DNA Liquid Crystals Research Articles

Water structural effects on DNA–DNA interactions and homologous recognition

Comprehending the principles underlying the interaction between DNA molecules in electrolyte solution is of crucial importance for understanding the phenomena of DNA condensation, recognition of homologous genes, and properties of DNA liquid crystals. Although DNA was considered in all its helical complexity over the last two decades, only a primitive, local, electrostatic model of the aqueous solution was considered. The forces acting between DNA molecules however must be influenced by the structure of the liquid separating them. In this paper we make a step towards unravelling earlier neglected effects of water structure on DNA–DNA interactions. We develop a model of DNA interaction accounting for the nonlocal dielectric response of water and of the electrolyte plasma dissolved in it. We focus particularly on the study of the dipolar overscreening effect, which leads to decaying oscillations of the electrostatic potential about DNA, and how it will affect electrostatic energy surfaces as a function of interaxial separation and mutual azimuthal orientation of the parallelly aligned interacting DNAs. We found that going beyond the classical electrostatic description of water (the so-called primitive model) reveals a complex oscillatory interaction surface in space, with many possible metastable configurations. These however vanish rapidly with smearing of the DNA charge distribution, due to dephasing of the oscillatory components of the interaction. This dephasing results in the suppression of oscillation amplitudes and leads to the dominance of non-oscillatory components in spatial dipolar correlations and the Debye screening. These dominant correlation patterns are shown to lead to a substantial enhancement of the difference between the interaction of homologous and nonhomologous DNA sequences, deepening and sharpening the homology recognition well.

DNA liquid crystals with AIE effect toward humidity-indicating biomaterials.

In this study, by fabricating DNA doped with tetraphenylethene-containing ammonium surfactant, the resulting solvent-free DNA ionic complex could undergo a humidity-induced phase change that could be well tracked by the fluorescence signal of the surfactant. Taking advantage of the humidity-induced change in fluorescence, the reported ionic DNA complex could accurately indicate the humidity in real time.

Self‐Assembly of All‐DNA Rods with Controlled Patchiness

AbstractDouble‐stranded DNA (dsDNA) fragments exhibit noncovalent attractive interactions between their tips. It is still unclear how DNA liquid crystal self‐assembly is affected by such blunt‐end attractions. It is demonstrated that stiff dsDNA fragments with moderate aspect ratio can specifically self‐assemble in concentrated aqueous solutions into different types of smectic mesophases on the basis of selectively screening of blunt‐end DNA stacking interactions. To this end, this type of attractions are engineered at the molecular level by constructing DNA duplexes where the attractions between one or both ends are screened by short hairpin caps. All‐DNA bilayer and monolayer smectic‐A type of phases, as well as a columnar phase, can be stabilized by controlling attractions strength. The results imply that the so far elusive smectic‐A in DNA rod‐like liquid crystals is a thermodynamically stable phase. The existence of the bilayer smectic phase is confirmed by Monte‐Carlo simulations of hard cylinders decorated with one attractive terminal site. This work demonstrates that DNA blunt‐ends behave as well‐defined monovalent attractive patches whose strength and position can be potentially precisely tuned, highlighting unique opportunities concerning the stabilization of nonconventional DNA‐based lyotropic liquid crystal phases assembled by all‐DNA patchy particles with arbitrary geometry and composition.

Superhelical DNA liquid crystals from dendrimer-induced DNA compaction.

Electrostatic compaction of double stranded DNA induced by a positively charged poly(amidoamine) (PAMAM) dendrimer of generation four (G4) was found to produce two unique types of DNA mesophases, in which the DNA bent into superhelices packed in a tetragonal or hexagonal lattice. The structure formed at a lower dendrimer charge density was three-dimensionally (3D) ordered, as characterized by the P41212 space group with a 41 screw axis in a tetragonal arrangement, showing that the weakly bent DNA superhelices with a pitch length of ca. 5.0 nm possessed both identical handedness and phase conservation. The 3D ordered structure transformed into a 2D mesophase at a higher dendrimer charge density, wherein the strongly bent superhelices with a pitch length of ca. 4.0 nm organized in a hexagonal lattice without lateral coherence of helical trajectory. The counterion valency of the protonic acid that is used to charge the dendrimer was found to influence the phase diagram. Under a given dendrimer charge density, the complex with a multivalent acid-protonated dendrimer tended to form structures with less curved DNA, attesting that the driving force of charge matching was reduced by increasing the counterion valency of the dendrimer.

DNA Self-Assembly Mediated by Programmable Soft-Patchy Interactions.

