Dynamic light scattering and fluorescence study of the interaction between double-stranded DNA and poly(amido amine) dendrimers

The interaction between a cationic poly(amido amine) (PAMAM) dendrimer of generation 4 and double-stranded salmon sperm DNA in 10 mM NaBr solution has been investigated using dynamic light scattering (DLS) and steady-state fluorescence spectroscopy. The structural parameters of the formed aggregates as well as the complex formation process were studied in dilute solutions. When DNA is mixed with PAMAM dendrimers, it undergoes a transition from a semiflexible coil to a more compact conformation due to the electrostatic interaction present between the cationic dendrimer and the anionic polyelectrolyte. The DLS results reveal that one salmon sperm DNA molecule forms a discrete aggregate in dilute solution with several PAMAM dendrimers with a mean apparent hydrodynamic radius of 50 nm. These discrete complexes coexist with free DNA at low molar ratios of dendrimer to DNA, which shows that cooperativity is present in the complex formation. The formation of the complexes was confirmed by agarose gel electrophoresis measurements. DNA in the complexes was also found to be significantly more protected against DNase catalyzed digestion compared to free DNA. The number of dendrimers per DNA chain in the complexes was found to be approximately 35 as determined by steady-state fluorescence spectroscopy.     

Surfactant-DNA gel particles: formation and release characteristics

Aqueous mixtures of oppositely charged polyelectrolytes undergo associative phase separation, resulting in coacervation, gelation, or precipitation. This phenomenon has been exploited here to form DNA gel particles by interfacial diffusion. We report on the formation of DNA gel particles by mixing solutions of DNA (either single-stranded (ssDNA) or double-stranded (dsDNA)) with solutions of cationic surfactant cetyltrimetrylammonium bromide (CTAB). By using CTAB, the formation of DNA reservoir gel particles, without adding any kind of cross-linker or organic solvent, has been demonstrated. Particles have been characterized with respect to the degree of DNA entrapment, surface morphology, and secondary structure of DNA in the particles. The swelling/deswelling behavior and the DNA release have been investigated in response to salt additions. Analysis of the data has suggested a higher degree of interaction between ssDNA and the cationic surfactant, confirming the stronger amphiphilic character of the denatured DNA. Fluorescence microscopy studies have suggested that the formation of these particles is associated with a conservation of the secondary structure of DNA.     

Quasielastic light scattering by biopolymers. IV. Tertiary collapse of calf thymus DNA in 5.5M LiCl

Circular dichroism has been commonly employed to infer the conformation of DNA in solution. The basis of the conformational assignments is the work of Tunis-Schneider and Maestre, wherein CD spectra of DNA were obtained under conditions comparable to those employed in the x-ray diffraction studies of A-, B-, and C-DNA. It has recently been suggested that the CD spectrum of DNA in chromatin, which is similar to the CD spectrum of the C-form DNA, is a superposition of the normal B-DNA spectrum and a single negative band, centered at 275 nm. This negative band is qualitatively identical to the spectrum for condensed Ψ-form DNA. We have employed the hydrodynamic methods of quasielastic light scattering and sedimentation velocity to determine the extent of DNA tertiary structural alteration in 5.5M LiCl as a possible explanation of the C-form CD spectrum. These studies suggest an eightfold contraction of the Stokes hydrodynamic volume for calf thymus DNA in going from 0.4M NH₄Ac to 5.5M LiCl, with no change in molecular weight. The estimated maximum presistence length of DNA in 5.5M LiCl is estimated to be 20.0 nm compared to the “minimum” value of 44.7 nm in NaCl solutions. The value 20.0 nm corresponds to a maximum radius of 16.7 nm for a “continuously coiled” cylinder of DNA, which compares with the value 5.0 nm of DNA in the nucleosome unit of chromatin.     

