DNA−Protein Interactions as the Source of Large-Length-Scale Chirality Evident in the Liquid Crystal Behavior of Filamentous Bacteriophages

Dynamics in the Intact fd Bacteriophage Revealed by Pseudo 3D REDOR-Based Magic Angle Spinning NMR

The development of robust NMR methodologies to probe dynamics on the atomic scale is vital to elucidate the close relations between structure, motion, and function in biological systems. Here, we present an automated protocol to measure, using magic-angle spinning NMR, the effective 13C-15N dipolar coupling constants between multiple spin pairs simultaneously with high accuracy. We use the experimental dipolar coupling constants to quantify the order parameters of multiple C-N bonds in the thousands of identical copies of the coat protein in intact fd-Y21M filamentous bacteriophage virus and describe its overall dynamics on the submillisecond time scale. The method is based on combining three pseudo three-dimensional NMR experiments, where a rotational echo double resonance (REDOR) dephasing block, designed to measure internuclear distances, is combined with three complementary 13C-13C mixing schemes: dipolar-assisted rotational resonance, through-bond transfer-based double quantum/single quantum correlation, and radio frequency driven recoupling. These mixing schemes result in highly resolved carbon spectra with correlations that are created by different transfer mechanisms. We show that the helical part of the coat protein undergoes a uniform small (∼30°) amplitude motion, while the N-terminus is highly flexible. In addition, our results suggest that the reduced mobility of lysine sidechains at the C-terminus are a signature of binding to the single stranded DNA.

Cross-domain Chirality Transfer in Self-Assembly of Chiral Block Copolymers

Chirality transfer is essential to acquire helical hierarchical superstructures from the self-assembly of supramolecular materials. By taking advantage of chirality transfers at different length scales through intra-chain and inter-chain chiral interactions, helical phase (H*) can be formed from the self-assembly of chiral block copolymers (BCPs*). In this study, chiral triblock terpolymers, polystyrene-b-poly(ethylene oxide)-b-poly(L-lactide) (PS-PEO-PLLA), and polystyrene-b-poly(4-vinylpyridine)-b-poly(L-lactide) (PS-P4VP-PLLA) are synthesized for self-assembly. For PS-PEO-PLLA with an achiral PEO mid-block that is compatible with PLLA (chiral end-block), H* can be formed while the block length is below a critical value. By contrast, for the one with achiral P4VP mid-block that is incompatible with PLLA, the formation of H* phase would be suppressed regardless of the length of the mid-block, giving cylinder phase. Those results elucidate a new type of chirality transfer across the phase domain that is referred as cross-domain chirality transfer, providing complementary understanding of the chirality transfer at the interface of phase-separated domains.

Biophysical basis of filamentous phage tactoid-mediated antibiotic tolerance in P. aeruginosa

Inoviruses are filamentous phages infecting numerous prokaryotic phyla. Inoviruses can self-assemble into mesoscale structures with liquid-crystalline order, termed tactoids, which protect bacterial cells in Pseudomonas aeruginosa biofilms from antibiotics. Here, we investigate the structural, biophysical, and protective properties of tactoids formed by the P. aeruginosa phage Pf4 and Escherichia coli phage fd. A cryo-EM structure of the capsid from fd revealed distinct biochemical properties compared to Pf4. Fd and Pf4 formed tactoids with different morphologies that arise from differing phage geometries and packing densities, which in turn gave rise to different tactoid emergent properties. Finally, we showed that tactoids formed by either phage protect rod-shaped bacteria from antibiotic treatment, and that direct association with a tactoid is required for protection, demonstrating the formation of a diffusion barrier by the tactoid. This study provides insights into how filamentous molecules protect bacteria from extraneous substances in biofilms and in host-associated infections.

Modulation of Biofilm Mechanics by DNA Structure and Cell Type

Deoxyribonucleic acid (DNA) evolved as a tool for storing and transmitting genetic information within cells, but outside the cell, DNA can also serve as “construction material” present in microbial biofilms or various body fluids, such as cystic fibrosis, sputum, and pus. In the present work, we investigate the mechanics of biofilms formed from Pseudomonas aeruginosa Xen 5, Staphylococcus aureus Xen 30, and Candida albicans 1408 using oscillatory shear rheometry at different levels of compression and recreate these mechanics in systems of entangled DNA and cells. The results show that the compression-stiffening and shear-softening effects observed in biofilms can be reproduced in DNA networks with the addition of an appropriate number of microbial cells. Additionally, we observe that these effects are cell-type dependent. We also identify other mechanisms that may significantly impact the viscoelastic behavior of biofilms, such as the compression-stiffening effect of DNA cross-linking by bivalent cations (Mg²⁺, Ca²⁺, and Cu²⁺) and the stiffness-increasing interactions of P. aeruginosa Xen 5 biofilm with Pf1 bacteriophage produced by P. aeruginosa. This work extends the knowledge of biofilm mechanobiology and demonstrates the possibility of modifying biopolymers toward obtaining the desired biophysical properties.

