One challenge in supramolecular chemistry is the design of versatile, self-assembling building blocks to attain total control of arrangement of matter at a molecular level. We have achieved reliable prediction and design of the three-dimensional structure of artificial RNA building blocks to generate molecular jigsaw puzzle units called tectosquares. They can be programmed with control over their geometry, topology, directionality, and addressability to algorithmically self-assemble into a variety of complex nanoscopic fabrics with predefined periodic and aperiodic patterns and finite dimensions. This work emphasizes the modular and hierarchical characteristics of RNA by showing that small RNA structural motifs can code the precise topology of large molecular architectures. It demonstrates that fully addressable materials based on RNA can be synthesized and provides insights into self-assembly processes involving large populations of RNA molecules.

Spider capture silk is a natural material that outperforms almost any synthetic material in its combination of strength and elasticity. The structure of this remarkable material is still largely unknown, because spider-silk proteins have not been crystallized. Capture silk is the sticky spiral in the webs of orb-weaving spiders. Here we are investigating specifically the capture spiral threads from Araneus, an ecribellate orb-weaving spider. The major protein of these threads is flagelliform protein, a variety of silk fibroin. We present models for molecular and supramolecular structures of flagelliform protein, derived from amino acid sequences, force spectroscopy (molecular pulling) and stretching of bulk capture web. Pulling on molecules in capture-silk fibres from Araneus has revealed rupture peaks due to sacrificial bonds, characteristic of other self-healing biomaterials. The overall force changes are exponential for both capture-silk molecules and intact strands of capture silk.

Sacrificial bonds and hidden length in structural molecules and composites have been found to greatly increase the fracture toughness of biomaterials by providing a reversible, molecular-scale energy-dissipation mechanism. This mechanism relies on the energy, of order 100 eV, needed to reduce entropy and increase enthalpy as molecular segments are stretched after being released by the breaking of weak bonds, called sacrificial bonds. This energy is relatively large compared to the energy needed to break the polymer backbone, of order a few eV. In many biological cases, the breaking of sacrificial bonds has been found to be reversible, thereby additionally providing a "self-healing" property to the material. Due to the nanoscopic nature of this mechanism, single molecule force spectroscopy using an atomic force microscope has been a useful tool to investigate this mechanism. Especially when investigating natural molecular constructs, force versus distance curves quickly become very complicated. In this work we propose various types of sacrificial bonds, their combination, and how they appear in single molecule force spectroscopy measurements. We find that by close analysis of the force spectroscopy curves, additional information can be obtained about the molecules and their bonds to the native constructs.

We compare the ''long-range hydrophobic forces'' measured (i) in the ''symmetric'' system between two mica surfaces that had been rendered hydrophobic by the adsorption of a double-chained cationic surfactant, and (ii) between one such hydrophobic surface and a hydrophilic surface of bare mica (''asymmetric'' case). In both cases, the forces were purely attractive, stronger than van der Waals, and of long-range, as previously reported, with those of the asymmetric, hydrophobic-hydrophilic system being even stronger and of longer range. Atomic force microscopy images of these surfaces show that the monolayers transform into patchy bilayers when the surfaces are immersed in water, and that the resulting surfaces contain large micrometer-sized regions of positive charges (bilayer) and negative charges (bare mica) while remaining overall neutral. The natural alignment of oppositely charged domains as two such surfaces approach would result in a long-range electrostatic attraction in water, but the short-range, ''truly hydrophobic'' interaction is not explained by these results.forces ͉ hydrophobic ͉ Langmuir-Blodgett films ͉ surfactant monolayers T he hydrophobic interaction is among the most important nonspecific interactions in biological and many colloidal systems. The significant role of the hydrophobic interaction has led to a great deal of study and yet, over 20 years since the first direct measurement of the attraction between two nominally hydrophobic surfaces (1, 2), no single theory is able to account for all observed experimental behavior. One source of confusion in determining the origins of the long-range hydrophobic interaction is the apparent existence of two different force regimes. It has been suggested (3-6) that the measured force between hydrophobic surfaces is in fact a combination of a ''truly hydrophobic'' short-range force (D Ͻ 10 nm) and a longerranged force (D Ͼ 10 nm) due to a mechanism unrelated or only indirectly related to the hydrophobicity of the surfaces. Suggested mechanisms for the long-range attraction include electrostatic charge or correlated dipole-dipole interactions (7-13), water structure (2, 14), phase metastability (15, 16), and preexisting submicroscopic bubbles that bridge the surfaces (17-19). Although there is convincing evidence of bridging nanobubbles between some types of surfaces (18,20), it has become clear that none of these models can explain all of the forces observed between the many different surfaces studied so far.Langmuir-Blodgett (LB)-deposited monolayers of cationic surfactants such as dimethyl-dioctadecyl-ammonium bromide (DODAB) have been used often in the past 25 years to study the hydrophobic interaction (3,15,16,(21)(22)(23), but the data presented in this article indicate that the long-range attraction between such surfaces may not be directly related to their hydrophobicity. In this article, surface forces apparatus (SFA) force measurements and atomic force microscopy (AFM) imaging are combined. Both symmetric (hydrophobic-hydrophobic) and asymmet...

