Information capacity of specific interactions

Specific interactions are a hallmark feature of self-assembly and signal-processing systems in both synthetic and biological settings. Specificity between components may arise from a wide variety of physical and chemical mechanisms in diverse contexts, from DNA hybridization to shape-sensitive depletion interactions. Despite this diversity, all systems that rely on interaction specificity operate under the constraint that increasing the number of distinct components inevitably increases off-target binding. Here we introduce “capacity,” the maximal information encodable using specific interactions, to compare specificity across diverse experimental systems and to compute how specificity changes with physical parameters. Using this framework, we find that “shape” coding of interactions has higher capacity than chemical (“color”) coding because the strength of off-target binding is strongly sublinear in binding-site size for shapes while being linear for colors. We also find that different specificity mechanisms, such as shape and color, can be combined in a synergistic manner, giving a capacity greater than the sum of the parts.Specific interactions between many species of components are the bedrock of biochemical function, allowing signal transduction along complex parallel pathways and self-assembly of multicomponent molecular machines. Inspired by their role in biology, engineered specific interactions have opened up tremendous opportunities in materials synthesis, achieving new morphologies of self-assembled structures with varied and designed functionality. The two major design approaches for programming specific interactions use either chemical specificity or shape complementarity.Chemical specificity is achieved by dividing binding sites into smaller regions, each of which can be given one of A “colors” or unique chemical identities. Sites bind to each other based on the sum of the interactions between corresponding regions. For example, a recent two-color system paints the flat surfaces of three-dimensional polyhedra with hydrophobic and hydrophilic patterns (1) or with a pattern of solder dots (2), allowing polyhedra to stick to each other based on the registry between their surface patterns. Another popular approach uses DNA hybridization, where specific matching of complementary sequences has been used to self-assemble structures purely from DNA strands (3, 4) and from nanoparticles coated with carefully chosen DNA strands (5–9).Shape complementarity uses the shapes of the component surfaces to achieve specific binding, even though the adhesion is via a nonspecific, typically short-range potential. In the synthetic context, shape-based modulation of attractive forces over a large dynamic range was first proposed and experimentally demonstrated for colloidal particles (10, 11), using tunable depletion forces (12, 13). Recent experiments have explored the range of possibilities opened up by such ideas, from lithographically designed planar particles (14) with undulating profile patterns to “Pacman” particles with cavities that exactly match smaller complementary particles (15). The number of possible shapes that can be made using these types of methods depends on fabrication constraints but the possibilities can be quite rich (16, 17). Using only nonspecific surface attraction, experiments have achieved numerous and complex morphologies such as clusters, crystals, glasses, and superlattices (10, 18–21).A further class of programmable specific interactions combines both chemical specificity and shape complementarity. The canonical example is protein-binding interactions (22); the binding interactions between two cognate proteins are specified by their amino acid sequence, which programs binding pockets with complex shape and chemical specificity. Recent efforts (23, 24) aim to rationally design these protein interactions for self-assembly. Because both the shape of the binding pocket and its chemical specificity are determined by the same amino acid sequence, these two features cannot be controlled independently. Other synthetic systems offer the promise of independent control of chemical and shape binding specificity, giving a larger set of possible interactions.These diverse systems achieve specific interactions through disparate physical mechanisms, with different control parameters for tuning binding specificity. However, they must all solve a common problem (25, 26): create a family of N “lock” and “key” pairs that bind well within pairs but avoid off-target binding across pairs (“crosstalk”). Any crosstalk limits the efficacy of the locks and keys. For example, in the context of DNA-based affinities, although there are 4^L unique sequences of length L, the strong off-target binding severely restricts the number that can be productively used. Analogously, for colloidal systems driven by depletion interactions, there can be significant off-target binding due to partial contact. The performance of a system of specific interactions depends acutely on how the system constraints (e.g., number of available bases, fabrication length scale, etc.) limit its ability to avoid crosstalk.In this paper, we develop a general information theory-based framework for quantitatively analyzing specificity in both natural and synthetic systems. We use a metric based on mutual information to derive a bound on the number of different interacting particles that a system can support before crosstalk overwhelms interaction specificity. Increasing the number of nominally distinct pairs beyond this limit cannot increase the effective number of distinguishable species. We compute this information-theoretic “capacity” for different experimental systems of recent interest, including DNA-based affinities and colloidal experiments in shape complementarity. We show that shape-based coding fundamentally results in lower crosstalk and higher capacity than color-based coding. We also find that shape- and color-based coding can be combined synergistically, giving a superadditive capacity that is greater than the sum of the color and shape parts.     