Spontaneous Alignment of Microtubules Via Tubulin Polymerization in a Narrow Space Under a Temperature Gradient

In this chapter, protocols for spontaneous alignment of microtubules (MTs), such as helices and spherulites, via tubulin polymerization in a narrow space and under a temperature gradient are presented for tubulin solutions and tubulin-polymer mixtures. These protocols provide an easy route for hierarchical MT assembly and may extend our current understanding of cytoskeletal protein self-assembly under dissipative conditions.

Patience is a virtue: self-assembly and physico-chemical properties of cellulose nanocrystal allomorphs

Cellulose nanocrystals (CNCs) are bio-based rod-like nanoparticles with a quickly expanding market. Despite the fact that a variety of production routes and starting cellulose sources are employed, all industrially produced CNCs consist of cellulose I (CNC-I), the native crystalline allomorph of cellulose. Here a comparative study of the physico-chemical properties and liquid crystalline behavior of CNCs produced from cellulose II (CNC-II) and typical CNC-I is reported. CNC-I and CNC-II are isolated by sulfuric acid hydrolysis of cotton and mercerized cotton, respectively. The two allomorphs display similar surface charge densities and ζ-potentials and both have a right-handed twist, but CNC-II have a slightly smaller average length and aspect ratio, and are less hygroscopic. Interestingly, the self-assembly behavior of CNC-I and CNC-II in water is different. Whilst CNC-I forms a chiral nematic phase, CNC-II initially phase separates into an upper isotropic and a lower nematic liquid crystalline phase, before a slow reorganization into a large-pitch chiral nematic texture occurs. This is potentially caused by a combination of factors, including the inferred faster rotational diffusion of CNC-II and the different crystal structures of CNC-I and CNC-II, which are responsible for the presence and absence of a giant dipole moment, respectively.

Helical Nanostructures with Circularly Polarized Luminescence from the Multicomponent Assembly of π-Conjugated N-terminal Amino Acids

Self-assembled structures with circularly polarized luminescence (CPL) have attracted great attention in recent years. π-conjugated N-terminal amino acids with chiral amino acid residues and luminophores are capable of forming self-assembled structures at hierarchical levels, whereby chirality can be transferred to the macroscopic scale with easily modulated CPL properties. Due to the presence of multiple noncovalent binding sites, including hydrogen bonding and aromatic interactions, π-conjugated N-terminal amino acids are emerging core candidates for incorporation into multicomponent self-assembled architectures, accomplishing rational control over supramolecular chirality as well as showing rich chiroptical properties. In this Minireview, we provide a brief summary of multiple-component coassembled systems comprising π-conjugated N-terminal amino acids, small organic species and metal ions. The synthesis of helical structures and manipulation of supramolecular chirality by controlling the self-assembled species is introduced, and the CPL properties of multiple-component π-conjugated N-terminal amino acids are also briefly summarized.

Pf Bacteriophage and Their Impact on Pseudomonas Virulence, Mammalian Immunity, and Chronic Infections

Pf bacteriophage are temperate phages that infect the bacterium Pseudomonas aeruginosa, a major cause of chronic lung infections in cystic fibrosis (CF) and other settings. Pf and other temperate phages have evolved complex, mutualistic relationships with their bacterial hosts that impact both bacterial phenotypes and chronic infection. We and others have reported that Pf phages are a virulence factor that promote the pathogenesis of P. aeruginosa infections in animal models and are associated with worse skin and lung infections in humans. Here we review the biology of Pf phage and what is known about its contributions to pathogenesis and clinical disease. First, we review the structure, genetics, and epidemiology of Pf phage. Next, we address the diverse and surprising ways that Pf phages contribute to P. aeruginosa phenotypes including effects on biofilm formation, antibiotic resistance, and motility. Then, we cover data indicating that Pf phages suppress mammalian immunity at sites of bacterial infection. Finally, we discuss recent literature implicating Pf in chronic P. aeruginosa infections in CF and other settings. Together, these reports suggest that Pf bacteriophage have direct effects on P. aeruginosa infections and that temperate phages are an exciting frontier in microbiology, immunology, and human health.

