19 research outputs found
Parallel and perpendicular cascades in solar wind turbulence
MHD-scale fluctuations in the velocity, magnetic, and density fields of the solar wind are routinely observed. The evolution of these fluctuations, as they are transported radially outwards by the solar wind, is believed to involve both wave and turbulence processes. The presence of an average magnetic field has important implications for the anisotropy of the fluctuations and the nature of the turbulent wavenumber cascades in the directions parallel and perpendicular to this field. In particular, if the ratio of the rms magnetic fluctuation strength to the mean field is small, then the parallel wavenumber cascade is expected to be weak and there are difficulties in obtaining a cascade in frequency. The latter has been invoked in order to explain the heating of solar wind fluctuations (above adiabatic levels) via energy transfer to scales where ion-cyclotron damping can occur. Following a brief review of classical hydrodynamic and magnetohydrodynamic (MHD) cascade theories, we discuss the distinct nature of parallel and perpendicular cascades and their roles in the evolution of solar wind fluctuations
Structural Heterogeneity in Polynucleotide-Facilitated Assembly of Phenothiazine Dyes
The assembly of stacked dyes on DNA
is of interest for electron
transfer, light harvesting, sensing, and catalysis applications. A
combination of UV/vis absorption, linear dichroism (LD), and circular
dichroism (CD) was applied to characterize thoroughly the aggregation
with DNA of the phenothiazine dyes methylene blue, azure B, and thionine.
Aggregates of each dye with [polyĀ(dG-dC)]<sub>2</sub>, [polyĀ(dA-dT)]<sub>2</sub>, and calf thymus DNA were explored at high dye:DNA binding
ratios, where excess dye groove-binds after all intercalation sites
are filled. The organization of the aggregates (dimers, trimers, and
multimers) with polydeoxynucleotides displays a structural diversity
that depends on DNA sequence, extent of methylation of dye exocyclic
amine groups, and ionic strength. The dyes typically form right-handed
H-aggregates having negative LD, consistent with stepped stacking
along the minor groove. However, aggregates in some dye:DNA aggregates
show left-handed chirality or positive LD, indicating unusual modes
of aggregation such as formation of adventitious dimers between intercalated
and minor groove bound dye. In terms of sequence-dependence, methylene
blue shows more extensive aggregation with [polyĀ(dA-dT)]<sub>2</sub>, while thionine aggregates more with [polyĀ(dG-dC)]<sub>2</sub>.
Azure B has distinctive behavior that is unlike either other dyes.
Thus, although these phenothiazine dyes possess a common tricyclic
framework, the organization of their polynucleotide-facilitated aggregates
depends sensitively on the extent of methylation of the exocyclic
amines
Chemical-to-Mechanical Energy Conversion in Biomacromolecular Machines: A Plasmon and Optimum Control Theory for Directional Work. 1. General Considerations
Short Oligonucleotides Aligned in Stretched Humid Matrix: Secondary DNA Structure in Poly(vinyl alcohol) Environment
We report that short, synthetic, double- as well as single-stranded
DNA can be aligned in stretched humid polyĀ(vinyl alcohol) (PVA) matrix,
and the secondary structure (nucleobase orientation) can be characterized
with linear dichroism (LD) spectroscopy. Oligonucleotides of lengths
varying between 10 (3.4 nm) and 60 bases (20.4 nm) were investigated
with respect to structural properties in the gel-like polymer environment.
The DNA conformation as a function of relative humidity reveals a
strong dependence of helical structure of DNA on PVA hydration level,
results of relevance for nanotechnical studies of DNA-based supramolecular
systems. Also, the PVA gel could provide possibilities to test models
for nucleic acid interactions and distribution in cell contexts, including
structural stability of genetic material in the cell and PVA-packaging
for gene delivery. A method by which duplex oligonucleotides, with
sequences designed to provide specific binding sites, become amenable
to polarized-light spectroscopy opens up new possibilities for studying
structure in DNA complexes with small adduct molecules as well as
proteins
Effects of PEGylation and acetylation of PAMAM dendrimers on DNA Binding, cytotoxicity and in vitro transfection efficiency
Poly(amidoamine) (PAMAM) dendrimers are promising multipotent gene delivery vectors, providing favorable DNA condensation properties also in combination with the possibility of conjugation of different targeting ligands to their surface. They have been used for transfection both in vitro and in vivo, but their application is currently somewhat limited due to inherent cytotoxicity. In this work we investigate how two types of surface modification, acetylation and PEGylation, affect the DNA binding characteristics, the cytotoxicity and the in vitro transfection efficiency of generation 4 and 5 PAMAM dendrimers. Particularly, we address how the morphology of DNA?dendrimer complexes, formed under low salt conditions, changes upon dilution in cell growth medium, an event that inevitably occurs before the complexes reach the cell surface in any transfection experiment. We find that acetylation and PEGylation essentially eliminates the inherent dendrimer cytotoxicity. However, the transfection efficiency of the modified dendrimers is lower than that of the corresponding unmodified dendrimers, which can be rationally understood by our observations that DNA is less condensed when complexed with these modified dendrimers. Although small DNA?dendrimer particles are formed, the availability for ethidium intercalation and nuclease degradation is significantly higher in the modified DNA?dendrimer complexes than in unmodified ones. Dilution in cell growth medium has a drastic effect on these electrostatically assembled complexes, resulting in increase in size and DNA availability. Our results strongly add to the notion that it is of importance to perform a biophysical characterization under conditions as close to the transfection situation as possible, to enable conclusions regarding structure?activity relations of gene delivery vectors.<br/
