nonprotonated. We concluded that carbon nanotubes do not improve the stability of the spatial structure of i-motif also when it is a part of a bigger structure like the iG. Such an effect was described in literature in reference to carboxylated nanotubes. Our current results suggest that the stabilization of i-motif is most probably related to easy formation of semiprotonated cytosine pairs at neutral pH due to interaction with carboxylated carbon nanotubes.

Block Copolymers as Dispersants for Single-Walled Carbon Nanotubes: Modes of Surface Attachment and Role of Block Polydispersity

When using amphiphilic polymers to exfoliate and disperse carbon nanotubes in water, the balance between the hydrophobic and hydrophilic moieties is critical and nontrivial. Here, we investigate the mode of surface attachment of a triblock copolymer, Pluronics F127, composed of a central hydrophobic polypropylene oxide block flanked by hydrophilic polyethylene oxide blocks, onto single-walled carbon nanotubes (SWNTs). Crucially, we analyze the composition in dispersant of both the as-obtained dispersion (the supernatant) and the precipitate-containing undispersed materials. For this, we combine the carefully obtained data from ¹H NMR peak intensities and self-diffusion and thermogravimetric analysis. The molecular motions behind the observed NMR features are clarified. We find that the hydrophobic blocks attach to the dispersed SWNT surface and remain significantly immobilized leading to ¹H NMR signal loss. On the other hand, the hydrophilic blocks remain highly mobile and thus readily detectable by NMR. The dispersant is shown to possess significant block polydispersity that has a large effect on dispersibility. Polymers with large hydrophobic blocks adsorb on the surface of the carbonaceous particles that precipitate, indicating that although a larger hydrophobic block is good for enhancing adsorption, it may be less effective in dispersing the tubes. A model is also proposed that consistently explains our observations in SWNT dispersions and some contradicting findings obtained previously in carbon nanohorn dispersions. Overall, our findings help elucidating the molecular picture of the dispersion process for SWNTs and are of interest when looking for more effective (i.e., well-balanced) polymeric dispersants.

Liquid interfaces with pH-switchable nanoparticle arrays

Stimuli-responsive 2D nanoscale systems offer intriguing opportunities for creating switchable interfaces. At liquid interfaces, such systems can provide control over interfacial energies, surface structure, and rheological and transport characteristics, which is relevant, for example, to bio- and chemical reactors, microfluidic devices, and soft robotics. Here, we explore the formation of a pH-responsive membrane formed from gold nanoparticles grafted with DNA (DNA-NPs) at a liquid-vapor interface. A DNA-NP 2D hexagonal lattice can be reversibly switched by pH modulation between an expanded state of non-connected nanoparticles at neutral pH and a contracted state of linked nanoparticles at acidic pH due to the AH+-H+A base pairing between A-motifs. Our in situ surface X-ray scattering studies reveal that the reversible lattice contraction can be tuned by the length of pH-activated linkers, with up to ∼71% change in surface area.

Coumarin centered copper(ii) complex with appended-imidazole as cancer chemotherapeutic agents against lung cancer: molecular insight via DFT-based vibrational analysis

Synthesis and structural characterization of the novel copper complex, DFT based vibrational analysis, DNA binding studies. In vitro cytotoxicity against A549 cancer cell lines and estimation of GSH, ROS, LPO levels, have been reported.

Thermo-reversible capture and release of DNA by zwitterionic surfactants

The thermo-reversible capture and release of DNA were studied by the protonation and deprotonation of alkyldimethylamine oxide (CnDMAO, n = 10, 12 and 14) in Tris-HCl buffer solution. DNA/C14DMAO in Tris-HCl buffer solution with pH = 7.2 is transparent at 25 °C, indicating that DNA molecules exist mainly in individuals and the binding of C14DMAO is weak. With the increase of temperature, the pH of the buffer solution continuously decreases, which leads to protonation of C14DMAO (C14DMAO + H(+)→ C14DMAOH(+)) and an obvious increase of the turbidity of the samples. This indicates a stronger binding of the protonated C14DMAOH(+) to DNA. Further investigations demonstrated the formation of DNA/C14DMAOH(+) complexes, in which the stretched DNA molecules are effectively compacted as evidenced from UV-vis absorptions, circular dichroism (CD) measurements, atomic force microscopy (AFM) observations, dynamic light scattering (DLS) measurements and agarose gel electrophoresis (AGE). Interestingly, when the temperature is turned back to 25 °C, the compacted DNA molecules can fully recover to the stretched conformation. This cycle can be repeated several times without obvious loss of efficiency. The effect of the chain length of CnDMAO has also been investigated. When C14DMAO was replaced by C12DMAO, similar phenomena can be observed with a slightly higher critical surfactant concentration for DNA compaction and a slightly lower pH of Tris-HCl buffer solution with pH = 6.8. For the DNA/C10DMAO system, however, no DNA compaction was observed even in Tris-HCl buffer solution with a much lower pH and a much higher C10DMAO concentration. The negative charges of DNA molecules can easily be neutralized by positive charges of cationic CnDMAOH(+) (n = 12 and 14) micelles. DNA was compacted and then insoluble DNA/CnDMAOH(+) complexes were formed. Because of the much higher critical micelle concentration (cmc) of the shorter chain length C10DMAOH(+), cationic C10DMAOH(+) micelles cannot form under the studied condition to compact DNA. The strategy may provide an efficient and alternative approach for stimuli-responsive gene therapy and drug release.