Compartmentalized host spaces accommodating guest aromatic molecules in a chiral way in a helix-peptide-aromatic framework

A novel host molecular assembly of a free-standing flat nanosheet with compartmentalized spaces was prepared using a bolaamphiphilic peptide composed of two amphiphilic helical peptides and an oligo(naphthaleneethynylene) (ONE) unit at the center of the molecule. The nanosheet possesses void host spaces that can accommodate two mol-equivalent ONE groups to form columns of ONE groups in a right-handed helical way and ONE channels over a long distance. The present molecular system therefore can provide a chiral pore channel for relatively large molecules.

Hierarchical bounding structures for efficient virial computations: Towards a realistic molecular description of cholesterics

We detail the application of bounding volume hierarchies to accelerate second-virial evaluations for arbitrary complex particles interacting through hard and soft finite-range potentials. This procedure, based on the construction of neighbour lists through the combined use of recursive atom-decomposition techniques and binary overlap search schemes, is shown to scale sub-logarithmically with particle resolution in the case of molecular systems with high aspect ratios. Its implementation within an efficient numerical and theoretical framework based on classical density functional theory enables us to investigate the cholesteric self-assembly of a wide range of experimentally relevant particle models. We illustrate the method through the determination of the cholesteric behavior of hard, structurally resolved twisted cuboids, and report quantitative evidence of the long-predicted phase handedness inversion with increasing particle thread angles near the phenomenological threshold value of 45°. Our results further highlight the complex relationship between microscopic structure and helical twisting power in such model systems, which may be attributed to subtle geometric variations of their chiral excluded-volume manifold.

Speeding up Monte Carlo simulation of patchy hard cylinders

The hard cylinder model decorated with attractive patches proved to be very useful recently in studying physical properties of several colloidal systems. Phase diagram, elastic constants and cholesteric properties obtained from computer simulations based on a simple hard cylinder model have been all successfully and quantitatively compared to experimental results. Key to these simulations is an efficient algorithm to check the overlap between hard cylinders. Here, we propose two algorithms to check the hard cylinder overlap and we assess their efficiency through a comparison with an existing method available in the literature and with the well-established algorithm for simulating hard spherocylinders. In addition, we discuss a couple of optimizations for performing computer simulations of patchy anisotropic particles and we estimate the speed-up which they can provide in the case of patchy hard cylinders.

Filamentous Bacteriophage Viruses: Preparation, Magic-Angle Spinning Solid-State NMR Experiments, and Structure Determination

Filamentous bacteriophages are elongated semi-flexible viruses that infect bacteria. They consist of a circular single-stranded DNA (ssDNA) wrapped by a capsid consisting of thousands of copies of a major coat protein subunit. Given the increasing number of discovered phages and the existence of only a handful of structures, the development of methods for phage structure determination is valuable for biophysics and structural virology. In recent years, we developed and applied techniques to elucidate the 3D atomic-resolution structures of intact bacteriophages using experimental magic-angle spinning (MAS) solid-state NMR data. The flexibility in sample preparation - precipitated homogeneous solids - and the fact that ssNMR presents no limitation on the size, weight or morphology of the system under study makes it an ideal approach to study phage systems in detail.In this contribution, we describe approaches to prepare isotopically carbon-13 and nitrogen-15 enriched intact phage samples in high yield and purity, and we present experimental MAS NMR methods to study the capsid secondary and tertiary structure, and the DNA-capsid interface. Protocols for the capsid structure determination using the Rosetta modeling software are provided. Specific examples are given from studies of the M13 and fd filamentous bacteriophage viruses.

Chirality Control and Its Memory at Microphase-Separated Interface of Self-Assembled Chiral Block Copolymers for Nanostructured Chiral Materials

Here, we show the induced chirality of an achiral chromophoric dye as a joint of polylactide-containing chiral block copolymers (BCPs*) driven by self-assembly, giving the achiral dyes preferentially arranged in a one-handed helical array at the microphase-separated interface. This helical arrangement of the achiral dyes can be "memorized" after hydrolysis of the polylactides in the BCPs* and serves as a chiral template for further chirality induction of different achiral dyes, probably through attractive aromatic π-π interactions at the interface, producing nanostructured chiral materials with tunable circular dichroism signals at desired wavelengths.

