Hydrodynamic properties and structure of fd virus

Phage probes couple to DNA relaxation dynamics to reveal universal behavior across scales and regimes

Microrheology has become an indispensable tool for measuring the dynamics of macromolecular systems. Yet, its ability to characterize polymer dynamics across spatiotemporal scales, which vary among polymers and concentration regimes, is limited by the selection of probe morphologies and sizes. Here, we introduce semiflexible M13 phage as a powerful microrheological probe able to circumvent these constraints to robustly capture the dynamics of polymeric solutions across decades of concentrations, sizes, and ionic conditions. We show that phage mobility directly couples to the relaxation dynamics of DNA solutions spanning from semidilute to entangled regimes with ionic strengths varying by four orders of magnitude. Phage mobility metrics across a broad range of timescales collapse onto universal master curves that are unexpectedly insensitive to ionic strength and exhibit robust crossovers from semidilute to entangled regime scaling, not captured by current theoretical models. Our results open the door to the use of phage probes to elucidate the complex dynamics of systems exhibiting a spectrum of thermal and active relaxation processes.

Mesoscale simulations of diffusion and sedimentation in shape-anisotropic nanoparticle suspensions

We determine the long-time self-diffusion coefficient and sedimentation coefficient for suspensions of nanoparticles with anisotropic shapes (octahedra, cubes, tetrahedra, and spherocylinders) as a function of nanoparticle concentration using mesoscale simulations. We use a discrete particle model for the nanoparticles, and we account for solvent-mediated hydrodynamic interactions between nanoparticles using the multiparticle collision dynamics method. Our simulations are compared to theoretical predictions and experimental data from existing literature, demonstrating good agreement in the majority of cases. Further, we find that the self-diffusion coefficient of the regular polyhedral shapes can be estimated from that of a sphere whose diameter is the average of their inscribed and circumscribed sphere diameters.

Dynamics of anisotropic colloidal systems: What to choose, DLS, DDM or XPCS?

Investigation of the dynamics of colloids in bulk can be hindered by issues such as multiple scattering and sample opacity. These challenges are exacerbated when dealing with inorganic materials. In this study, we employed a model system of Akaganeite colloidal rods to assess three leading dynamics measurement techniques: 3D-(depolarized) dynamic light scattering (3D-(D)DLS), polarized-differential dynamic microscopy (P-DDM), and x-ray photon correlation spectroscopy (XPCS). Our analysis revealed that the translational and rotational diffusion coefficients captured by these methods show a remarkable alignment. Additionally, by examining the q-ranges and maximum volume fractions for each approach, we offer insights into the best technique for investigating the dynamics of anisotropic systems at the colloidal scale.

Self-Assembled Single-Stranded DNA Nano-Networks in Solution and at Surfaces

We studied the directed self-assembly of two types of complementary single-stranded DNA (ssDNA) strands [i.e., poly(dA) and poly(dT)] into more complex, organized, and percolating networks in dilute solutions and at surfaces. Understanding ssDNA self-assembly into 2D networks on surfaces is important for the use of such networks in the fabrication of well-defined nanotechnological devices, as, for instance, required in nanoelectronics or for biosensing. To control the formation of 2D networks on surfaces, it is important to know whether DNA assemblies are formed already in dilute solutions or only during the drying/immobilization process at the surface, where the concentration automatically increases. Fluorescence cross-correlation spectroscopy clearly shows the presence of larger DNA complexes in mixed poly(dA) and poly(dT) solutions already at very low DNA concentrations (<1 nM), that is, well below the overlap concentration. Here, we describe for the first time such supramolecular complexes in solution and how their structure depends on the ssDNA length and concentration and ionic strength. Hence, future attempts to control such networks should also focus on network precursors in solution and not only on their immobilization on surfaces.

Quantification of Peptide-Bound Particles: A Phage Mimicking Approach via Site-Selective Immobilization on Glass

The increasing complexity and need of high-tech materials for modern electronics raise the demand for rare earth elements. While recycling rates are still negligible for most elements, geopolitical tensions, circular economy, and the aim for a carbon-neutral society put pressure on conventional supply strategies and emphasize the need for new ideas for recycling. Our research group works on the development of phage surface display (PSD)-derived peptide-based recycling methods for electronic waste. This study focuses on LaPO4:Ce,Tb (LAP), a component of electronic waste from compact energy-saving lamps containing rare earth element-enriched fluorescent powders. While free solution-phase peptides show little to no interaction with the target material, we re-enabled the binding capability by immobilizing them on various glass supports. We shine a spotlight on the transition from phage-bound to free peptides and present the first proof of successful peptide-LAP particle interactions of previously reported PSD-derived sequences. Therefore, we introduce a method to investigate peptide-particle-interactions qualitatively and quantitatively. Additionally, a calibration curve allowed the quantification of peptide-bound particles. Combined with the quantification of the immobilized peptide on the surface, it was possible to calculate a potential dosage of peptides for future recycling processes.