New dimeric carbazole-benzimidazole mixed ligands for the stabilization of human telomeric G-quadruplex DNA and as telomerase inhibitors. A remarkable influence of the spacer

The development of G-quadruplex (G4) DNA binding small molecules has become an important strategy for selectively targeting cancer cells. Herein, we report the design and evolution of a new kind of carbazole-based benzimidazole dimers for their efficient telomerase inhibition activity. Spectroscopic titrations reveal the ligands high affinity toward the G4 DNA with significantly higher selectivity over duplex-DNA. The electrophoretic mobility shift assay shows that the ligands efficiently promote the formation of G4 DNA even at a lower concentration of the stabilizing K(+) ions. The TRAP-LIG assay demonstrates the ligand's potential telomerase inhibition activity and also establishes that the activity proceeds via G4 DNA stabilization. An efficient nuclear internalization of the ligands in several common cancer cells (HeLa, HT1080, and A549) also enabled differentiation between normal HFF cells in co-cultures of cancer and normal ones. The ligands induce significant apoptotic response and antiproliferative activity toward cancer cells selectively when compared to the normal cells.

Use of a Ureido-Substituted Deoxycytidine Module for DNA Assemblies

Ureido-substituted cytosine derivatives are promising for constructing self-assembly structures that can be applied to nanotechnology research. However, conventional cytosine modules achieve assembly in organic solvents. In this study, an N-phenylcarbamoyl deoxycytidine nucleoside was incorporated into a C-rich oligonucleotide to achieve self-assembly in aqueous solution. The results show that the capability of the module to form DNA assemblies varied depending on the number of modules incorporated. The deoxycytidine derivative has a potential application in the development of smart materials based on DNA assembly.

Carbon-Nanotube-Mediated Electrochemical Transition in a Redox-Active Supramolecular Hydrogel Derived from Viologen and an l-Alanine-Based Amphiphile

A two-component hydrogelator (16-A)2 -V(2+) , comprising an l-alanine-based amphiphile (16-A) and a redox-active viologen based partner (V(2+) ), is reported. The formation the hydrogel depended, not only on the acid-to-amine stoichiometric ratio, but on the choice of the l-amino acid group and also on the hydrocarbon chain length of the amphiphilic component. The redox responsive property and the electrochemical behavior of this two-component system were further examined by step-wise chemical and electrochemical reduction of the viologen nucleus (V(2+) /V(+) and V(+) /V(0) ). The half-wave reduction potentials (E1/2 ) associated with the viologen ring shifted to more negative values with increasing amine component. This indicates that higher extent of salt formation hinders reduction of the viologen moiety. Interestingly, the incorporation of single-walled carbon nanotubes in the electrochemically irreversible hydrogel (16-A)2 -V(2+) transformed it into a quasi-reversible electrochemical system.

Regulation of telomeric i-motif stability by 5-methylcytosine and 5-hydroxymethylcytosine modification

The two important epigenetic markers in the human genome, 5-methylcytosine (mC) and 5-hydroxymethylcytosine (hmC), are involved in gene regulation processes. As a major epigenetic target, cytosines in a C-rich DNA sequence were substituted with mC and hmC to investigate the thermal stability and pH sensitivity of the corresponding i-motifs. Circular Dichroism (CD) studies indicate the formation of i-motifs at acidic pH (<6.5) for mC- and hmC-modified DNA sequences. Thermal denaturation results suggest that DNA i-motifs are stabilized when modified with one or two mCs. However, hypermethylation with mC and single modification with hmC cause destabilization of the structure. A biomimetic crowding agent does not alter the stability effect trends resulting from mC and hmC modifications, though the corresponding i-motifs show elevated melting temperatures without significant changes in pKa values.