Structural Effects of Single Mutations in a Filamentous Viral Capsid Across Multiple Length Scales

Filamentous bacteriophage (phage) are single-stranded DNA viruses that infect bacteria. Single-site mutants of fd phage have been studied by magic-angle spinning nuclear magnetic resonance and by small-angle X-ray scattering. Detailed analysis has been performed that provides insight into structural variations on three length scales. The results, analyzed in conjunction with existing literature data, suggest that a single charge mutation on the capsid surface affects direct interviral interactions but not the structure of individual particles or the macroscale organization. On the other hand, a single hydrophobic mutation located at the hydrophobic interface that stabilizes capsid assembly alters the atomic structure of the phage, mainly affecting intersubunit interactions, affects its macroscale organization, that is, the pitch of the cholesteric liquid crystal formed by the particles, but skips the nanoscale hence does not affect direct interparticle interactions. An X-ray scattering under osmotic pressure assay provides the effective linear charge density of the phage and we obtain values of 0.6 Å^-1 and 0.4 Å^-1 for fd and M13 phage, respectively. These values agree with a simple consideration of a single cylinder with protein and DNA charges spread according to the most recent atomic-resolution models of the phage.

Efficient assignment and NMR analysis of an intact virus using sequential side-chain correlations and DNP sensitization

An experimental strategy has been developed to increase the efficiency of dynamic nuclear polarization (DNP) in solid-state NMR studies. The method makes assignments simpler, faster, and more reliable via sequential correlations of both side-chain and Cα resonances. The approach is particularly suited to complex biomolecules and systems with significant chemical-shift degeneracy. It was designed to overcome the spectral congestion and line broadening that occur due to sample freezing at the cryogenic temperatures required for DNP. Nonuniform sampling (NUS) is incorporated to achieve time-efficient collection of multidimensional data. Additionally, fast (25 kHz) magic-angle spinning (MAS) provides optimal sensitivity and resolution. Data collected in <1 wk produced a virtually complete de novo assignment of the coat protein of Pf1 virus. The peak positions and linewidths for samples near 100 K are perturbed relative to those near 273 K. These temperature-induced perturbations are strongly correlated with hydration surfaces.

Filamentous Bacteriophage Promote Biofilm Assembly and Function

Biofilms-communities of bacteria encased in a polymer-rich matrix-confer bacteria with the ability to persist in pathologic host contexts, such as the cystic fibrosis (CF) airways. How bacteria assemble polymers into biofilms is largely unknown. We find that the extracellular matrix produced by Pseudomonas aeruginosa self-assembles into a liquid crystal through entropic interactions between polymers and filamentous Pf bacteriophages, which are long, negatively charged filaments. This liquid crystalline structure enhances biofilm function by increasing adhesion and tolerance to desiccation and antibiotics. Pf bacteriophages are prevalent among P. aeruginosa clinical isolates and were detected in CF sputum. The addition of Pf bacteriophage to sputum polymers or serum was sufficient to drive their rapid assembly into viscous liquid crystals. Fd, a related bacteriophage of Escherichia coli, has similar biofilm-building capabilities. Targeting filamentous bacteriophage or the liquid crystalline organization of the biofilm matrix may represent antibacterial strategies.

Into the polymer brush regime through the "grafting-to" method: densely polymer-grafted rodlike viruses with an unusual nematic liquid crystal behavior

The current work reports an intriguing discovery of how the force exerted on protein complexes like filamentous viruses by the strong interchain repulsion of polymer brushes can induce subtle changes of the constituent subunits at the molecular scale. Such changes transform into the macroscopic rearrangement of the chiral ordering of the rodlike virus in three dimensions. For this, a straightforward "grafting-to" PEGylation method has been developed to densely graft a filamentous virus with poly(ethylene glycol) (PEG). The grafting density is so high that PEG is in the polymer brush regime, resulting in straight and thick rodlike particles with a thin viral backbone. Scission of the densely PEGylated viruses into fragments was observed due to the steric repulsion of the PEG brush, as facilitated by adsorption onto a mica surface. The high grafting density of PEG endows the virus with an isotropic-nematic (I-N) liquid crystal (LC) phase transition that is independent of the ionic strength and the densely PEGylated viruses enter into the nematic LC phase at much lower virus concentrations. Most importantly, while the intact virus and the one grafted with PEG of low grafting density can form a chiral nematic LC phase, the densely PEGylated viruses only form a pure nematic LC phase. This can be traced back to the secondary to tertiary structural change of the major coat protein of the virus, driven by the steric repulsion of the PEG brush. Quantitative parameters characterising the conformation of the grafted PEG derived from the grafting density or the I-N LC transition are elegantly consistent with the theoretical prediction.