The effect of chain length on the melting temperature and size of dialkyldimethylammonium bromide vesicles

Differential scanning calorimetry (DSC) and dynamic light scattering (DLS) were used to obtain the gel to liquid-crystalline phase transition temperature (Tm) and the apparent hydrodynamic radius (Rh) of spontaneously formed cationic vesicles of dialkyldimethylammonium bromide salts (CnH2n+1)2(CH3)2N+.Br-, with varying chain lengths. The preparation of cationic vesicles from aqueous solution of these surfactants, for n=12, 14, 16 and 18 (DDAB, DTDAB, DHDAB and DODAB, respectively), requires the knowledge of the surfactant gel to liquid-crystalline phase transition temperature, or melting temperature (Tm) since below this temperature these surfactants are poorly or not soluble in water. That series of cationic surfactants has been widely investigated as vesicle-forming surfactants, although C12 and C18, DDAB and DODAB are by far the most investigated from this series. The dependence of Tm of these surfactants on the number n of carbons in the surfactant tails is reported. The Tm obtained by DSC increases non-linearly with n, and the vesicle apparent radius Rh is about the same for DHDAB and DODAB, but much smaller for DDAB.     

Molecular size determination of a membrane protein in surfactants by light scattering

The molecular size of an outer surface protein from the photosynthetic bacterium Chlorobium tepidum was studied by dynamic light scattering (DLS) and HPLC gel filtration. For that purpose, the membrane protein was isolated and studied in four different nonionic surfactants, namely t-octylphenoxypolyethenoxyethanol (Triton X-100), (methyl-6-O-(N)-heptyl-carbamoyl)-alpha-D-glucopyranoside (Hecameg), dodecyl-beta-D-maltoside (DDM) and n-octyl-oligo-oxyethylene (Octyl-POE). The protein was isolated by solubilization of the membranes with Triton X-100. The final purification step was a gel filtration, which was also used for surfactant exchange. Light scattering reveals the simultaneous presence of particles of different sizes in the 3-6 and 20-110 nm range, respectively. The smaller size is related to the hydrodynamic radius of the individual protein/surfactant complexes, whereas the larger size is associated with the presence of complex aggregates.     

Determination of a molecular shape for netrin-4 from hydrodynamic and small angle X-ray scattering measurements

As part of a continuing investigation of netrins, an emerging class of extracellular matrix proteins that are involved in axon guidance activity, we have used dynamic light scattering (DLS) and small angle X-ray scattering to investigate the solution conformation of a truncated version of netrin-4 (Δnetrin-4) that lacks the C-terminal portion. The protein is characterized by a hydrodynamic (Stokes) radius (r(H)) of 4.60 (±0.20) nm, a radius of gyration (r(G)) of 4.42 (±0.20) nm and a maximum particle dimension (D(max)) of 16nm. More detailed ab initio modeling of the SAXS data indicates an extended rod like conformation for Δnetrin-4 in solution-a concept supported by the excellent agreement observed between experimental parameter estimates and those calculated for the ab initio models for Δnetrin-4 by the HYDROPRO program.     

Molecular characterisation of soybean polysaccharides: an approach by size exclusion chromatography, dynamic and static light scattering methods

Water soluble polysaccharides from soybean (SSPS) have a pectin-like structure and are used as stabilisers in acidified beverages. Physicochemical properties such as structure, molecular weight and shape or conformation are primary factors controlling their functional properties. Two soybean polysaccharides, a native SSPS and a modified SSPS treated with beta-(1-->4)-D-galactosidase (GPase/SSPS) were studied by dynamic and static light scattering (DLS, SLS) and size exclusion chromatography (SEC). Consecutive filtrations using a range of membrane pore size removed a small fraction of macromolecular aggregates from dilute polysaccharide solutions with relatively little effect on the major component molecules as monitored by DLS and SEC measurements. Access to aggregate-free dilute solutions of SSPS and GPase/SSPS allowed the direct measurement of molecular characteristics. SLS results showed that SSPS had a weight average molecular weight of (645+/-11)x 10(3)g/mol and a radius of gyration, Rg, of (23.5+/-2.8)nm. By comparing R(g) with the hydrodynamic radius, Rh (21.1+/-0.5 nm) obtained from DLS, the structural parameter rho (Rg/Rh) was found to be 1.1, suggesting that SSPS has an overall globular shape due to a highly branched structure. The modified SSPS had a significantly lower molecular weight (287+/-18)x 10(3)g/mol but a similar radius of gyration (23.2+/-1.7 nm). The structure parameter rho of GPase/SSPS was higher (rho=1.3) because of a smaller hydrodynamic radius (17.7+/-1.8 nm). This suggests that GPase/SSPS has a much less branched structure yet still differs significantly from a linear random coil conformation (rho=1.7-2.0). The results derived from SLS and DLS are in agreement with the conclusions obtained from a chemical analysis where the reduction of molecular weight of GPase/SSPS was caused by the cleavage of galactan side chains.     