The Role of Rotational Motion in Diffusion NMR Experiments on Supramolecular Assemblies: Application to Sup35NM Fibrils

Pulsed-field gradient (PFG) NMR is an important tool for characterization of biomolecules and supramolecular assemblies. However, for micrometer-sized objects, such as amyloid fibrils, these experiments become difficult to interpret because in addition to translational diffusion they are also sensitive to rotational diffusion. We have constructed a mathematical theory describing the outcome of PFG NMR experiments on rod-like fibrils. To test its validity, we have studied the fibrils formed by Sup35NM segment of the prion protein Sup35. The interpretation of the PFG NMR data in this system is fully consistent with the evidence from electron microscopy. Contrary to some previously expressed views, the signals originating from disordered regions in the fibrils can be readily differentiated from the similar signals representing small soluble species (e.g. proteolytic fragments). This paves the way for diffusion-sorted NMR experiments on complex amyloidogenic samples.

Self-Assembly of Model Amphiphilic Peptides in Nonaqueous Solvents: Changing the Driving Force for Aggregation Does Not Change the Fibril Structure

Within the homologous series of amphiphilic peptides A_nK, both A₈K and A₁₀K self-assemble in water to form twisted ribbon fibrils with lengths around 100 nm. The structure of the fibrils can be described in terms of twisted β-sheets extending in the direction of the fibrils, laminated to give a constant cross section of 4 nm by 8 nm. The finite width of the twisted ribbons can be reasonably explained within a simple thermodynamic model, considering a free energy penalty for the stretching of hydrogen bonds along the twisted β-sheets and an interfacial free energy gain for the lamination of the hydrophobic β-sheets. In this study, we characterize the self-assembly behavior of these peptides in nonaqueous solutions as a route to probe the role of hydrophobic interaction in fibril stabilization. Both peptides, in methanol and N,N-dimethylformamide, were found to form fibrillar aggregates with the same β-sheet structure as in water but with slightly smaller cross-sectional sizes. However, the gel-like texture, the slow relaxation in dynamic light scattering experiments, and a correlation peak in the small-angle X-ray scattering pattern highlighted enhanced interfibril interactions in the nonaqueous solvents in the same concentration range. This could be ascribed to a higher effective volume of the aggregates because of enhanced fibril growth and length, as suggested by light scattering and cryogenic transmission electron microscopy analyses. These effects can be discussed considering how the solvent properties affect the different energetic contributions (hydrophobic, electrostatic, and hydrogen bonding) to fibril formation. In the analyzed case, the decreased hydrogen bonding propensity of the nonaqueous solvents makes the hydrogen bond formation along the fibril a key driving force for peptide assembly, whereas it represents a nonrelevant contribution in water.

Arrested dynamics in a model peptide hydrogel system

We report here on a peptide hydrogel system, which in contrast to most other such systems, is made up of relatively short fibrillar aggregates, discussing resemblance with colloidal rods. The synthetic model peptides A₈K and A₁₀K, where A denotes alanine and K lysine, self-assemble in aqueous solutions into ribbon-like aggregates having an average length 〈L〉 on the order of 100 nm and with a diameter d≈ 6 nm. The aggregates can be seen as weakly charged rigid rods and they undergo an isotropic to nematic phase transition at higher concentrations. Translational motion perpendicular to the rod axis gets strongly hindered when the concentration is increased above the overlap concentration. Similarly, the rotational motion is hindered, leading to very long stress relaxation times. The peptide self-assembly is driven by hydrophobic interactions and due to a net peptide charge the system is colloidally stable. However, at the same time short range, presumably hydrophobic, attractive interactions appear to affect the rheology of the system. Upon screening the long range electrostatic repulsion, with the addition of salt, the hydrophobic attraction becomes more dominant and we observe a transition from a repulsive glassy state to an attractive gel-state of the rod-like peptide aggregates.