Thermoresponsive Chiral to Nonchiral Ordering Transformation in the Nematic Liquid-Crystal Phase of Rodlike Viruses: Turning the Survival Strategy of a Virus into Valuable Material Properties

The current work investigates the thermoresponsive in situ chiral to nonchiral ordering transformation of a rodlike virus in the naturally assembled state-the chiral nematic liquid crystal (CLC) phase. We take this as an elegant example of reconfigurable self-assembly, through which it is possible to realize in situ transformation from one assembled state to another without disrupting the preformed assembly in general or going through a secondary assembling procedure of the disassembled building blocks. The detailed investigation presented here reveals many unique characteristics of the thermoresponsive 3D chiral ordering of rodlike viruses induced by heat stress. The chiral to nonchiral ordering transformation is highly reversible in the temperature range of up to 60 °C and can be repeated many times. There exists a critical temperature around 40 °C which is independent of the ionic strength and virus concentration. Such reconfigurable ordering in the CLC phase stems from the intrinsic structure change of constituent coat proteins without disrupting the structural integrity of the virus, as revealed by three analytical techniques targeting levels ranging from the molecular, secondary conformation of the constituent proteins to the whole single virus, respectively. Such structural flexibility, also termed polymorphism, is relative to the survival strategies of a biological organism such as the virus and can be transformed into very precious material properties. The potential of the virus-based CLC phase as the chiral matrix to regulate chiro-optical properties of gold nanorods is also presented.

Helical alignment inversion of microtubules in accordance with a structural change in their lattice

Giant helical (oriented chiral nematic) alignments of microtubules of nanometer to centimeter lengths are known to form over a temperature gradient during anisotropic spiral propagation via tubulin dimer addition in a capillary cell. Such helical alignments may be modified by the addition of either paclitaxel or dimethyl sulfoxide, which induces a lattice (helical) structural change in the microtubule itself. In this study, we found that the lattice structural change of microtubules brings about inversion of microtubule alignments in the helical ordering. Based on microscopy and scattering data, a mechanism for the helical ordering of microtubules is discussed in relation to their lattice (helical) structure.

Magic-angle spinning NMR of intact bacteriophages: insights into the capsid, DNA and their interface

Bacteriophages are viruses that infect bacteria. They are complex macromolecular assemblies, which are composed of multiple protein subunits that protect genomic material and deliver it to specific hosts. Various biophysical techniques have been used to characterize their structure in order to unravel phage morphogenesis. Yet, most bacteriophages are non-crystalline and have very high molecular weights, in the order of tens of MegaDaltons. Therefore, complete atomic-resolution characterization on such systems that encompass both capsid and DNA is scarce. In this perspective article we demonstrate how magic-angle spinning solid-state NMR has and is used to characterize in detail bacteriophage viruses, including filamentous and icosahedral phage. We discuss the process of sample preparation, spectral assignment of both capsid and DNA and the use of chemical shifts and dipolar couplings to probe the capsid-DNA interface, describe capsid structure and dynamics and extract structural differences between viruses.

Nucleotide-type chemical shift assignment of the encapsulated 40 kbp dsDNA in intact bacteriophage T7 by MAS solid-state NMR

The icosahedral bacteriophage T7 is a 50 MDa double-stranded DNA (dsDNA) virus that infects Escherichia coli. Although there is substantial information on the physical and morphological properties of T7, structural information, based mostly on Raman spectroscopy and cryo-electron microscopy, is limited. Here, we apply the magic-angle spinning (MAS) solid-state NMR (SSNMR) technique to study a uniformly (13)C and (15)N labeled wild-type T7 phage. We describe the details of the large-scale preparation and purification of an isotopically enriched phage sample under fully hydrated conditions, and show a complete (13)C and a near-complete (15)N nucleotide-type specific assignment of the sugar and base moieties in the 40 kbp dsDNA of T7 using two-dimensional (13)C-(13)C and (15)N-(13)C correlation experiments. The chemical shifts are interpreted as reporters of a B-form conformation of the encapsulated dsDNA. While MAS SSNMR was found to be extremely useful in determining the structures of proteins in native-like environments, its application to nucleic acids has lagged behind, leaving a missing (13)C and (15)N chemical shift database. This work therefore expands the (13)C and (15)N database of real B-form DNA systems, and opens routes to characterize more complex nucleic acid systems by SSNMR.

