Nucleic acid liquids

The confluence of recent discoveries of the roles of biomolecular liquids in living systems and modern abilities to precisely synthesize and modify nucleic acids (NAs) has led to a surge of interest in liquid phases of NAs. These phases can be formed primarily from NAs, as driven by basepairing interactions, or from the electrostatic combination (coacervation) of negatively charged NAs and positively charged molecules. Generally, the use of sequence-engineered NAs provides the means to tune microsopic particle properties, and thus imbue specific, customizable behaviors into the resulting liquids. In this way, researchers have used NA liquids to tackle fundamental problems in the physics of finite valence soft materials, and to create liquids with novel structured and/or multi-functional properties. Here, we review this growing field, discussing the theoretical background of NA liquid phase separation, quantitative understanding of liquid material properties, and the broad and growing array of functional demonstrations in these materials. We close with a few comments discussing remaining open questions and challenges in the field.

Controlling the size and adhesion of DNA droplets using surface- enriched DNA molecules

Liquid droplets of biomolecules serve as organizers of the cellular interior and are of interest in biosensing and biomaterials applications. Here, we investigate means to tune the interfacial properties of a model biomolecular liquid consisting of multi-armed DNA 'nanostar' particles. We find that long DNA molecules that have binding affinity for the nanostars are preferentially enriched on the interface of nanostar droplets, thus acting as surfactants. Fluorescent measurements indicate that, in certain conditions, the interfacial density of the surfactant is around 20 per square micron, indicative of a sparse brush-like structure of the long, polymeric DNA. Increasing surfactant concentration leads to decreased droplet size, down to the sub-micron scale, consistent with droplet coalesence being impeded by the disjoining pressure created by the brush-like surfactant layer. Added DNA surfactant also keeps droplets from adhering to both hydrophobic and hydrophilic solid surfaces, apparently due to this same disjoining effect of the surfactant layer. We thus demonstrate control of the size and adhesive properties of droplets of a biomolecular liquid, with implications for basic biophysical understanding of such droplets, as well as for their applied use.

Dynamical Approach to the Jamming Problem

A simple dynamical model, biased random organization (BRO), appears to produce configurations known as random close packing (RCP) as BRO's densest critical point in dimension d=3. We conjecture that BRO likewise produces RCP in any dimension; if so, then RCP does not exist in d=1-2 (where BRO dynamics lead to crystalline order). In d=3-5, BRO produces isostatic configurations and previously estimated RCP volume fractions 0.64, 0.46, and 0.30, respectively. For all investigated dimensions (d=2-5), we find that BRO belongs to the Manna universality class of dynamical phase transitions by measuring critical exponents associated with the steady-state activity and the long-range density fluctuations. Additionally, BRO's distribution of near contacts (gaps) displays behavior consistent with the infinite-dimensional theoretical treatment of RCP when d≥4. The association of BRO's densest critical configurations with random close packing implies that RCP's upper-critical dimension is consistent with the Manna class d_{uc}=4.

Vacuole dynamics and popping-based motility in liquid droplets of DNA

Liquid droplets of biomolecules play key roles in organizing cellular behavior, and are also technologically relevant, yet physical studies of dynamic processes of such droplets have generally been lacking. Here, we investigate and quantify the dynamics of formation of dilute internal inclusions, i.e., vacuoles, within a model system consisting of liquid droplets of DNA 'nanostar' particles. When acted upon by DNA-cleaving restriction enzymes, these DNA droplets exhibit cycles of appearance, growth, and bursting of internal vacuoles. Analysis of vacuole growth shows their radius increases linearly in time. Further, vacuoles pop upon reaching the droplet interface, leading to droplet motion driven by the osmotic pressure of restriction fragments captured in the vacuole. We develop a model that accounts for the linear nature of vacuole growth, and the pressures associated with motility, by describing the dynamics of diffusing restriction fragments. The results illustrate the complex non-equilibrium dynamics possible in biomolecular condensates.