Investigation on the analytical application of cationic Gemini surfactant 12‐4‐12 and its interaction with DNA

The quantitative determination of nucleic acids is of great importance in fundamental research and clinical diagnosis. In this work, the interaction between DNA and cationic Gemini surfactant 12‐4‐12, which changes the conformation of DNA, was investigated by UV‐vis absorption, FT‐IR spectra and steady‐state fluorescence techniques. A hydrophobic pyrene probe was used to investigate the microenvironment change and calculate the critical micelle concentration (CMC) of Gemini surfactant 12‐4‐12 (0.69 mmol/L), which is close to the value obtained from the conductivity method (0.79 mmol/L). A new detection assay for DNA is proposed with Gemini surfactant 12‐4‐12, using the resonance light‐scattering (RLS) technique. The formation of DNA–12‐4‐12 complex resulted in enhanced RLS signals at 368 nm, which is proportional to DNA concentration in the range 0.304–5.32 mg/L, with a detection limit of 35 µg/L. Most coexisting substances do not interfere in the detection and four synthetic samples were analyzed satisfactorily. Copyright © 2011 John Wiley & Sons, Ltd.     

Compaction of DNA in an anionic micelle environment followed by assembly into phosphatidylcholine liposomes

A difficult problem concerning the interaction of DNA with amphiphiles of opposite charge above their critical micelle concentration is the propensity for aggregation of the condensed DNA complexes. In this study, this problem was addressed by attenuating amphiphile charge density within a cholate micelle environment. The amphiphile consisted of a cationic peptide, acetyl-CWKKKPKK-amide, conjugated to dilaurylphosphatidylethanolamine. In the presence of cholate, multiple equivalents of cationic charge were required to bring about the completion of DNA condensation. At the end point of condensation, stable, soluble DNA–micelle complexes were formed, which by dynamic light scattering exhibited apparent hydrodynamic diameters between 30 and 60 nm. Aggregation, as measured by static light scattering at 90° and by turbidity, was not observed until further additions of peptide–lipid conjugate were made beyond the end point of DNA condensation. Liposome complexes containing the non-aggregated, compacted DNA were formed by adding dioleoylphosphatidylcholine followed by removing the cholate by dialysis. The resulting complexes were distributed within a narrow density range, the DNA was quantitatively assembled into the liposomes, and liposomes without DNA were not detected. Small particles were formed with a mean hydrodynamic diameter of 77 nm. The liposomal DNA showed complete retention of its supercoiled form and no detectable sensitivity to DNase (25 U/10 µg DNA, 1.5 h, 37°C). The use of an anionic, dialyzable amphiphile to attenuate charge interactions between DNA and cationic amphiphiles is a useful technology for the quantitative assembly of compacted DNA into conventional liposomes, with complete protection against nuclease activity.     

Structural changes of ultraviolet-irradiated DNA derived from hydrodynamic measurements

The paper reports on sedimentation and viscosity measurements performed on ultraviolet-irradiated DNA from T7 phage and calf thymus. From the hydrodynamic data the relative changes in the mean molecular weight, radius of gyration, and effective Kuhn statistical segment length were calculated. The results show that ultraviolet irradiation (254 nm) leads to a significant decrease of the effective statistical segment length of DNA which may be due to small local helix kinks (produced by the generation of photodimers) and a local increase of chain flexibility. Alterations in the overall DNA conformation may be observed even at low fluences where the mean molecular weight almost stays constant. The locally distorted helix regions possibly may serve as recognition sites in the first step of excision repair.     