Stimuli responsive chiral liquid crystal phases of phenylboronic acid functionalized rodlike viruses and their interaction with biologically important diols

M13 viruses decorated with phenylboronic acid moieties form pH-responsive chiral LC phases that are regulated by binding with biological diols.

Control of helical handedness in DNA and PNA nanostructures

Helical handedness and the twist and tilt parameters of the base pairs in duplex DNA can be affected by base sequence variation and change in environmental conditions as occurs in the transformation between right-handed B-DNA and left-handed Z-DNA. For duplexes of DNA with oligonucleotide analogs such as peptide nucleic acids (PNAs), less is known about the effects on structure such as the base pair twist and tilt parameters and handedness. However, in PNA:PNA duplexes, the absence of chiral information determining helical handedness allows the relationship between preferred helical handedness and structural design to be manipulated and, therefore, better understood. In this chapter, we report a protocol for switching between B- and Z-DNA:DNA duplexes, and the experimental procedures for obtaining right- or left-handed PNA:PNA duplexes.

Chemical shifts for the unusual DNA structure in Pf1 bacteriophage from dynamic-nuclear-polarization-enhanced solid-state NMR spectroscopy

Solid-state NMR spectra, including dynamic nuclear polarization enhanced 400 MHz spectra acquired at 100 K, as well as non-DNP spectra at a variety of field strengths and at temperatures in the range 213-243 K, have allowed the assignment of the (13)C and (15)N resonances of the unusual DNA structure in the Pf1 virion. The (13)C chemical shifts of C3' and C5', considered to be key reporters of deoxyribose conformation, fall near or beyond the edges of their respective ranges in available databases. The (13)C and (15)N chemical shifts of the DNA bases have above-average values for AC4, AC5, CC5, TC2, and TC5, and below average values for AC8, GC8, and GN2, pointing to an absence of Watson-Crick hydrogen bonding, yet the presence of some type of aromatic ring interaction. Crosspeaks between Tyr40 of the coat protein and several DNA atoms suggest that Tyr40 is involved in this ring interaction. In addition, these crosspeak resonances and several deoxyribose resonances are multiply split, presumably through the effects of ordered but differing interactions between capsid protein subunits and each type of nucleotide in each of the two DNA strands. Overall, these observations characterize and support the DNA model proposed by Liu and Day and refined by Tsuboi et al., which calls for the most highly stretched and twisted naturally occurring DNA yet encountered.

Right-handed double-helix ultrashort DNA yields chiral nematic phases with both right- and left-handed director twist

Concentrated solutions of duplex-forming DNA oligomers organize into various mesophases among which is the nematic (N(∗)), which exhibits a macroscopic chiral helical precession of molecular orientation because of the chirality of the DNA molecule. Using a quantitative analysis of the transmission spectra in polarized optical microscopy, we have determined the handedness and pitch of this chiral nematic helix for a large number of sequences ranging from 8 to 20 bases. The B-DNA molecule exhibits a right-handed molecular double-helix structure that, for long molecules, always yields N(∗) phases with left-handed pitch in the μm range. We report here that ultrashort oligomeric duplexes show an extremely diverse behavior, with both left- and right-handed N(∗) helices and pitches ranging from macroscopic down to 0.3 μm. The behavior depends on the length and the sequence of the oligomers, and on the nature of the end-to-end interactions between helices. In particular, the N(∗) handedness strongly correlates with the oligomer length and concentration. Right-handed phases are found only for oligomers shorter than 14 base pairs, and for the sequences having the transition to the N(∗) phase at concentration larger than 620 mg/mL. Our findings indicate that in short DNA, the intermolecular double-helical interactions switch the preferred liquid crystal handedness when the columns of stacked duplexes are forced at high concentrations to separations comparable to the DNA double-helix pitch, a regime still to be theoretically described.