Random Close Packing as a Dynamical Phase Transition

Sphere packing is an ancient problem. The densest packing is known to be a face-centered cubic (FCC) crystal, with space-filling fraction ϕ_{FCC}=π/sqrt[18]≈0.74. The densest "random packing," random close packing (RCP), is yet ill defined, although many experiments and simulations agree on a value ϕ_{RCP}≈0.64. We introduce a simple absorbing-state model, biased random organization (BRO), which exhibits a Manna class dynamical phase transition between absorbing and active states that has as its densest critical point ϕ_{c_{max}}≈0.64≈ϕ_{RCP} and, like other Manna class models, is hyperuniform at criticality. The configurations we obtain from BRO appear to be structurally identical to RCP configurations from other protocols. This leads us to conjecture that the highest-density absorbing state for an isotropic biased random organization model produces an ensemble of configurations that characterizes the state conventionally known as RCP.

Hyperuniform Structures Formed by Shearing Colloidal Suspensions

In periodically sheared suspensions there is a dynamical phase transition, characterized by a critical strain amplitude γ_{c}, between an absorbing state where particle trajectories are reversible and an active state where trajectories are chaotic and diffusive. Repulsive nonhydrodynamic interactions between "colliding" particles' surfaces have been proposed as a source of this broken time reversal symmetry. A simple toy model called random organization qualitatively reproduces the dynamical features of this transition. Random organization and other absorbing state models exhibit hyperuniformity, a strong suppression of density fluctuations on long length scales quantified by a structure factor S(q→0)∼q^{α} with α>0, at criticality. Here we show experimentally that the particles in periodically sheared suspensions organize into structures with anisotropic short-range order but isotropic, long-range hyperuniform order when oscillatory shear amplitudes approach γ_{c}.

Optimizing a reconfigurable material via evolutionary computation

Rapid prototyping by combining evolutionary computation with simulations is becoming a powerful tool for solving complex design problems in materials science. This method of optimization operates in a virtual design space that simulates potential material behaviors and after completion needs to be validated by experiment. However, in principle an evolutionary optimizer can also operate on an actual physical structure or laboratory experiment directly, provided the relevant material parameters can be accessed by the optimizer and information about the material's performance can be updated by direct measurements. Here we provide a proof of concept of such direct, physical optimization by showing how a reconfigurable, highly nonlinear material can be tuned to respond to impact. We report on an entirely computer controlled laboratory experiment in which a 6×6 grid of electromagnets creates a magnetic field pattern that tunes the local rigidity of a concentrated suspension of ferrofluid and iron filings. A genetic algorithm is implemented and tasked to find field patterns that minimize the force transmitted through the suspension. Searching within a space of roughly 10^{10} possible configurations, after testing only 1500 independent trials the algorithm identifies an optimized configuration of layered rigid and compliant regions.

Dense suspension splat: monolayer spreading and hole formation after impact

We use experiments and minimal numerical models to investigate the rapidly expanding monolayer formed by the impact of a dense suspension drop against a smooth solid surface. The expansion creates a lacelike pattern of particle clusters separated by particle-free regions. Both the expansion and the development of the spatial inhomogeneity are dominated by particle inertia and, therefore, are robust and insensitive to details of the surface wetting, capillarity, and viscous drag.

Fast imaging technique to study drop impact dynamics of non-Newtonian fluids

In the field of fluid mechanics, many dynamical processes not only occur over a very short time interval but also require high spatial resolution for detailed observation, scenarios that make it challenging to observe with conventional imaging systems. One of these is the drop impact of liquids, which usually happens within one tenth of millisecond. To tackle this challenge, a fast imaging technique is introduced that combines a high-speed camera (capable of up to one million frames per second) with a macro lens with long working distance to bring the spatial resolution of the image down to 10 µm/pixel. The imaging technique enables precise measurement of relevant fluid dynamic quantities, such as the flow field, the spreading distance and the splashing speed, from analysis of the recorded video. To demonstrate the capabilities of this visualization system, the impact dynamics when droplets of non-Newtonian fluids impinge on a flat hard surface are characterized. Two situations are considered: for oxidized liquid metal droplets we focus on the spreading behavior, and for densely packed suspensions we determine the onset of splashing. More generally, the combination of high temporal and spatial imaging resolution introduced here offers advantages for studying fast dynamics across a wide range of microscale phenomena.