Virus lasers for biological detection

The selective amplification of DNA in the polymerase chain reaction is used to exponentially increase the signal in molecular diagnostics for nucleic acids, but there are no analogous techniques for signal enhancement in clinical tests for proteins or cells. Instead, the signal from affinity-based measurements of these biomolecules depends linearly on the probe concentration. Substituting antibody-based probes tagged for fluorescent quantification with lasing detection probes would create a new platform for biomarker quantification based on optical rather than enzymatic amplification. Here, we construct a virus laser which bridges synthetic biology and laser physics, and demonstrate virus-lasing probes for biosensing. Our virus-lasing probes display an unprecedented > 10,000 times increase in signal from only a 50% increase in probe concentration, using fluorimeter-compatible optics, and can detect biomolecules at sub-100 fmol mL⁻¹ concentrations.

Many ligand-binding assays still rely on signals that scale linearly with probe concentration. The authors present lasing detection probes with a dye-labelled virus as the gain medium to optically amplify the signal, which could enable much higher signals than for fluorescent quantification.

Filamentous phages as building blocks for reconfigurable and hierarchical self-assembly

Filamentous bacteriophages such as fd-like viruses are monodisperse rod-like colloids that have well defined properties of diameter, length, rigidity, charge and chirality. Engineering these viruses leads to a library of colloidal rods, which can be used as building blocks for reconfigurable and hierarchical self-assembly. Their condensation in an aqueous solution with additive polymers, which act as depletants to induce attraction between the rods, leads to a myriad of fluid-like micronic structures ranging from isotropic/nematic droplets, colloid membranes, achiral membrane seeds, twisted ribbons, π-wall, pores, colloidal skyrmions, Möbius anchors, scallop membranes to membrane rafts. These structures, and the way that they shape-shift, not only shed light on the role of entropy, chiral frustration and topology in soft matter, but also mimic many structures encountered in different fields of science. On the one hand, filamentous phages being an experimental realization of colloidal hard rods, their condensation mediated by depletion interactions constitutes a blueprint for the self-assembly of rod-like particles and provides a fundamental foundation for bio- or material-oriented applications. On the other hand, the chiral properties of the viruses restrict the generalities of some results but vastly broaden the self-assembly possibilities.

Conformations and membrane-driven self-organization of rodlike fd virus particles on freestanding lipid membranes

Membrane-mediated interactions and aggregation of colloidal particles adsorbed to responsive elastic membranes are challenging problems relevant for understanding the microscopic organization and dynamics of biological membranes. We experimentally study the behavior of rodlike semiflexible fd virus particles electrostatically adsorbed to freestanding cationic lipid membranes and find that their behavior can be controlled by tuning the membrane charge and ionic strength of the surrounding medium. Three distinct interaction regimes of rodlike virus particles with responsive elastic membranes can be observed. (i) A weakly charged freestanding cationic lipid bilayer in a low ionic strength medium represents a gentle quasi-2D substrate preserving the integrity, structure, and mechanical properties of the membrane-bound semiflexible fd virus, which under these conditions is characterized by a monomer length of 884 ± 4 nm and a persistence length of 2.5 ± 0.2 μm, in perfect agreement with its properties in bulk media. (ii) An increase in the membrane charge leads to the membrane-driven collapse of fd virus particles on freestanding lipid bilayers and lipid nanotubes into compact globules. (iii) When the membrane charge is low, and the mutual electrostatic repulsion of membrane-bound virus particles is screened to a considerable degree, membrane-driven self-organization of membrane-bound fd virus particles into long linear tip-to-tip aggregates showing dynamic self-assembly/disassembly and quasi-semiflexible behavior takes place. These observations are in perfect agreement with the results of recent theoretical and simulation studies predicting that membrane-mediated interactions can control the behavior of colloidal particles adsorbed on responsive elastic membranes.