Intersubunit hydrophobic interactions in Pf1 filamentous phage

Magic angle spinning solid-state NMR has been used to study the structural changes in the Pf1 filamentous bacteriophage, which occur near 10 °C. Comparisons of NMR spectra recorded above and below 10 °C reveal reversible perturbations in many NMR chemical shifts, most of which are assigned to atoms of hydrophobic side chains of the 46-residue subunit. The changes mainly involve groups located in patches on the interfaces between neighboring capsid subunits. The observations show that the transition adjusts the hydrophobic interfaces between fairly rigid subunits. The low temperature form has been generally more amenable to structure determination; spin diffusion experiments on this form revealed unambiguous contacts between side chains of neighboring subunits. These contacts are important constraints for structure modeling.

Charge reversal of the rodlike colloidal fd virus through surface chemical modification

There is increasing interest in the use of viruses as model systems for fundamental research and as templates for nanomaterials. In this work, the rodlike fd virus was subjected to chemical modifications targeting different solvent-exposed functional groups in order to tune its surface properties, especially reversing the surface charge from negative to positive. The carboxyl groups of fd were coupled with different kinds of organic amines by carbodiimide chemistry, resulting in modified viruses that are positively charged over a wide range of pH. Care was taken to minimize intervirus cross linking, which often occurs because of such modifications. The surface amino groups were also grafted with poly(ethylene glycol) (PEG) end-functionalized with an active succinimidyl ester in order to introduce a steric stabilization effect. By combining charge reversal with PEG grafting, a reversible attraction between positively and negatively charged PEG-grafted fd viruses could be realized, which was tuned by the ionic strength of the solution. In addition, a charge-reversed fd virus forms only a pure nematic phase in contrast to the cholesteric phase of the wild type. These modified viruses might be used as model systems in soft condensed matter physics, for example, in the study of polyelectrolyte complexes or lyotropic liquid-crystalline phase behavior.

Bacteriophage Bundles with Pre-Aligned Ca Initiate the Oriented Nucleation and Growth of Hydroxylapatite

Inorganic ions may direct the self-assembly of biomacromolecules into nanostructures which can further be used as a reactant and matrix for nanomaterials synthesis and assembly. Here we use bone mineral and filamentous bacteriophage as a model to demonstrate this concept. Divalent calcium ions are found to trigger the electrostatic self-assembly of anionic nanofiber-like bacteriophages into bundle structures where calcium ions are pre-organized between bacteriophage nanofibers. The resultant Ca(2+)-bacteriophage bundles can be separated and purified from the aqueous solution. The nanostructures of the bundles are verified by zeta potential analysis, small angle x-ray scattering and transmission electron microscopy. Because of the transcription of the bacteriophage chiral surface to the periodic alignment of pre-loaded Ca(2+), the Ca(2+)-bacteriphage bundles can serve as both Ca sources and biotemplates to initiate the oriented nucleation and growth of nanocrystalline hydroxyapatite in phosphate solution or in simulated body fluid. This work provides new insights into biomineralization and represents a new approach to the fabrication of biomolecular-inorganic hybrid layered nanostructures.

Direct measurement of the twist penetration length in a single smectic A layer of colloidal virus particles

In the 1970s, deGennes discussed the fundamental geometry of smectic liquid crystals and established an analogy between the smectic A phase and superconductors. It follows that smectic layers expel twist deformations in the same way that superconductors expel magnetic field. We make a direct observation of the penetration of twist at the edge of a single isolated smectic A layer composed of chiral fd virus particles subjected to a depletion interaction. Using the LC-PolScope, we make quantitative measurements of the spatial dependence of the birefringence due to molecular tilt near the layer edges. We match data to theory for the molecular tilt penetration profile and determine the twist penetration length for this system.

Braided bundles and compact coils: the structure and thermodynamics of hexagonally packed chiral filament assemblies

Molecular chirality frustrates the two-dimensional assembly of filamentous molecules, a fact that reflects the generic impossibility of imposing a global twisting of layered materials. We explore the consequences of this frustration for hexagonally ordered assemblies of chiral filaments that are finite in lateral dimension. Specifically, we employ a continuum-elastic description of cylindrical bundles of filaments, allowing us to consider the most general resistance to and preference for chiral ordering of the assembly. We explore two distinct mechanisms by which chirality at the molecular scale of the filament frustrates the assembly into aggregates. In the first, chiral interactions between filaments impart an overall twisting of filaments around the central axis of the bundle. In the second, we consider filaments that are inherently helical in structure, imparting a writhing geometry to the central axis. For both mechanisms, we find that a thermodynamically stable state of dispersed bundles of finite width appears close to but below the point of bulk filament condensation. The range of thermodynamic stability of dispersed bundles is sensitive only to the elastic cost and preference for chiral filament packing. The self-limited assembly of chiral filaments has particular implications for a large class of biological molecules--DNA, filamentous proteins, viruses, and bacterial flagella--which are universally chiral and are observed to form compact bundles under a broad range of conditions.