Adding shape and interaction anisotropy to a colloidal particle offers exquisitely tunable routes to engineer a rich assortment of complex-architected structures. Inspired by the hierarchical self-assembly concept with block copolymers and DNA liquid crystals and exploiting the unique assembly properties of DNA, we report here the construction and self-assembly of DNA-based soft-patchy anisotropic particles with a high degree of modularity in the system's design. By programmable positioning of thermoresponsive polymeric patches on the backbone of a stiff DNA duplex with linear and star-shaped architecture, we reversibly drive the DNA from a disordered ensemble to a diverse array of long-range ordered multidimensional nanostructures with tunable lattice spacing, ranging from lamellar to bicontinuous double-gyroid and double-diamond cubic morphologies, through the alteration of temperature. Our results demonstrate that the proposed hierarchical self-assembly strategy can be applied to any kind of DNA nanoarchitecture, highlighting the design principles for integration of self-assembly concepts from the physics of liquid crystals, block copolymers, and patchy colloids into the continuously growing interdisciplinary research field of structural DNA nanotechnology.

Elasticity and Viscosity of DNA Liquid Crystals.

Concentrated solutions of blunt-ended DNA oligomer duplexes self-assemble in living polymers and order into lyotropic nematic liquid crystal phase. Using the optical torque provided by three distinct illumination geometries, we induce independent splay, twist, and bend deformations of the DNA nematic and measure the corresponding elastic coefficients K1, K2, and K3, and viscosities ηsplay, ηtwist, and ηbend. We find the viscoelasticity of the system to be remarkably soft, as the viscoelastic coefficients are smaller than in other lyotropic liquid crystals. We find K1 > K3 > K2, in agreement with the elasticity of the nematic phase of flexible polymers, and ηbend > ηsplay > ηtwist a behavior that is nonconventional in the context of chromonic, polymeric, and thermotropic liquid crystals, indicating a possible role of the weakness and reversibility of the DNA aggregates.

Nature-Inspired Emerging Chiral Liquid Crystal Nanostructures: From Molecular Self-Assembly to DNA Mesophase and Nanocolloids.

Liquid crystals (LCs) are omnipresent in living matter, whose chirality is an elegant and distinct feature in certain plant tissues, the cuticles of crabs, beetles, arthropods, and beyond. Taking inspiration from nature, researchers have recently devoted extensive efforts toward developing chiral liquid crystalline materials with self-organized nanostructures and exploring their potential applications in diverse fields ranging from dynamic photonics to energy and safety issues. In this review, an account on the state of the art of emerging chiral liquid crystalline nanostructured materials and their technological applications is provided. First, an overview on the significance of chiral liquid crystalline architectures in various living systems is given. Then, the recent significant progress in different chiral liquid crystalline systems including thermotropic LCs (cholesteric LCs, cubic blue phases, achiral bent-core LCs, etc.) and lyotropic LCs (DNA LCs, nanocellulose LCs, and graphene oxide LCs) is showcased. The review concludes with a perspective on the future scope, opportunities, and challenges in these truly advanced functional soft materials and their promising applications.

Photochemical analysis of structural transitions in DNA liquid crystals reveals differences in spatial structure of DNA molecules organized in liquid crystalline form

The anisotropic shape of DNA molecules allows them to form lyotropic liquid crystals (LCs) at high concentrations. This liquid crystalline arrangement is also found in vivo (e.g., in bacteriophage capsids, bacteria or human sperm nuclei). However, the role of DNA liquid crystalline organization in living organisms still remains an open question. Here we show that in vitro, the DNA spatial structure is significantly changed in mesophases compared to non-organized DNA molecules. DNA LCs were prepared from pBluescript SK (pBSK) plasmid DNA and investigated by photochemical analysis of structural transitions (PhAST). We reveal significant differences in the probability of UV-induced pyrimidine dimer photoproduct formation at multiple loci on the DNA indicative of changes in major groove architecture.

DNA liquid crystals doped with AuAg nanoclusters: One-photon and two-photon imaging

Many essential similarities between the behavior and arrangement of biological structures and liquid crystals can be found. Moreover, some of biomacromolecules, such as DNA, are shown to exhibit lyotropic liquid crystalline phases both in vitro and in vivo. In this study, we used natural DNA concentration condition to form DNA liquid crystal (LC) phases as a simplified in vitro model of DNA self-ordering in cells. Due to the increasing interest in the use of nanoparticles as optical markers, we investigated possible applications of silver-doped gold nanoclusters (AuAgNCs) for one- and two-photon imaging in condensed DNA samples. We studied the influence of NCs doping on the DNA LC properties and the distribution of NCs within the liquid crystalline matrix. Depending on the type of DNA liquid crystalline phase we observed different emission patterns of AuAgNCs correlated with the degree of DNA ordering.

Two-Photon Imaging of 3D Organization of Bimetallic AuAg Nanoclusters in DNA Matrix.