Silica biomineralization via the self-assembly of helical biomolecules

The biomimetic synthesis of relevant silica materials using biological macromolecules as templates via silica biomineralization processes attract rapidly rising attention toward natural and artificial materials. Biomimetic synthesis studies are useful for improving the understanding of the formation mechanism of the hierarchical structures found in living organisms (such as diatoms and sponges) and for promoting significant developments in the biotechnology, nanotechnology and materials chemistry fields. Chirality is a ubiquitous phenomenon in nature and is an inherent feature of biomolecular components in organisms. Helical biomolecules, one of the most important types of chiral macromolecules, can self-assemble into multiple liquid-crystal structures and be used as biotemplates for silica biomineralization, which renders them particularly useful for fabricating complex silica materials under ambient conditions. Over the past two decades, many new silica materials with hierarchical structures and complex morphologies have been created using helical biomolecules. In this review, the developments in this field are described and the recent progress in silica biomineralization templating using several classes of helical biomolecules, including DNA, polypeptides, cellulose and rod-like viruses is summarized. Particular focus is placed on the formation mechanism of biomolecule-silica materials (BSMs) with hierarchical structures. Finally, current research challenges and future developments are discussed in the conclusion.

High-throughput DNA separation in nanofilter arrays

We numerically investigated the dynamics of short double-stranded DNA molecules moving through a deep-shallow alternating nanofilter, by utilizing Brownian dynamics simulation. We propose a novel mechanism for high-throughput DNA separation with a high electric field, which was originally predicted by Laachi et al. [Phys. Rev. Lett. 2007, 98, 098106]. In this work, we show that DNA molecules deterministically move along different electrophoretic streamlines according to their length, owing to geometric constraint at the exit of the shallow region. Consequently, it is more probable that long DNA molecules pass over a deep well region without significant lateral migration toward the bottom of the deep well, which is in contrast to the long dwelling time for short DNA molecules. We investigated the dynamics of DNA passage through a nanofilter facilitating electrophoretic field kinematics. The statistical distribution of the DNA molecules according to their size clearly corroborates our assumption. On the other hand, it was also found that the tapering angle between the shallow and deep regions significantly affects the DNA separation performance. The current results show that the nonuniform field effect combined with geometric constraint plays a key role in nanofilter-based DNA separation. We expect that our results will be helpful in designing and operating nanofluidics-based DNA separation devices and in understanding the polymer dynamics in confined geometries.

Glass transition of repulsive charged rods (fd-viruses)

It has recently been shown that suspensions of long and thin charged fibrous viruses (fd) form a glass at low ionic strengths. The corresponding thick electric double layers give rise to long-ranged repulsive electrostatic interactions, which lead to caging and structural arrest at concentrations far above the isotropic-nematic coexistence region. Structural arrest and freezing of the orientational texture are found to occur at the same concentration. In addition, various types of orientational textures are equilibrated below the glass transition concentration, ranging from a chiral-nematic texture with a large pitch (of about 100 μm), an X-pattern, and a tightly packed domain texture, consisting of helical domains with a relatively small pitch (of about 10 μm) and twisted boundaries. The dynamics of both particles as well as the texture are discussed, below and above the glass transition. Dynamic light scattering correlation functions exhibit two dynamical modes, where the slow mode is attributed to the elasticity of helical domains. On approach of the glass-transition concentration, the slow mode increases in amplitude, while as the amplitudes of the fast and slow mode become equal at the glass transition. Finally, interesting features of the "transient" behaviors of charged fd-rod glass are shown as the initial caging due to structural arrest, the propagation of flow originating from stress release, and the transition to the final metastable glass state. In addition to the intensity correlation function, power spectra are presented as a function of the waiting time, at the zero-frequency limit that may access to the thermal anomalities in a charged system.

An electric-field induced dynamical state in dispersions of charged colloidal rods

The response of concentrated dispersions of charged colloids to low-frequency electric fields is governed by field-induced inter-colloidal interactions resulting from the polarization of electric double layers and the layer of condensed ions, association and dissociation of condensed ions, as well as hydrodynamic interactions through field-induced electro-osmotic flow. The phases and states that can be formed by such field-induced interactions are an essentially unexplored field of research. Experiments on concentrated suspensions of rod-like colloids (fd-virus particles), within the isotropic-nematic phase coexistence region, showed that a number of phases/states are induced, depending on the field amplitude and frequency [Soft Matter, 2010, 6, 273]. In particular, a dynamical state is found where nematic domains form and melt on a time scale of the order of seconds. We discuss the microscopic origin of this dynamical state, which is attributed to the cyclic, electric-field induced dissociation and association of condensed ions. A semi-quantitative theory is presented for the dynamics of melting and formation of nematic domains, including a model for the field-induced dissociation/association of condensed ions. The resulting equation of motion for the orientational order parameter is solved numerically for parameters complying with the fd-virus system. A limit-cycle is found, with a cycling-time that diverges at the transition line in the field-amplitude versus frequency plane where the dynamical state first appears, in accord with experimental findings.