γ-PGA-g-β-CD自组装及其医用纳米涂层材料

以生物大分子γ-聚谷氨酸 (γ-PGA)、β-环糊精 (β-CD)为反应单元,通过酯化反应,制备接枝共聚物 (γ-PGA-g-β-CD),用氢核磁共振(1H-NMR)对共聚物进行结构表征。接着将γ-PGA-g-β-CD在选择性溶剂中进行自组装,形成自组装胶束纳米粒子,利用纳米粒度分析仪及原子力显微镜（AFM）对胶束粒子的粒径和形貌进行表征。最后以γ-PGA-g-β-CD自组装胶束粒子溶液为电解液,结合恒电位电沉积技术,在镁合金表面制备γ-PGA-g-β-CD生物纳米涂层材料,利用傅里叶变换红外光谱（FT-IR）、扫描电子显微镜（SEM）及电化学工作站分别对涂层的化学组分、表面形貌以及电化学腐蚀性能进行表征。研究结果显示：β-CD的接枝率为28%,γ-PGA-g-β-CD自组装胶束粒子的流体动力学直径为(168±5.3) nm,所制备的γ-PGA-g-β-CD生物涂层可降低镁合金的腐蚀速率,具有较好的防护作用。     

Symmetry breaking in self-assembled M4L6 cage complexes

Here we describe the phenomenon of symmetry breaking within a series of M₄L₆ container molecules. These containers were synthesized using planar rigid bis-bidentate ligands based on 2,6-substituted naphthalene, anthracene, or anthraquinone spacers and Fe^II ions. The planarity of the ligand spacer favors a stereochemical configuration in which each cage contains two metal centers of opposite handedness to the other two, which would ordinarily result in an S₄-symmetric, achiral configuration. Reduction of symmetry from S₄ to C₁ is achieved by the spatial offset between each ligand’s pair of binding sites, which breaks the S₄ symmetry axis. Using larger Cd^II or Co^II ions instead of Fe^II resulted, in some cases, in the observation of dynamic motion of the symmetry-breaking ligands in solution. NMR spectra of these dynamic complexes thus reflected apparent S₄ symmetry owing to rapid interconversion between energetically degenerate, enantiomeric C₁-symmetric conformations.     

高分子量聚二茂铁衍生物的性质与应用

综述了近年来高分子量聚二茂铁衍生物性能及应用研究的进展。聚二茂铁衍生物均聚物和嵌段共聚物表现出独特的电、光、磁和氧化不原性质，在材料科学、超分子科学和纳米结构材料方面的应用前景良好。     

Peptide aggregates: a novel model system to study self-assembly of peptides

Ordered aggregates of Val-Leu-Pro-Phe, tetrapeptide 1 , have been found in aqueous solutions. Evidence for the formation of aggregates for the above peptide was obtained by conductometric, pH metric, UV and fluorescence spectroscopic techniques. Values of critical micelle concentration (CMC) for the above peptide obtained by these methods are in good agreement with each other. The formation of organized aggregates of the peptide is favoured upon increasing the temperature (viz. the process of aggregation is endothermic). The aggregation number has been determined at different temperatures. Values of ΔG°_mΔH°_mΔS°_m and ΔC°_p have also been estimated. Binding studies with the 8-anilinonaphthyl sulfonic acid (ANS) and pyrene indicate that the interior of the aggregate is nonpolar. There are two processes with regard to the change of thermodynamical parameters like ΔG°_mΔH°_mΔS°_mΔC°_p aggregation number (N). In the first process (from 5°C to 40°C) the driving force for aggregation seems to be the positive entropy because of water release due to intermolecular association of ionic moieties. The second process (from 40°C and above) is due to intramolecular ionic interaction. The chemical shifts of the amide protons of the peptide have been presented in the light of inter- and intramolecular hydrogen-bond formation, and forces implicated in aggregation for both the first and second processes. © Munksgaard 1995.     