Glycogen phosphorylase <Emphasis Type="Italic">b</Emphasis> and phosphorylase kinase binding to glycogen under molecular crowding conditions. Inhibitory effect of FAD

Dynamic light scattering was used to study the interaction of phosphorylase kinase (PhK) and glycogen phos-phorylase b (Phb) from rabbit skeletal muscle with glycogen under molecular crowding conditions arising from the presence of 1 M trimethylamine N-oxide and at physiological ionic strength. The mean value of hydrodynamic radius of the initial glycogen particles was 52 nm. Crowding stimulated Phb and PhK combined binding on glycogen particles. Two-stage character of PhK binding to glycogen particles containing adsorbed Phb was found in the presence of the crowding agent. At the initial stage, limited size particles with hydrodynamic radius of ～220 nm are formed, whereas the second stage is accompanied by linear growth of hydrodynamic radius. Flavin adenine dinucleotide (FAD) selectively inhibited PhK binding at the second stage. The data indicate that in the first stage Phb is involved in PhK binding by glycogen particles containing adsorbed Phb, whereas PhK binding in the second stage does not involve Phb.     

Aggregation-induced conformation changes dictate islet amyloid polypeptide (IAPP) membrane affinity

Islet amyloid polypeptide (IAPP) is a 37 residue intrinsically disordered protein whose aggregation is associated with Type II diabetes. Like most amyloids, it appears that the intermediate aggregates (“oligomers”) of IAPP are more toxic than the mature fibrils, and interaction with the cell membrane is likely to be an integral component of the toxicity. Here we probe the membrane affinity and the conformation of the peptide as a function of its aggregation state. We find that the affinity of the peptide for artificial lipid bilayers is more than 15 times higher in the small oligomeric state (hydrodynamic radius ~ 1.6 nm) compared to the monomeric state (hydrodynamic radius ~ 0.7 nm). Binding with RIN-m5F cell membranes also shows qualitatively similar behavior. The monomeric state, as determined by Forster Resonance Energy Transfer, has a much larger end to end distance than the oligomeric state, suggesting conformational change between the monomers and the oligomers. Raman and Infrared spectroscopic measurements show the presence of considerable alpha helical content in the oligomers, whereas the larger aggregates have largely beta sheet character. Therefore, the conformation of the small oligomers is distinct from both the smaller monomers and the larger oligomers, and this is associated with an enhanced membrane affinity. This provides a possible structural basis for the enhanced toxicity of amyloid oligomers. Such change is also reminiscent of amyloid beta, another aggregation prone amyloidogenic peptide, though the nature of the conformational change is quite different in the two cases. We infer that conformational change underlying oligomer formation is a key factor in determining the enhanced membrane affinity of disease causing oligomers, but the toxic “oligomer fold” may not be universal.     

Higher-order structures of chromatin in solution.

Neutron scatter studies have been made on gently prepared chicken erythrocyte chromatin over a range of ionic strength. At low ionic strength the mass per unit length of the '10 nm nucleofilament corresponds to one nucleosome per 8--12 nm and a DNA packing ratio of between 6 and 9. From the contrast dependence of the cross-section radius of gyration of the nucleofilament the following parameters have been obtained; RgDNA' the cross-section radius of gyration (Rg) when DNA dominates the scatter; RgP, the cross-section Rg when protein dominates the scatter; Rc, the cross-section Rg at infinite contrast and alpha, the constant which describes the dependence of the cross-section Rg on contrast variation. From our understanding of the structure of the core particle, various arrangement of core particles in the nucleofilament have been tested. In models consistent with the above parameters the core particles are arranged edge-to-edge or with the faces of the core particles inclined to within 20 degrees to the axis of the nucleofilament. With increase of ionic strength the transition to the second-order chromatin structure has been followed. This gave the interesting result that above 20 microM NaCL or 0.4 mM MgCL2 the cross-section Rg increases abruptly to about 9 nm with a packing ratio of 0.2 nucleosome/mn and with further increase of ionic strength the Rg increases to 9.5 nm while the packing ratio increases threefold to 0.6 nucleosome/nm. This suggests a family of supercoils of nucleosomes which contract with increasing ionic strength. In its most contracted form the diameter of the hydrated supercoil has been found from the radial distribution function to be 34 nm. Models for the arrangements of core particles in the 34-nm supercoil are discussed.     

DNA-surfactant interactions: coupled cooperativity in ligand binding leads to duplex stabilization.