Chemical modification of M13 bacteriophage and its application in cancer cell imaging

The M13 bacteriophage has been demonstrated to be a robust scaffold for bionanomaterial development. In this paper, we report on the chemical modifications of three kinds of reactive groups, i.e., the amino groups of lysine residues or N-terminal, the carboxylic acid groups of aspartic acid or glutamic acid residues, and the phenol group of tyrosine residues, on M13 surface. The reactivity of each group was identified through conjugation with small fluorescent molecules. Furthermore, the regioselectivity of each reaction was investigated by HPLC-MS-MS. By optimizing the reaction condition, hundreds of fluorescent moieties could be attached to create a highly fluorescent M13 bacteriophage. In addition, cancer cell targeting motifs such as folic acid could also be conjugated onto the M13 surface. Therefore, dual-modified M13 particles with folic acid and fluorescent molecules were synthesized via the selective modification of two kinds of reactive groups. Such dual-modified M13 particles showed very good binding affinity to human KB cancer cells, which demonstrated the potential applications of M13 bacteriophage in bioimaging and drug delivery.

Free energy calculations reveal rotating-ratchet mechanism for DNA supercoil relaxation by topoisomerase IB and its inhibition

Topoisomerases maintain the proper topological state of DNA. Human topoisomerase I removes DNA supercoils by clamping a duplex DNA segment, nicking one strand at a phosphodiester bond, covalently attaching to the 3' end of the nick, and allowing the DNA downstream of the cut to rotate around the intact strand. Using molecular dynamics simulations and umbrella sampling free energy calculations, we show that the rotation of downstream DNA in the grip of the enzyme that brings about release of positive or negative supercoils occurs by thermally assisted diffusion on ratchet energy profiles. The ratchetlike free-energy-versus-rotation profile that we compute provides a model for the function of topoisomerase in which the periodic maxima along the profile modulate the rate of supercoil relaxation, while the minima provide metastable conformational states for DNA religation. The results confirm previous experimental and computational work, and suggest that relaxation of the two types of supercoils involves distinct protein pathways. Additionally, simulations performed with the ternary complex of topoisomerase, DNA, and the chemotherapeutic drug topotecan show important differences in the mechanisms for supercoil relaxation when the drug is present, accounting for the relative values of relaxation rates measured in single-molecule experiments. Good agreement is found between rate constants from tweezer experiments and those calculated from simulations. Evidence is presented for the existence of semiopen states of the protein, which facilitate rotations after the initial one, as a result of biasing the protein into a conformation more favorable to strand rotation than the closed state required for nicking of the DNA.

Effect of coat protein mutations in bacteriophage fd studied by sedimentation analysis

(a) Bacteriophage fd is a filamentous virus that has previously been well characterized. (b) Earlier work using point mutagenesis indicated that a lysine residue at position 48 in the major coat protein plays a crucial role in interacting with the DNA and governing the assembly into an intact virion. (c) In this study the sedimentation properties (sedimentation velocity and equilibrium) of wild-type fd and two mutants substituted at lysine-48 (K48Q and K48A) were compared. (d) Both mutants are similar to each other [M(r) approximately (19.5 +/- 1.5) x 10(6)] but somewhat bigger than the wild-type [M(r) approximately (15.1 +/- 1.5) x 10(6)]. The value for the wild-type is consistent with earlier published values. (e) By combining these data with sedimentation coefficient data, it is possible to compare the contour lengths and relative flexibilities of the mutants with those of the wild-type virion. (f) The mutants are shown hydrodynamically to have larger contour lengths (as also observed by electron microscopy): the approximately 20% difference in values obtained assuming rigid particle hydrodynamics with those obtained from electron microscopy is strongly suggestive of some difference in flexibility between the wild-type and mutants.