Encapsulated-guest rotation in a self-assembled heterocapsule directed toward a supramolecular gyroscope

The self-assembled heterocapsule 1·2, which is formed by the hydrogen bonds of tetra(4-pyridyl)-cavitand 1 and tetrakis(4-hydroxyphenyl)-cavitand 2, encapsulates 1 molecule of guests such as 1,4-diacetoxybenzene 3a, 1,4-diacetoxy-2,5-dimethylbenzene 3b, 1,4-diacetoxy-2,5-dialkoxybenzenes (3c, OCH₃; 3d, OC₂H₅; 3e, OC₃H₇; 3f, OC₄H₉; 3g, OC₅H₁₁; 3h, OC₆H₁₃; 3i, OC₈H₁₇), 1,4-diacetoxy-2,5-difluorobenzene 4a, and 1,4-diacetoxy-2,3-difluorobenzene 4b. The X-ray crystallographic analysis of 3c@(1·2) showed that the acetoxy groups at the 1,4-positions of 3c are oriented toward the 2 aromatic cavity ends of 1·2 and that 3c can rotate along the long axis of 1·2. Thus, the 1·2 (stator) with the encapsulation guest (rotator) behaves as a supramolecular gyroscope. A variable temperature (VT) ¹H NMR study in CDCl₃ showed that 3a, 3b, 4a, and 4b within 1·2 rotate rapidly even at 218 K, whereas guest rotation is almost inhibited for 3h and 3i even at 323 K. In this respect, 4b with a large dipole moment is a good candidate for the rotator of 1·2. For 3c–3g, the enthalpic (ΔH^‡) and entropic (ΔS^‡) contributions to the free energy of activation (ΔG^‡) for the guest-rotational steric barriers within 1·2 were obtained from Eyring plots based on line-shape analysis of the VT ¹H NMR spectra. The value of ΔG^‡ increased in the order 3c < 3d < 3e < 3f < 3g. Thus, the elongation of the alkoxy chains at the 2,5-positions of 3 puts the brakes on guest rotation within 1·2.     

Discrete stack of an odd number of polarized aromatic compounds revealing the importance of net vs. local dipoles

Three polarized aromatic guest molecules (pyrene-4,5-dione, 1) form a triple-layered stack in the box-shaped cavity of an organic pillared coordination cage in water. The cavity size strictly limits the number of stacked planar guests but does not restrict guest orientation, and thus enables the study of discrete stacks of polarized guests and their preferred conformations. Crystallographic study shows that the guest molecules in the cavity are rotated 120° with respect to each other, canceling the net dipole moment rather than the local dipole moment. The unique conformation of a discrete, triple stack of 1 sharply contrasts to the standard head-to-tail conformation in infinite stacks of 1.     

钛种植体表面原位包裹大鼠骨髓基质细胞的研究

目的探讨钛种植体表面对大鼠骨髓基质细胞（bone marrow stromal cells,BMSCs）进行原位包裹的方法,为钛种植体表面组织工程支架构建提供实验基础。方法采用层层自组装技术在钛种植体表面构建以壳聚糖/海藻酸钠为组分的聚电解质多层膜结构,同时对BMSCs进行原位分层包裹,并通过扫描电镜及激光共聚焦显微镜观察包裹细胞的生长状态。结果扫描电镜及激光共聚焦显微镜观察证实BMSCs被成功包裹于钛种植体表面,并保持良好的生物学活性。结论钛种植体表面可以实现对BMSCs的原位分层包裹。     

Janus nanoparticles: materials,preparation and recent advances in drug delivery

Introduction: The term Janus particles was used to describe particles that are the combination of two distinct sides with differences in chemical nature and/or polarity on each face. Due to the exponential growth of interest on multifunctional nanotechnologies, such anisotropic nanoparticles are promising tools in the field of drug delivery.

Areas covered: The main preparation processes and the materials used have been described first. Then a specific focus has been done on therapeutic and/or diagnostic applications of Janus particles.

Expert opinion: Janus particles are demonstrated as interesting objects with advanced properties that combine features and functionalities of different materials in one single unit. Due to their dual structure, Janus particles are promising candidates for a variety of high-quality applications dealing with drug delivery purposes. Still, the main challenges for the future lie in the development of the preparation of shape-controlled and nano-sized particles with large-scale production processes and approved pharmaceutical excipients.