Reversible gelation of rod-like viruses grafted with thermoresponsive polymers

The synthesis and selected macroscopic properties of a new model system consisting of poly(N-isopropylacrylamide) (PNIPAM)-coated rod-like fd virus particles are presented. The sticky rod-like colloids can be used to study effect of particle shape on gelation transition, the structure and viscoelasticity of isotropic and nematic gels, and to make both open isotropic as well as ordered nematic particle networks. This model system of rod-like colloids, for which the strength of attraction between the particles is tunable, is obtained by chemically grafting highly monodisperse rod-like fd virus particles with thermoresponsive polymers, e.g. PNIPAM. At room temperature, suspensions of the resulting hybrid PNIPAM-fd are fluid sols which are in isotropic or liquid crystalline phases, depending on the particle concentration and ionic strength. During heating/cooling, the suspensions change reversibly between sol and gel state near a critical temperature of approximately 32 degrees C, close to the lower critical solution temperature of free PNIPAM. The so-called nematic gel, which exhibits a cholesteric feature, can therefore be easily obtained. The gelation behavior of PNIPAM-fd system and the structure of the nematic gel have been characterized by rheology, optical microscopy and small-angle X-ray scattering.

Supramolecular Helical Columns from the Self-Assembly of Chiral Rods

Chiral-bridged rod molecules (CBRs) that consisted of bis(penta-p-phenylene) conjugated to an opened or closed chiral bridging group as a rigid segment and oligoether dendrons as flexible segments were synthesized and characterized. In the bulk state, both molecules self-assemble into a hexagonal columnar structure, as confirmed by X-ray scatterings and transmission electron microscopy (TEM) observations. Interestingly, these structures display opposite Cotton effects in the chromophore of the aromatic unit in spite of the same chirality (R,R) of the chiral bridging groups. The molecules were observed to self-assemble into cylindrical micellar aggregates in aqueous solution, as confirmed by light scattering and TEM investigations, and exhibit intense signals in the circular dichroism (CD) spectra, which are indicative of one-handed helical conformations. The CD spectra of each molecule showed opposite signals to each other, which were similar to those in the bulk. Notably, when the opened CBR was added to a solution of closed CBRs up to a certain concentration, the CD signal of the closed CBR was amplified. This implies that both molecules co-assemble into a one-handed helical structure because the opened chiral bridge is conformationally flexible, which is inverted to co-assemble with the closed CBR. These results demonstrate that small structural modifications of the chiral moiety can transfer the chiral information to a supramolecular assembly in the opposite way.

Conformational indeterminism in protein misfolding: chiral amplification on amyloidogenic pathway of insulin

Unlike folding, protein aggregation is a multipathway, kinetically controlled process yielding different conformations of fibrils. The dynamics and determinism/indeterminism boundaries of misfolded conformations remain obscure. Here we show that, upon vortexing, insulin forms two distinct types of fibrils with opposite local chiral preferences, which manifest in the opposite twists of bound dye, thioflavin T. Occurrence of either type of fibrils in a test tube is only stochastically determined. By acting through an autocatalytic, "chiral amplification"-like mechanism, a random conformational fluctuation triggers conversion of the macroscopic amount of insulin into aggregates with uniformly biased chiral moieties, which bind and twist likewise the achiral dye. Although a convection-driven chiral amplification in achiral systems, which results in randomly distributed excesses of optically active forms, is known, observation of such a phenomenon in misfolded protein built of l-amino acids is unprecedented. The two optical variants of insulin fibrils show distinct morphologies and can propagate their chiral biases upon seeding to nonagitated insulin solutions. Our findings point to a new aspect of topological complexity of protein fibrils: a chiral feature of hierarchically assembled polypeptides, which is partly emancipated from the innate left-handedness of amino acids. Because altering chirality of a molecule changes dramatically its biological activity, the finding may have important ramifications in the context of the structural basis of "amyloid strains".