We report on two-photon excitation properties of small silver-doped gold nanoclusters (AuAgNCs) and on their three-dimensional arrangement in a hybrid system composed of DNA liquid crystals (LCs) and AuAgNCs. UV-vis and fluorescence spectroscopy, transmission electron microscopy (TEM), and multiphoton excitation spectroscopy were used to characterize the nanoparticles. We show that AuAgNCs exhibit two-photon excited luminescence (2PL) emission and second-harmonic generation (SHG) and that these properties remain the same in liquid crystalline matrix. The results are described in detail and discussed in the context of possible imaging application of AuAgNC and specific AuAgNCs organization induced by liquid crystalline ordering of DNA molecules.

Non-linear optical measurement of the twist elastic constant in thermotropic and DNA lyotropic chiral nematics

Throughout the whole history of liquid crystals science, the balancing of intrinsic elasticity with coupling to external forces has been the key strategy for most application and investigation. While the coupling of the optical field to the nematic director is at the base of a wealth of thoroughly described optical effects, a significant variety of geometries and materials have not been considered yet. Here we show that by adopting a simple cell geometry and measuring the optically induced birefringence, we can readily extract the twist elastic coefficient K22 of thermotropic and lyotropic chiral nematics (N*). The value of K22 we obtain for chiral doped 5CB thermotropic N* well matches those reported in the literature. With this same strategy, we could determine for the first time K22 of the N* phase of concentrated aqueous solutions of DNA oligomers, bypassing the limitations that so far prevented measuring the elastic constants of this class of liquid crystalline materials. The present study also enlightens the significant nonlinear optical response of DNA liquid crystals.

Controlling the volatility of the written optical state in electrochromic DNA liquid crystals.

Liquid crystals are widely used in displays for portable electronic information display. To broaden their scope for other applications like smart windows and tags, new material properties such as polarizer-free operation and tunable memory of a written state become important. Here, we describe an anhydrous nanoDNA–surfactant thermotropic liquid crystal system, which exhibits distinctive electrically controlled optical absorption, and temperature-dependent memory. In the liquid crystal isotropic phase, electric field-induced colouration and bleaching have a switching time of seconds. Upon transition to the smectic liquid crystal phase, optical memory of the written state is observed for many hours without applied voltage. The reorientation of the DNA–surfactant lamellar layers plays an important role in preventing colour decay. Thereby, the volatility of optoelectronic state can be controlled simply by changing the phase of the material. This research may pave the way for developing a new generation of DNA-based, phase-modulated, photoelectronic devices.

Mechanism for invalid detection of microcantilever-DNA biosensors due to environmental changes

Microcantilever-DNA biosensors can lose recognition signals under specific hybridization conditions; this could be termed as a type of invalid detection. Using a multiscale energy method, this paper presents an alternative mechanism for this invalid detection induced by bio-interactions and environmental changes in temperature and ionic strength. First, a scaling law for the nanoscale thickness of the DNA film, and a mesoscopic empirical potential for bio-interactions in DNA liquid crystal solution, were combined to update a multiscale analytical model revealing the relation between cantilever motion, temperature, ionic strength, elastic properties of multilayered cantilevers, and nanoscopic properties of DNA molecules. Second, we carried out isothermal and non-isothermal experiments for the bending motion during the formation of a self-assembled monolayer of thiolated single-stranded DNA covalently immobilized on the gold-coated side of the cantilevers, and during the subsequent hybridization with the complementary nucleic acid, in order to obtain the relevant model parameters, and also to validate the proposed analytical model. Third, the effects of temperature and ionic strength on the microcantilever deflections were investigated. Numerical results show that the competing interplay among electrostatic force, hydration force, and configurational entropy generates an invalid point of detection at a grafting density of about 0.05 chain nm−2. In the grafting density interval of 0.02–0.05 chain nm−2, the thermal effect induces distortion of signals; in the grafting density interval of 0.05–0.097 chain nm−2, fluctuations in ionic strength make detection fail. These findings will help to design and improve microcantilever-based biosensors with high sensitivity and robustness.

Stabilization of DNA liquid crystals on doping with gold nanorods.

We report on the impact of doping with gold nanorods (NRs) on the formation and stability of DNA liquid crystals (LCs). Cetyl trimethylammonium (CTAB)-stabilized gold NRs were synthesized using the wet chemistry method. Different textures of cholesteric and columnar mesophases, as well as phase transitions, were observed using a polarized light microscope. It was found that liquid crystalline phases formed in the samples were qualitatively the same and the phase appearance sequence was preserved in the samples regardless of the doping. We show that depending on the concentration of gold NRs present in the phase, nanoparticle-doped cholesteric and columnar hexagonal phases existed in wider temperature ranges compared to pure DNA LCs. The potential applications of these liquid crystal-nanoparticle hybrid systems may include the fabrication of new optoelectronic devices and sensors.