The cooperative nature of interaction of cationic surfactants with short oligonucleotides leading to eventual stabilization of DNA duplexes is demonstrated. At submicellar concentrations and DNA:surfactant charge ratios of 0.2 to 0.8, the association of single chain (CTAB) and double chain (DOTAP) surfactants to oligonucleotides is initiated by electrostatic interaction of cationic ligands with polyanionic DNA that aligns the surfactant molecules on the DNA template. This is followed by binding of new surfactant ligands to the initial complex, driven cooperatively by the hydrophobic forces, leading to in situ formation of surfactant-bound and bare duplexes as separate species. These exhibit independent melting behaviour characterised by double transition in thermal UV profiles, with a higher T(m) for surfactant-DNA complexes. Understanding the cooperative binding of the cationic surfactants to the DNA described here may have implications for rational design of DNA binding drugs and DNA delivery systems.     

Determination of a particle's radius by two-dimensional agarose gel electrophoresis

Electrophoresis in an agarose gel dilute enough to be almost nonretarding, followed by electrophoresis in an orthogonal direction into a more concentrated agarose gel, has been developed as a procedure to determine the radius of spherical particles. Unlike procedures of unidirectional electrophoresis in a single gel, the above procedure can be used to compare the radii of particles that differ in solid-support-free electrophoretic mobility. Accuracy of 0.3 nm has been achieved with particles 30 nm in radius. It was found that the apparent radius of the spherical capsid of bacteriophage P22 decreased by 3% during elevated temperature-induced ejection of DNA from the capsid. Though originally designed for use with multimolecular particles, the procedure described here should also be useful with monomolecular particles.     

Neutron scattering studies of chromatosomes

Neutron scattering data establish that the radius of gyration of the DNA in chicken erythrocyte chromatosome particles is significantly higher, by about 0.3 nm, than the radius of gyration of the DNA in the core particle. Corresponding information of the radius of gyration of the protein component in the chromatosomes (3.75 nm) indicated an enlargement, compared to the radius of gyration of the octamer of histone proteins both in core particles and in the histone octamer stabilised in 2 M NaCl (3.25 nm). From the latter data, we could calculate the distance in the chromatosome between the centre of mass of the linker histone and the histone octamer as 5.5 nm. These results impose severe limitations for the organisation of the 22 bp extra DNA and the possible location of H1/H5 in the chromatosome, implying that the H1/H5 is close to the centre turn of the core particle DNA.     

Neutral postgrafted colloidal particles for gene delivery

Surface modification of cationic lipoplexes has been carried out by means of a postgrafting reaction. The original lipoplexes described comprise a cationic lipid, a neutral lipid, poly(ethylene glycol)-cholesterol (with or without a targeting ligand) and DNA. Modifying their surface via a chemical, postgrafting reaction did not alter their size (approximately 100 nm) nor their ability to compact DNA, but did give a reduced zeta potential (approximately 0 mV) to afford surface neutral particles. With the modified lipoplexes nonspecific NIH3T3 cell surface binding in vitro was inhibited. Intravenous injection of the neutralized lipoplexes in mice showed decreased accumulation of the particles in the lung as compared to PEGylated cationic lipoplexes. Tumor targeting was also achieved in vivo by the addition of an RGD-PEG-Cholesterol as a lipid-ligand in the postgrafted lipoplex formulation.     

Adsorption of DNA onto positively charged amidine colloidal spheres and the resultant bridging interaction

The complexation behaviour of duplex linear DNA (negatively charged) with amidine functionalised sub-micron latex spheres (positively charged) was studied using dynamic light scattering (DLS) and a PALS interferrometric zeta potential sizer. Four types of DNA-sphere complex were investigated as a function of component concentration by combining amidine functionalised polystyrene microspheres with radii of 10.5 nm and 60 nm, and herring DNA of lengths of 35 nm and 85 nm. At low DNA concentrations (c(DNA)), the undercharged complexes showed a small increase in measured hydrodynamic radius (R(h)) and a decrease in zeta potential with increasing c(DNA). Within a critical DNA concentration range R(h) was seen to peak sharply, and the zeta potentials were approximately 0 mV, corresponding to the formation of unstable neutral complexes. Immediately above this concentration region the measured R(h) values became comparable with those at low c(DNA), and the zeta potential became negative, indicating the formation of stable overcharged complexes. The small and large spheres formed multi-sphere and single sphere overcharged aggregates respectively, which is thought to be determined by the relative magnitude of the chain persistence length (approximately 50 nm) and the sphere radius, switching on or off the DNA bridging interaction.