Structural characterization of nonionic mixed micelles formed by C12EO6 surfactant and P123 triblock copolymer

A structural characterization of mixed micelles formed in aqueous solution by the PEO-PPO-PEO triblock copolymer P123 and the nonionic surfactant C(12)EO(6) was carried out using various techniques, including ultralow shear viscosimetry, depolarized dynamic light scattering (VH-DLS), depolarized static light scattering (VH-SLS), and small-angle X-ray scattering (SAXS). The sphere-to-rod transition of the mixed micelles was studied in a diluted regime (P123 concentrations ranging from 0.5 to 10 wt %) at C(12)EO(6)/P123 molar ratios of 2.2, 3.2, 6.0, and 11 as well as for the pure C(12)EO(6). The data from VH-SLS and viscosimetry displayed a sharp increase in the intensity and viscosity, respectively, at the sphere-to-rod transition, and the results from the two methods were in accordance. In both techniques, an increased transition temperature with increasing content of C(12)EO(6) (in the molar ratio regime from 2.2 to 11) was observed. SAXS was used as the main technique, and a thorough structural characterization was performed, where indirect Fourier transformation (IFT) and generalized indirect Fourier transformation (GIFT) were employed in the analysis procedure of the SAXS data. The p(r) functions obtained from the IFT (employed at low P123 concentrations, i.e., 1.0 and 2.0 wt %) and GIFT (employed above 2.0 wt %) analyses revealed increased inhomogeneities in the mixed micelles when the molar ratio was increased. This suggested that the C(12)EO(6) organized themselves at the interface between the PPO core and the PEO corona of the P123 micelles, with the C(12) alkyl chain stretching into the hydrophobic core and the EO(6) part residing in the hydrophilic corona. The structure factor parameters obtained with GIFT for a molar ratio of 2.2 at a P123 concentration of 5.0 wt % showed radius values smaller than what was estimated from the p(r) functions. This was explained by an interpenetration of the PEO chains from one mixed micelle into a neighboring one. VH-DLS was performed on the mixed micelles at a temperature 3 degrees C above the transition temperature and at a molar ratio of 2.2. From the analyzed data, the average length L of the rods was estimated to be 102 nm.

Is DNA a worm-like chain in Couette flow? In search of persistence length, a critical review

Persistence length is the foremost measure of DNA flexibility. Its origins lie in polymer theory which was adapted for DNA following the determination of BDNA structure in 1953. There is no single definition of persistence length used, and the links between published definitions are based on assumptions which may, or may not be, clearly stated. DNA flexibility is affected by local ionic strength, solvent environment, bound ligands and intrinsic sequence-dependent flexibility. This article is a review of persistence length providing a mathematical treatment of the relationships between four definitions of persistence length, including: correlation, Kuhn length, bending, and curvature. Persistence length has been measured using various microscopy, force extension and solution methods such as linear dichroism and transient electric birefringence. For each experimental method a model of DNA is required to interpret the data. The importance of understanding the underlying models, along with the assumptions required by each definition to determine a value of persistence length, is highlighted for linear dichroism data, where it transpires that no model is currently available for long DNA or medium to high shear rate experiments.

Hydrodynamic studies on defined heterochromatin fragments support a 30-nm fiber having six nucleosomes per turn

We have compared the physical properties of a 15.51-kb constitutive heterochromatin segment and a 16.17-kb facultative heterochromatin segment that form part of the chicken beta-globin locus. These segments were excised from an avian erythroleukemia cell line by restriction enzyme digestion and released from the nucleus, thus allowing measurement of the sedimentation coefficients by use of calibrated sucrose gradients. A determination of the buoyant density of the cross-linked particle in CsCl led to the total mass of the particles and their frictional coefficients, f. Despite the slight differences in nucleosome density, the measured value of f for both fragments was consistent with a rodlike particle having a diameter of 33-45 nm and a length corresponding to approximately six to seven nucleosomes per 11-nm turn. At higher ionic strengths we found no evidence of any abrupt conformational change, demonstrating that these chromatin fragments released from the nucleus did not assume the more compact conformations recently described for some reconstituted structures.

Unexpected slow near wall dynamics of spherical colloids in a suspension of rods

In this paper, we will show the influence of an additional rodlike component, that is, fd-virus, on the diffusion of spherical polystyrene colloids close to a wall. The sphere diffusivity normal to the wall, D perpendicular, is strongly affected by the presence of the rods, while the effect on the parallel diffusivity, D||, is less pronounced except in the immediate vicinity of the wall. We show that this observation cannot be explained by describing the effect of the rods as a simple mean field depletion potential alone.

