Formation and healing of micrometer-sized channel networks on highly mobile Au(111) surfaces.

Practical protocols are presented to reproducibly prepare micrometer-sized Au(111) substrates. Au(111) terraces of micrometer dimensions and atomic smoothness were crystallized by flame-annealing vacuum-deposited gold films on glass and on millimetric amorphous gold shots. Gold films and shots that were slowly cooled in a moderately applied stream of nitrogen gas exhibited large and stable crystal surfaces with Au(111) morphologies. Similarly, flame-annealed gold samples cooled with another protocol--in much rougher streams of nitrogen gas--produced morphologically unstable and highly mobile Au(111) layers. Within the first hour after preparation, however, rapid microscale restructuring in the layers produced complex morphologies of hexagonal channel networks and islands that were predominantly triangular. These channeled gold layers fused slowly in the following hours, with velocities of 0.01-0.2 A/s, as quantified by digital image correlation (DIC). Atomically smooth, stable, and predominantly triangular Au(111) terraces on the scale of micrometers were observed approximately 24 h after the sample preparations.

Building programmable jigsaw puzzles with RNA.

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.

Atomic force microscopy imaging and pulling of nucleic acids.

Recent advances in atomic force microscopy (AFM) imaging of nucleic acids include the visualization of DNA and RNA incorporated into devices and patterns, and into structures based on their sequences or sequence recognition. AFM imaging of nuclear structures has contributed to advances in telomere research and to our understanding of nucleosome formation. Highlights of force spectroscopy or pulling of nucleic acids include the use of DNA as a programmable force sensor, and the analysis of RNA flexibility and drug binding to DNA.

Molecular nanosprings in spider capture-silk threads.

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.

Artificial human telomeres from DNA nanocircle templates.

Human telomerase is a reverse-transcriptase enzyme that synthesizes the multikilobase repeating hexamer telomere sequence (TTAGGG)n at the ends of chromosomes. Here we describe a designed approach to mimicry of telomerase, in which synthetic DNA nanocircles act as essentially infinite catalytic templates for efficient synthesis of long telomeres by DNA polymerase enzymes. Results show that the combination of a nanocircle and a DNA polymerase gives a positive telomere-repeat amplification protocol assay result for telomerase activity, and similar to the natural enzyme, it is inhibited by a known telomerase inhibitor. We show that artificial telomeres can be engineered on human chromosomes by this approach. This strategy allows for the preparation of synthetic telomeres for biological and structural study of telomeres and proteins that interact with them, and it raises the possibility of telomere engineering in cells without expression of telomerase itself. Finally, the results provide direct physical support for a recently proposed rolling-circle mechanism for telomerase-independent telomere elongation.

The backbone conformational entropy of protein folding: experimental measures from atomic force microscopy.

The energy dissipated during the atomic force microscopy-based mechanical unfolding and extension of proteins is typically an order of magnitude greater than their folding free energy. The vast majority of the "excess" energy dissipated is thought to arise due to backbone conformational entropy losses as the solvated, random-coil unfolded state is stretched into an extended, low-entropy conformation. We have investigated this hypothesis in light of recent measurements of the energy dissipated during the mechanical unfolding of "polyproteins" comprised of multiple, homogeneous domains. Given the assumption that backbone conformational entropy losses account for the vast majority of the energy dissipated (an assumption supported by numerous lines of experimental evidence), we estimate that approximately 19(+/-2)J/(mol K residue) of entropy is lost during the extension of three mechanically stable beta-sheet polyproteins. If, as suggested by measured peak-to-peak extension distances, pulling proceeds to near completion, this estimate corresponds to the absolute backbone conformational entropy of the unfolded state. As such, it is exceedingly close to previous theoretical and semi-empirical estimates that place this value at approximately 20J/(mol K residue). The estimated backbone conformational entropy lost during the extension of two helical polyproteins, which, in contrast to the mechanically stable beta-sheet polyproteins, rupture at very low applied forces, is three- to sixfold less. Either previous estimates of the backbone conformational entropy are significantly in error, or the reduced mechanical strength of the helical proteins leads to the rupture of a subsequent domain before full extension (and thus complete entropy loss) is achieved.