Maytansine is a potent microtubule-targeted compound that induces mitotic arrest and kills tumor cells at subnanomolar concentrations. However, its side effects and lack of tumor specificity have prevented successful clinical use. Recently, antibody-conjugated maytansine derivatives have been developed to overcome these drawbacks. Several conjugates show promising early clinical results. We evaluated the effects on microtubule polymerization and dynamic instability of maytansine and two cellular metabolites (S-methyl-DM1 and S-methyl-DM4) of antibody-maytansinoid conjugates that are potent in cells at picomolar levels and that are active in tumor-bearing mice. Although S-methyl-DM1 and S-methyl-DM4 inhibited polymerization more weakly than maytansine, at 100 nmol/L they suppressed dynamic instability more strongly than maytansine (by 84% and 73%, respectively, compared with 45% for maytansine). However, unlike maytansine, S-methyl-DM1 and S-methyl-DM4 induced tubulin aggregates detectable by electron microscopy at concentrations ≥2 μmol/L, with S-methyl-DM4 showing more extensive aggregate formation than S-methyl-DM1. Both maytansine and S-methyl-DM1 bound to tubulin with similar K D values (0.86 ± 0.2 and 0.93 ± 0.2 μmol/L, respectively). Tritiated S-methyl-DM1 bound to 37 highaffinity sites per microtubule (K D , 0.1 ± 0.05 μmol/L). Thus, S-methyl-DM1 binds to high-affinity sites on microtubules 20-fold more strongly than vinblastine. The high-affinity binding is likely at microtubule ends and is responsible for suppression of microtubule dynamic instability. Also, at higher concentrations, S-methyl-DM1 showed low-affinity binding either to a larger number of sites on microtubules or to sedimentable tubulin aggregates. Overall, the maytansine derivatives that result from cellular metabolism of the antibody conjugates are themselves potent microtubule poisons, interacting with microtubules as effectively as or more effectively than the parent molecule. Mol Cancer Ther; 9(10); 2689-99. ©2010 AACR.

Lubricin (LUB) is a glycoprotein of the synovial cavity of human articular joints, where it serves as an antiadhesive, boundary lubricant, and regulating factor for the cartilage surface. It has been proposed that these properties are related to the presence of a long, extended, heavily glycosylated and highly hydrated mucinous domain in the central part of the LUB molecule. In this work, we show that LUB has a contour length of 220 +/- 30 nm and a persistence length of < or =10 nm. LUB molecules aggregate in oligomers where the protein extremities are linked by disulfide bonds. We have studied the effect of proteolytic digestion by chymotrypsin and removal of the disulfide bonds, both of which mainly affect the N- and C- terminals of the protein, on the adsorption, normal forces, friction (lubrication) forces, and wear of LUB layers adsorbed on smooth, negatively charged mica surfaces, where the protein naturally forms lubricating polymer brush-like layers. After in situ digestion, the surface coverage was drastically reduced, the normal forces were altered, and both the coefficient of friction and the wear were dramatically increased (the COF increased to mu = 1.1-1.9), indicating that the mucinous domain was removed from the surface. Removal of disulfide bonds did not change the surface coverage or the overall features of the normal forces; however, we find an increase in the friction coefficient from mu = 0.02-0.04 to mu = 0.13-1.17 in the pressure regime below 6 atm, which we attribute to a higher affinity of the protein terminals for the surface. The necessary condition for LUB to be a good lubricant is that the protein be adsorbed to the surface via its terminals, leaving the central mucin domain free to form a low-friction, surface-protecting layer. Our results suggest that this "end-anchoring" has to be strong enough to impart the layer a sufficient resistance to shear, but without excessively restricting the conformational freedom of the adsorbed proteins.

Despite its remarkable materials properties, the structure of spider dragline silk has remained unsolved. Results from two probe microscopy techniques provide new insights into the structure of spider dragline silk. A soluble synthetic protein from dragline silk spontaneously forms nanofibers, as observed by atomic force microscopy. These nanofibers have a segmented substructure. The segment length and amino acid sequence are consistent with a slab-like shape for individual silk protein molecules. The height and width of nanofiber segments suggest a stacking pattern of slab-like molecules in each nanofiber segment. This stacking pattern produces nano-crystals in an amorphous matrix, as observed previously by NMR and x-ray diffraction of spider dragline silk. The possible importance of nanofiber formation to native silk production is discussed. Force spectra for single molecules of the silk protein demonstrate that this protein unfolds through a number of rupture events, indicating a modular substructure within single silk protein molecules. A minimal unfolding module size is estimated to be around 14 nm, which corresponds to the extended length of a single repeated module, 38 amino acids long. The structure of this spider silk protein is distinctly different from the structures of other proteins that have been analyzed by single-molecule force spectroscopy, and the force spectra show correspondingly novel features.

Maytansine and its analogues (maytansinoids) are potent microtubule-targeted compounds that inhibit proliferation of cells at mitosis. Antibody-maytansinoid conjugates consisting of maytansinoids (DM1 and DM4) attached to tumor-specific antibodies have shown promising clinical results. To determine the mechanism by which the antibody-DM1 conjugates inhibit cell proliferation, we examined the effects of the cleavable anti-EpCAM-SPP-DM1 and uncleavable anti-EpCAM-SMCC-DM1 conjugates on MCF7 human breast tumor cells. We also examined the effects of the free maytansinoids, maytansine and S-methyl DM1 (a version of DM1 that is stable in cell culture medium), for comparison. Both the conjugates and free maytansinoids potently inhibited MCF7 cell proliferation at nanomolar and subnanomolar concentrations, respectively, by arresting the cells in mitotic prometaphase/metaphase. Arrest occurred in concert with the internalization and intracellular processing of both conjugates under conditions that induced abnormal spindle organization and suppressed microtubule dynamic instability. Microtubule depolymerization occurred only at significantly higher drug concentrations. The results indicate that free maytansinoids, antibody-maytansinoid conjugates, and their metabolites exert their potent antimitotic effects through a common mechanism involving suppression of microtubule dynamic instability.