Thermodynamics for the Formation of Double-Stranded DNA-Single-Walled Carbon Nanotube Hybrids

For the first time, the thermodynamics are described for the formation of double-stranded DNA (ds-DNA)-single-walled carbon nanotube (SWNT) hybrids. This treatment is applied to the exchange reaction of sodium cholate (SC) molecules on SWNTs and the ds-DNAs d(A)20 -d(T)20 and nuclear factor (NF)-κB decoy. UV/Vis/near-IR spectroscopy with temperature variations was used for analyzing the exchange reaction on the SWNTs with four different chiralities: (n,m)=(8,3), (6,5), (7,5), and (8,6). Single-stranded DNAs (ss-DNAs), including d(A)20 and d(T)20, are also used for comparison. The d(A)20-d(T)20 shows a drastic change in its thermodynamic parameters around the melting temperature (Tm ) of the DNA oligomer. No such Tm dependency was measured, owing to high Tm in the NF-κB decoy DNA and no Tm in the ss-DNA.

Non-covalent and reversible functionalization of carbon nanotubes

Carbon nanotubes (CNTs) have been proposed and actively explored as multipurpose innovative nanoscaffolds for applications in fields such as material science, drug delivery and diagnostic applications. Their versatile physicochemical features are nonetheless limited by their scarce solubilization in both aqueous and organic solvents. In order to overcome this drawback CNTs can be easily non-covalently functionalized with different dispersants. In the present review we focus on the peculiar hydrophobic character of pristine CNTs that prevent them to easily disperse in organic solvents. We report some interesting examples of CNTs dispersants with the aim to highlight the essential features a molecule should possess in order to act as a good carbon nanotube dispersant both in water and in organic solvents. The review pinpoints also a few examples of dispersant design. The last section is devoted to the exploitation of the major quality of non-covalent functionalization that is its reversibility and the possibility to obtain stimuli-responsive precipitation or dispersion of CNTs.

Conjugated polymer-assisted dispersion of single-wall carbon nanotubes: the power of polymer wrapping

The future application of single-walled carbon nanotubes (SWNTs) in electronic (nano)devices is closely coupled to the availability of pure, semiconducting SWNTs and preferably, their defined positioning on suited substrates. Commercial carbon nanotube raw mixtures contain metallic as well as semiconducting tubes of different diameter and chirality. Although many techniques such as density gradient ultracentrifugation, dielectrophoresis, and dispersion by surfactants or polar biopolymers have been developed, so-called conjugated polymer wrapping is one of the most promising and powerful purification and discrimination strategies. The procedure involves debundling and dispersion of SWNTs by wrapping semiflexible conjugated polymers, such as poly(9,9-dialkylfluorene)s (PFx) or regioregular poly(3-alkylthiophene)s (P3AT), around the SWNTs, and is accompanied by SWNT discrimination by diameter and chirality. Thereby, the π-conjugated backbone of the conjugated polymers interacts with the two-dimensional, graphene-like π-electron surface of the nanotubes and the solubilizing alkyl side chains of optimal length support debundling and dispersion in organic solvents. Careful structural design of the conjugated polymers allows for a selective and preferential dispersion of both small and large diameter SWNTs or SWNTs of specific chirality. As an example, with polyfluorenes as dispersing agents, it was shown that alkyl chain length of eight carbons are favored for the dispersion of SWNTs with diameters of 0.8-1.2 nm and longer alkyls with 12-15 carbons can efficiently interact with nanotubes of increased diameter up to 1.5 nm. Polar side chains at the PF backbone produce dispersions with increased SWNT concentration but, unfortunately, cause reduction in selectivity. The selectivity of the dispersion process can be monitored by a combination of absorption, photoluminescence, and photoluminescence excitation spectroscopy, allowing identification of nanotubes with specific coordinates [(n,m) indices]. The polymer wrapping strategy enables the generation of SWNT dispersions containing exclusively semiconducting nanotubes. Toward the applications in electronic devices, until now most applied approach is a direct processing of such SWNT dispersions into the active layer of network-type thin film field effect transistors. However, to achieve promising transistor performance (high mobility and on-off ratio) careful removal of the wrapping polymer chains seems crucial, for example, by washing or ultracentrifugation. More defined positioning of the SWNTs can be accomplished in directed self-assembly procedures. One possible strategy uses diblock copolymers containing a conjugated polymer block as dispersing moiety and a second block for directed self-assembly, for example, a DNA block for specific interaction with complementary DNA strands. Another strategy utilizes reactive side chains for controlled anchoring onto patterned surfaces (e.g., by interaction of thiol-terminated alkyl side chains with gold surfaces). A further promising application of purified SWNT dispersions is the field of organic (all-carbon) or hybrid solar cell devices.