Single M13 bacteriophage tethering and stretching

The ability to present biomolecules on the highly organized structure of M13 filamentous bacteriophage is a unique advantage. Where previously this viral template was shown to direct the orientation and nucleation of nanocrystals and materials, here we apply it in the context of single-molecule (SM) biophysics. Genetically engineered constructs were used to display different reactive species at each of the filament ends and along the major capsid, and the resulting hetero-functional particles were shown to consistently tether microscopic beads in solution. With this system, we report the development of a SM assay based on M13 bacteriophage. We also report the quantitative characterization of the biopolymer's elasticity by using an optical trap with nanometer-scale position resolution. Expanding the fluctuating rod limit of the wormlike chain to incorporate enthalpic polymer stretching yielded a model capable of accurately capturing the full range of extensions. Fits of the force-extension measurements gave a mean persistence length of approximately 1,265 nm, lending SM support for a shorter filamentous bacteriophage persistence length than previously thought. Furthermore, a predicted stretching modulus roughly two times that of dsDNA, coupled with the system's linkage versatility and load-bearing capability, makes the M13 template an attractive candidate for use in tethered bead architectures.

Controlling dimensions of polymerized micelles: micelle template versus reaction conditions

The polymerization of elongated micellar structures offers a novel approach to the production of high aspect ratio, water-soluble amphiphilic nanoparticles. Three different surfactants were synthesized consisting of a cationic surfactant of the form (C(X)H(2X+1))trimethylammonium (where X = 14, 16, or 18) and a vinyl-containing counterion, 4-vinylbenzoate. The resulting polymer-surfactant aggregates have been polymerized to produce high aspect ratio nanoparticles which are insensitive to changes in solution conditions. The radius of the initial template is maintained on polymerization, whereas the template length is not. The aggregate radius is varied by changing the length of the surfactant tail, in this case producing aggregates with radii of 1.7, 2.0, or 2.4 nm. Variation of the initiator decomposition half-life, by means of using different initiators and varying temperature, is used to control the aggregate length between 80 and 500 nm. Through the process discussed here, both the radius and length of the aggregates are controlled independently.

Static and dynamic solution properties of monodisperse oligofluorenes

Dynamic light scattering techniques were employed for the study of molecular and collective properties of newly synthesized oligomers (n = 3-7) of the polyfluorene in toluene solutions. At low concentrations, the molar mass, interaction parameter, optical anisotropy and the transport coefficients for translational and rotational diffusion provide a consistent description using a rigid rod model with thickness b = 0.6 nm and length L = nl (l = 0.75 nm). This description is in agreement with the persistence length (6-7 nm) reported for the fluorene polymers. In the non-dilute regime, the estimated concentration for the lyotropic transition further supports the proposed molecular shape and the second slow process in the intermediate scattering function relates to the formation of almost spherical clusters above about 30%.

Physical properties of a genomic condensed chromatin fragment

We have studied the physical properties of a segment of condensed chromatin that lies upstream of the chicken beta-globin locus. This segment can be excised from an avian erythroleukemia cell line by restriction enzyme digestion and released from the nucleus as an essentially homogeneous fragment about 15.5 kbp long. Because of this homogeneity we could measure its sedimentation coefficient quite accurately by a combination of sucrose gradient and analytical ultracentrifugation. By measuring additionally the buoyant density of the cross-linked particle in CsCl we could deduce the total mass of the particle, hence its frictional coefficient, f, directly related to its shape. The measured value of f is consistent with a rod-like particle of the approximate length and diameter proposed earlier for the 30 nm chromatin fiber. The method is generally applicable to homogeneous particles of unique sequence at genomic abundance.

Analysis of the intrinsic bend in the M13 origin of replication by atomic force microscopy

Atomic force microscopy (AFM) has been used to image a 471-bp bent DNA restriction fragment derived from the M13 origin of replication in plasmid LITMUS 28, and a 476-bp normal, unbent fragment from plasmid pUC19. The most probable angle of curvature of the 471-bp DNA fragment is 40-50 degrees, in reasonably good agreement with the bend angle determined by transient electric birefringence, 38 degrees +/- 7 degrees. The normal 476-bp DNA fragment exhibited a Gaussian distribution of bend angles centered at 0 degrees, indicating that this fragment does not contain an intrinsic bend. The persistence length, P, was estimated to be 60 +/- 8 and 62 +/- 8 nm for the 471- and 476-bp fragments, respectively, from the observed mean-square end-to-end distances in the AFM images. Since the P-values of the normal and bent fragments are close to each other, the overall flexibility of DNA fragments of this size is only marginally affected by the presence of a stable bend. The close agreement of AFM and transient electric birefringence results validates the suitability of both methods for characterizing DNA bending and flexibility.

