Compositional Analysis of ssDNA-Coated Single-Wall Carbon Nanotubes through UV Absorption Spectroscopy.

Aqueous suspensions of single-wall carbon nanotubes (SWCNTs) coated by ssDNA are analyzed using UV absorption and total carbon measurements. The results give absolute average concentrations of both components in samples without free ssDNA. From those values, the average mid-UV SWCNT absorptivity is deduced for three different batches of relatively small diameter nanotubes: two HiPco and one CoMoCAT. The absorptivity values enable the use of simple spectrophotometry to measure absolute concentrations of similar SWCNT samples in aqueous SDS. The results also quantify the mass ratio of ssDNA to SWCNT, defining the average number of nanotube carbon atoms suspended by one ssDNA strand of T15GT15 or T30G. Comparing this experimental parameter with results from replica exchange molecular dynamics simulations of one ssDNA strand freely adsorbed on a (6,5) segment shows close agreement between the computed number of SWCNT atoms covered per strand and the measured number of SWCNT atoms suspended per strand.

Charge-Free, Stabilizing Amide-π Interactions Can Be Used to Control Collagen Triple-Helix Self-Assembly.

There is a noted lack of understood, controllable interactions for directing the organization of collagen triple helices. While the field has had success using charge-pair interactions and cation-π interactions in helix design, these alone are not adequate for achieving the degree of specificity desirable for these supramolecular structures. Furthermore, because of the reliance on electrostatic interactions, designed heterotrimeric systems have been heavily charged, a property undesirable in some applications. Amide-π interactions are a comparatively understudied class of charge-free interactions, which could potentially be harnessed for triple-helix design. Herein, we propose, validate, and utilize pairwise amino acid amide-π interactions in collagen triple-helix design. Glutamine-phenylalanine pairs, when arranged in an axial geometry, are found to exhibit a moderately stabilizing effect, while in the lateral geometry, this pair is destabilizing. Together this allows glutamine-phenylalanine pairs to effectively set the register of triple helices. In contrast, interactions between asparagine and phenylalanine appear to have little effect on triple-helical stability. After deconvoluting the contributions of these amino acids to triple-helix stability, we demonstrate these new glutamine-phenylalanine interactions in the successful design of a heterotrimeric triple helix. The results of all of these analyses are used to update our collagen triple-helix thermal stability prediction algorithm, Scoring function for Collagen Emulating Peptides' Temperature of Transition (SCEPTTr).

Surfactant-Controlled Mobility of Oil Droplets in Mineral Nanopores.

Polymer flooding is one of the widely used enhanced oil recovery (EOR) methods. However, tuning polymer properties to achieve improved performance in porous mineral rocks of diverse oil reservoirs remains one of the challenges of EOR processes. Here, we use molecular dynamics (MD) simulations to examine decane/water mixtures with surfactant additives in calcite and kaolinite mineral nanopores and characterize surfactant properties associated with increased fluid mobility and improved wettability in planar and constricted nanopore geometries. Cetyltrimethylammonium chloride (CTAC) and sodium dodecyl sulfate (SDS) surfactants are found to modulate the contact angles of decane droplets and reduce the decane density on mineral surfaces. CTAC can enhance and unblock the flow of decane droplets through narrowing nanopores with constricted geometries while aiding in decane droplet shape deformation, whereas SDS leads to decane droplets stalling in front of constrictions in nanopores. We hypothesize that the inability of the cationic CTAC headgroup to form hydrogen bonds is one of the key factors leading to enhanced CTAC-coated decane flow through constricted nanopores. The obtained molecular view of equilibrium and dynamic properties of complex fluids typical of oil reservoirs can provide a basis for the future design of new molecules for EOR processes.

Ultralarge Modulation of Fluorescence by Neuromodulators in Carbon Nanotubes Functionalized with Self-Assembled Oligonucleotide Rings.

Noncovalent interactions between single-stranded DNA (ssDNA) oligonucleotides and single wall carbon nanotubes (SWNTs) have provided a unique class of tunable chemistries for a variety of applications. However, mechanistic insight into both the photophysical and intermolecular phenomena underlying their utility is lacking, which results in obligate heuristic approaches for producing ssDNA-SWNT based technologies. In this work, we present an ultrasensitive "turn-on" nanosensor for neuromodulators dopamine and norepinephrine with strong relative change in fluorescence intensity (Δ F/ F0) of up to 3500%, a signal appropriate for in vivo neuroimaging, and uncover the photophysical principles and intermolecular interactions that govern the molecular recognition and fluorescence modulation of this nanosensor synthesized from the spontaneous self-assembly of (GT)6 ssDNA rings on SWNTs. The fluorescence modulation of the ssDNA-SWNT conjugate is shown to exhibit remarkable sensitivity to the ssDNA sequence chemistry, length, and surface density, providing a set of parameters with which to tune nanosensor dynamic range, analyte selectivity and strength of fluorescence turn-on. We employ classical and quantum mechanical molecular dynamics simulations to rationalize our experimental findings. Calculations show that (GT)6 ssDNA form ordered rings around (9,4) SWNTs, inducing periodic surface potentials that modulate exciton recombination lifetimes. Further evidence is presented to elucidate how dopamine analyte binding modulates SWNT fluorescence. We discuss the implications of our findings for SWNT-based molecular imaging applications.

Guanine-Specific Chemical Reaction Reveals ssDNA Interactions on Carbon Nanotube Surfaces.

Understanding the conformations of physisorbed single-stranded DNA (ssDNA) oligos on single-wall carbon nanotube (SWCNT) surfaces is important for advancing basic nanoscience and for developing applications in biomedicine and quantum information processing. Here we report evidence that the ssDNA strands are partly desorbed from the nanotube surface under common conditions. SWCNT suspensions were prepared in eight ssDNA oligos, each containing 1 guanine and 30 thymine bases but differing in the position of the guanine within the strand. Singlet oxygen exposure then covalently functionalized the guanine to the SWCNT surface, red-shifting the nanotube fluorescence by an amount reflecting the guanine spatial density at the surface. Spectral shifts were greatest for central guanine positions and smallest for end positions. In conjunction with steered molecular dynamics simulations, the results suggest that steric interference between neighboring ssDNA strands on an individual nanotube causes significant dislocation or desorption of the strand ends while central regions remain better wrapped around the nanotube. This effect decreases with decreasing concentrations of free ssDNA.

Dye Quenching of Carbon Nanotube Fluorescence Reveals Structure-Selective Coating Coverage.

Many properties and applications of single-wall carbon nanotubes (SWCNTs) depend strongly on the coatings that allow their suspension in aqueous media. We report that SWCNT fluorescence is quenched by reversible physisorption of dye molecules such as methylene blue, and that measurements of that quenching can be used to infer structure-specific exposures of the nanotube surface to the surrounding solution. SWCNTs suspended in single-stranded DNA oligomers show quenching dependent on the combination of nanotube structure and ssDNA base sequence. Several sequences are found to give notably high or low surface coverages for specific SWCNT species. These effects seem correlated with the selective recognitions used for DNA-based structural sorting of nanotubes. One notable example is that dye quenching of fluorescence from SWCNTs coated with the (ATT)4 base sequence is far stronger for one (7,5) enantiomer than for the other, showing that coating coverage is associated with the coating affinity difference reported previously for this system. Equilibrium modeling of quenching data has been used to extract parameters for comparative complexation constants and accessible surface areas. Further insights are obtained from molecular dynamics simulations, which give estimated contact areas between ssDNA and SWCNTs that correlate with experimentally inferred surface exposures and account for the enantiomeric discrimination of (ATT)4.