Structure-property relationship of anilino-squaraines in organic solar cells

Soluble molecular semiconductors are a promising alternative to semiconducting polymers in the field of organic photovoltaics. Here, three custom-made symmetric 1,3-bis(N,N-alkylated-2,6-dihydroxy-anilino)squaraines containing systematic variations in their molecular structures are compared regarding their applicability as donor materials in bulk-heterojunction solar cells. The terminal substitution pattern of the squaraines is varied from cyclic over linear to branched including a stereogenic center. Single crystal structures are determined, and, in the case of chiral squaraine, unusual formation of stereoisomer co-crystals is revealed. The thin film absorbance spectra show characteristic signatures of H- and J-bands or hint at the formation of tautomers. The general feasibility of these model compounds for photovoltaic applications is studied by light-induced electron spin resonance spectroscopy. The impact of the different molecular substitution patterns on aggregation behavior and, consequently, their optoelectronic solid state properties including charge carrier mobility and finally the solar cell performance are investigated.

Treatment of testicular intraepithelial neoplasia (intratubular germ cell neoplasia unspecified) with local radiotherapy or with platinum-based chemotherapy: a survey of the German Testicular Cancer Study Group

BACKGROUND

The treatment of testicular intraepithelial neoplasia (TIN), the progenitor of testicular germ cell tumours (GCTs), is based on little data.

PATIENTS AND METHODS

Two hundred and twenty-eight GCT patients with contralateral TIN were retrospectively enrolled. Ten had surveillance, 122 radiotherapy to testis with 18-20 Gy, 30 cisplatin-based chemotherapy (two cycles), 51 chemotherapy (three cycles), and 15 carboplatin. The study end point was a malignant event (ME), defined as detection of TIN upon control biopsy or occurrence of a second GCT. The Secondary end point was hypogonadism during follow-up.

RESULTS

Numbers, proportions of ME, and median event-free survival (EFS) times were: radiotherapy N = 3, 2.5%, 11.08 years; chemotherapy (two cycles) N = 15, 50%, 3.0 years; chemotherapy (three cycles) N = 12, 23.5%, 9.83 years; carboplatin N = 10, 66%, 0.9 years; surveillance N = 5, 50%, 7.08 years. EFS is significantly different among the groups. Hypogonadism rates were in radiotherapy patients 30.8%, chemotherapy (two cycles) 13%, chemotherapy (three cycles) 17.8%, carboplatin 40%, surveillance 40%.

CONCLUSIONS

Local radiotherapy is highly efficacious in curing TIN. Chemotherapy is significantly less effective and the cure rates are dose-dependent. Though hypogonadism occurs in one-third of patients, radiotherapy with 20 Gy remains the standard management of TIN.

A putative helical domain in the MalK subunit of the ATP-binding-cassette transport system for maltose of Salmonella typhimurium (MalFGK2) is crucial for interaction with MalF and MalG. A study using the LacK protein of Agrobacterium radiobacter as a tool