DNA persistence length revisited

DNA restriction fragments ranging from 79 to 789 base pairs in length have been characterized by transient electric birefringence (TEB) measurements at various temperatures between 4 and 43 degrees C. The DNA fragments do not contain runs of four or more adenine residues in a row and migrate with normal electrophoretic mobilities in polyacrylamide gels, indicating that they are not intrinsically curved or bent. The low ionic strength buffers used for the measurements contained 1 mM Tris Cl, pH 8.0, EDTA, and variable concentrations of Na(+) or Mg(2+) ions. The rotational relaxation times were obtained by fitting the TEB field-free decay signals with a nonlinear least-squared fitting program; the decay of the birefringence was monoexponential for fragments < or = 241 base pair (bp) in length and multiexponential for larger fragments. The terminal relaxation times, characteristic of the end-over-end rotation of the DNA molecules, were then used to determine the persistence length (p) and hydrodynamic radius (r) of DNA as a function of temperature and ionic strength, using several different hydrodynamic models. The specific values obtained for p and r are model dependent. The wormlike chain model of P. J. Hagerman and B. H. Zimm (Biopolymers 1981, Vol. 20, pp. 1481-1502) combined with the revised Broersma equation (J. Newman et al., Journal of Mol Biol 1997, Vol. 116, pp. 593-606) appears to be the most suitable for describing the flexibility of DNA in low ionic strength solutions. The values of p and r obtained from the global least squares fitting of this equation are independent of DNA length, and the deviations of the individual values from the average are reasonably small. The consensus r value calculated for DNA in various low ionic strength solutions containing 1 mM Tris buffer is 14.7 +/- 0.4 A at 20 degrees C. The consensus p values decrease from 814 approximately 564 A in solutions containing 1 mM Tris buffer plus 0.2-1 mM NaCl and decrease still further to 440 A in solutions containing 0.2 mM Mg(2+) ions. The persistence length exhibits a shallow maximum at 20 degrees C and decreases slowly upon either increasing or decreasing the temperature, regardless of the model used to fit the data. By contrast, the consensus values of the hydrodynamic radius are independent of temperature. The calculated persistence lengths and hydrodynamic radii are compared with other data in the literature.

Metal ion-induced lateral aggregation of filamentous viruses fd and M13

We report a detailed comparison between calculations of inter-filament interactions based on Monte-Carlo simulations and experimental features of lateral aggregation of bacteriophages fd and M13 induced by a number of divalent metal ions. The general findings are consistent with the polyelectrolyte nature of the virus filaments and confirm that the solution electrostatics account for most of the experimental features observed. One particularly interesting discovery is resolubilization for bundles of either fd or M13 viruses when the concentration of the bundle-inducing metal ion Mg(2+) or Ca(2+) is increased to large (>100 mM) values. In the range of Mg(2+) or Ca(2+) concentrations where large bundles of the virus filaments are formed, the optimal attractive interaction energy between the virus filaments is estimated to be on the order of 0.01 kT per net charge on the virus surface when a recent analytical prediction to the experimentally defined conditions of resolubilization is applied. We also observed qualitatively distinct behavior between the alkali-earth metal ions and the divalent transition metal ions in their action on the charged viruses. The understanding of metal ions-induced reversible aggregation based on solution electrostatics may lead to potential applications in molecular biology and medicine.

Applications of fluorescence correlation spectroscopy: measurement of size-mass relationship of native and denatured schizophyllan

Diffusion dynamics of a polysaccharide, schizophyllan has been studied by fluorescence correlation spectroscopy (FCS). Several different sizes of nondenatured and denatured schizophyllan have been labeled with rhodamine 6G in borate buffer. The length of the nondenatured schizophyllan was calculated from FCS data by using the Broersma's relationship for rod-like macromolecules. The obtained length was close to that obtained by atomic force microscopy (AFM) measurements. Denatured schizophyllan possesses a random coil conformation. Its hydrodynamic radius R(h) was measured by FCS. The relationship between R(h) and the molecular mass M has been studied and the scaling relationship R(h)--M(0.59) has been obtained, which is in agreement with the random coil model with excluded volume effect. The persistence length q(denat) of the denatured schizophyllan was determined by Hearst's relationship, to be equal to 5.16 +/- 0.75 (nm). The work demonstrates the utility of FCS method for dynamics investigations of biopolymers especially in diluted regime (concentration lower than 10(-8)M could be measured) where other techniques could not be used.