Interactions of a Photochromic Spiropyran with Liposome Model Membranes
The interactions between anionic or zwitterionic liposomes
and
a water-soluble, DNA-binding photochromic spiropyran are studied using
UV/vis absorption and linear dichroism (LD) spectroscopy. The spectral
characteristics as well as the kinetics of the thermal isomerization
process in the absence and presence of the two different liposome
types provide information about the environment and whether or not
the spiropyran resides in the liposome membrane. By measuring LD on
liposomes deformed and aligned by shear flow, further insight is obtained
about interaction and binding geometry of the spiropyran at the lipid
membranes. We show that the membrane interactions differ between the
two types of liposomes used as well as the isomeric forms of the spiropyran
photoswitch
UV Transition Moments of Tyrosine
To
assist polarized-light spectroscopy for protein-structure analysis,
the UV spectrum of <i>p</i>-cresol, the chromophore of tyrosine,
was studied with respect to transition moment directions and perturbation
by solvent environment. From linear dichroism (LD) spectra of <i>p</i>-cresol aligned in stretched matrices of polyĀ(vinyl alcohol)
and polyethylene, the lowest ĻāĻ* transition (L<sub>b</sub>) is found to have pure polarization over its entire absorption
(250ā300 nm) with a transition moment perpendicular to the
symmetry axis (C<sub>1</sub>āC<sub>4</sub>), both in polar
and nonpolar environments. For the second transition (L<sub>a</sub>), polarized parallel with the symmetry axis, a certain admixture
of intensity with orthogonal polarization is noticed, depending on
the environment. While the L<sub>b</sub> spectrum in cyclohexane shows
a pronounced vibrational structure, it is blurred in methanol, which
can be modeled as due to many microscopic polar environments. With
the use of quantum mechanical (QM) calculations, the transition moments
and solvent effects were analyzed with the B3LYP and ĻB97X-D
functionals in cyclohexane, water, and methanol using a combination
of implicit and explicit solvent models. The blurred L<sub>b</sub> band is explained by solvent hydrogen bonds, where both accepting
and donating a hydrogen causes energy shifts. The inhomogeneous solvent-shift
sensitivity in combination with robust polarization can be exploited
for analyzing tyrosine orientation distributions in protein complexes
using LD spectroscopy
Spectral Properties and Orientation of Voltage-Sensitive Dyes in Lipid Membranes
Voltage-sensitive dyes are frequently used for probing
variations
in the electric potential across cell membranes. The dyes respond
by changing their spectral properties: measured as shifts of wavelength
of absorption or emission maxima or as changes of absorption or fluorescence
intensity. Although such probes have been studied and used for decades,
the mechanism behind their voltage sensitivity is still obscure. We
ask whether the voltage response is due to electrochromism as a result
of direct field interaction on the chromophore or to solvatochromism,
which is the focus of this study, as result of changed environment
or molecular alignment in the membrane. The spectral properties of
three styryl dyes, di-4-ANEPPS, di-8-ANEPPS, and RH421, were investigated
in solvents of varying polarity and in model membranes using spectroscopy.
Using quantum mechanical calculations, the spectral dependence of
monomer and dimer ANEPPS on solvent properties was modeled. Also,
the kinetics of binding to lipid membranes and the binding geometry
of the probe molecules were found relevant to address. The spectral
properties of all three probes were found to be highly sensitive to
the local environment, and the probes are oriented nearly parallel
with the membrane normal. Slow binding kinetics and scattering in
absorption spectra indicate, especially for di-8-ANEPPS, involvement
of aggregation. On the basis of the experimental spectra and time-dependent
density functional theory calculations, we find that aggregate formation
may contribute to the blue-shifts seen for the dyes in decanol and
when bound to membrane models. In conclusion, solvatochromic and other
intermolecular interactions effects also need to be included when
considering electrochromic response voltage-sensitive dyes
DNA polymorphism as an origin of adenine-thymine tract length-dependent threading intercalation rate
Binuclear ruthenium complexes that bind DNA by threading intercalation have recently been found to exhibit an exceptional kinetic selectivity for long polymeric adenine?thymine (AT) DNA. A series of oligonucleotide hairpin duplexes containing a central tract of 6?44 alternating AT base pairs have here been used to investigate the nature of the recognition mechanism. We find that, above a threshold AT tract length corresponding to one helix turn of B-DNA, a dramatic increase in threading intercalation rate occurs. In contrast, such length dependence is not observed for rates of unthreading. Intercalation by any mechanism that depends on the open end of the hairpin was found not to be important in the series of oligonucleotides used, as verified by including in the study a hairpin duplex cyclized by a copper-catalyzed āclickā reaction. Our observations are interpreted in terms of a conformational pre-equilibrium, determined by the length of the AT tract. We finally find that mismatches or loops in the oligonucleotide facilitate the threading process, of interest for the development of mismatch-recognizing probes