A multi-scale model for the analysis of the inhomogeneity of elastic properties of DNA biofilm on microcantilevers

In nanoscale diagnostic systems, inhomogeneity in near-surface systems and flexibility in biostructures greatly influence the mechanical/electrical/thermal properties of biosensors and resultant detection signals. This study focuses on inhomogeneity and flexibility of DNA biofilm and characterizes its local interactions and mechanical properties. First, a flexible cylinder model of DNA chain is employed to capture the local geometric deformation characteristics of DNA molecules on microcantilever. In order to describe the inhomogeneous properties of DNA biofilm at thickness direction, the Strey's empirical formula for mesoscopic DNA liquid crystal theory is improved with the assumption of a net charge distribution in film. The model parameters are obtained by curve fitting with experimental data. Second, the biaxial iso-strain compression of thought experiment and the energy conservation law are used to predict macroscopic effective tangent modulus of DNA biofilm in terms of nanoscopic properties of dsDNA, buffer salt concentration.

Recovery of intact DNA nanostructures after agarose gel–based separation

Recovery of intact DNA nanostructures after agarose gel–based separation

Liquid crystal phases of DNA: Evaluation of DNA organization by two‐photon fluorescence microscopy and polarization analysis

We report on the investigation of the structure of DNA liquid crystal (LC) phases by means of polarization sensitive two-photon microscopy (PSTPM). DNA was stained with fluorescent dyes, an intercalator propidium iodide, or a groove binder Hoechst 3342, and the angular dependence of the intensity of two-photon excited fluorescence emitted by the dye was collected. The local orientation of DNA molecules in cholesteric and columnar LC phases was established on the basis of the relative angle between the transition dipole of the dye and the long axis of DNA helix. Three-dimensional images of the cholesteric phase were obtained making use of the intrinsic 3D resolving ability of two-photon microscopy. We also discuss the influence of dyes on the parameters of DNA LC phases and comment on advantages and limitations of the PSTPM technique in comparison with other LC characterization techniques.

Mechanical properties of double-stranded DNA biolayers immobilized on microcantilever under axial compression

In label-free biodetections based on microcantilever technology, double-stranded DNA (dsDNA) structures form through the linkage between probe single-stranded DNA (ssDNA) molecules immobilized on solid substrates and target ssDNA molecules in solutions. Mechanical/electrical properties of these biolayers are important factors for nanomechanical deflections of microcantilevers. In this paper, the biolayer immobilized on microcantilever is treated as a bar with a macroscopic elastic modulus on the basis of continuum mechanics viewpoints. In consideration of hydration force, screened electrostatic repulsion and conformational fluctuation in biolayers, load-deformation curves of dsDNA biolayers under axial compression are depicted with the help of the energy conservation law and a mesoscopic free energy presented by Strey et al. (1997, 1999) [Strey, H.H., Parsegian, V.A., Podgornik, R., 1997. Equation of state for DNA liquid crystals: fluctuation enhanced electrostatic double layer repulsion. Physical Review Letters 78, 895–898; Strey, H.H., Parsegian, V.A., Podgornik, R., 1999. Equation of state for polymer liquid crystals: theory and experiment. Physical Review E 59, 999–1008] from a liquid crystal theory. And the analytical relation between macroscopic Young's modulus of biolayers and nanoscopic geometrical properties of dsDNA, packing density, buffer salt solution concentration, etc. is also formulated.

An energy model for nanomechanical deflection of cantilever-DNA chip

Nanomechanical behavior of cantilever-DNA chip in label-free biodetection is investigated by the energy method. First, using an equation of state for DNA liquid crystals and an alternative two-variable model for laminated cantilever beams, a relationship between chip energy and some factors, such as nanogeometrical, physical, chemical characteristics of DNA molecules, microscopical geometric dimension, macroscopical mechanical properties of chip, etc., is formulated in consideration of electrostatic energy, hydration energy and configurational fluctuations of DNA layer as well as mechanical energy of chip. Second, theoretical predictions of nanomechanical deflection of DNA chip by the minimum principle of energy are compared with experimental data in Wu's experiments. Third, the influence of stochastic interchain distances and stochastic elastic modulus on chip deflection is investigated. The validity of the simplified two-layer-beam model is also studied. Numerical results show that chip deflection enhances with the increase in length of DNA chains, and the interchain distances should be carefully controlled no less than 4 nm during the process of probe molecules self-assembly.

Electrostatically driven self-assembly of hybrid elastin–DNA liquid crystals

Self-assembled, hybrid liquid crystals of elastin-like peptides complexed with DNA exhibit inverse temperature-transition behavior and demonstrate functional materials design strategies.