The ATP-binding-cassette (ABC) protein LacK of Agrobacterium radiobacter displays high sequence similarity to the MalK subunit of the Salmonella typhimurium maltose-transport system (MalFGK2). We have used LacK as a tool to identify sites of interaction of MalK with the membrane-integral components MalF and MalG. Small amounts of LacK, resulting from the expression of the plasmid-borne lacK gene, proved to be sufficient for partial restoration of growth of a malK strain of S. typhimurium on maltose. LacK failed to substitute for MalK in regulating the expression of maltose-inducible genes but the hybrid complex MalFGLacK2 was sensitive to inducer exclusion. The lacK gene also complemented a ugpC mutant of Escherichia coli to growth on sn-glycerol-3-phosphate as the phosphate source. Partially purified LacK exhibited a spontaneous ATPase activity comparable to that of MalK. A MalK"-'LacK chimeric protein was isolated (by in vivo recombination) in which the N-terminal 140 amino acids of MalK are fused to residues 141-363 of LacK. The protein substituted for MalK in maltose transport considerably better than LacK. Furthermore, random mutagenesis of the plasmid-borne lacK gene yielded three clones that were superior to wild-type lacK in complementing a malK mutation. Single mutations (V114M or L123F) substantially improved the growth of a malK strain on maltose, whereas a double mutation (L123F, S295N) resulted in growth and transport rates that were indistinguishable from those obtained with MalK. In contrast, the introduction of the single change S295N into LacK had no effect but combination with the V114M mutation led to a further twofold increase in transport activity. These results indicate that a putative helical domain in MalK, encompassing residues 89-140, is crucial for a functional, high-affinity interaction with MalF and MalG.

Nucleotide-induced conformational changes of MalK, a bacterial ATP binding cassette transporter protein

Nucleotide-induced structural rearrangements of MalK, the ATP-hydrolyzing component of the ATP binding cassette transporter for maltose from Salmonella typhimurium were investigated by means of analysis of intrinsic tryptophan fluorescence and limited proteolysis. ATP was found to decrease the tryptophan fluorescence of purified MalK by 37 +/- 1%. ADP or adenosine 5'-O-(3-(thio)triphosphate) (ATP gamma S) caused similar quenching while AMP was rather ineffective. Mg2+ ions were not required. Exposure of MalK to increasing concentrations of trypsin and subsequent analysis by SDS-polyacrylamide gel electrophoresis and immunoblotting revealed the formation of three major transiently stable peptide fragments of 24 (T2), 23 (T3), and 20 kDa (T4), respectively. In addition, a minor rapidly degraded fragment of 33 kDa (T1) was observed. However, in the presence of MgATP, fragment T1 as well as a substantial fraction of native MalK were strongly protected against proteolytic attack. Similar protection against the protease was observed in the presence of MgGTP or, to a lesser extent, MgCTP. In contrast, MgADP, ATP in the presence of EDTA, CaATP or nonhydrolyzable nucleotides such as MgATP gamma S or MgAMP-PNP (beta, gamma-imidoadenosine-5'-triphosphate) failed to significantly affect the susceptibility of MalK to the protease. MgATP similarly affected the tryptic digestion pattern of a mutant protein (MalKK42R) that exhibits only a much reduced ATPase activity but has retained the capability to bind nucleotides. N-terminal protein sequence analysis of the peptides revealed cleavage by trypsin at Arg66 (T1), Arg146 (T2), Arg153 (T3), and Arg185 (T4), respectively. These results indicate that (i) nucleotide binding to MalK is accompanied by a global conformational change of the protein; (ii) a very specific interaction occurs with substrates of the MalK-ATPase, resulting in structural changes that involve the helical domain from Arg66 to Arg146; and (iii) the C-terminal half of MalK is rather resistant to proteolysis.

Characterization of site-directed mutations in conserved domains of MalK, a bacterial member of the ATP-binding cassette (ABC) family [corrected]

Site-directed mutagenesis was used to change four amino acid residues (Q82, P152, L179, H192) in the MalK subunit of S. typhimurium maltose transport system which are highly conserved among members of the ATP-binding cassette (ABC) family. Replacement of H192 caused complete failure to complement the transport defect of a malK strain whereas changes of the other residues resulted in reduced or wild-type activity. The purified mutant proteins exhibited ATPase activity comparable to wild-type MalK.