Eukaryotic genomes are packaged into nucleosome particles that occlude the DNA from interacting with most DNA binding proteins. Nucleosomes have higher affinity for particular DNA sequences, reflecting the ability of the sequence to bend sharply, as required by the nucleosome structure. However, it is not known whether these sequence preferences have a significant influence on nucleosome position in vivo, and thus regulate the access of other proteins to DNA. Here we isolated nucleosome-bound sequences at high resolution from yeast and used these sequences in a new computational approach to construct and validate experimentally a nucleosome–DNA interaction model, and to predict the genome-wide organization of nucleosomes. Our results demonstrate that genomes encode an intrinsic nucleosome organization and that this intrinsic organization can explain ∼50% of the in vivo nucleosome positions. This nucleosome positioning code may facilitate specific chromosome functions including transcription factor binding, transcription initiation, and even remodelling of the nucleosomes themselves.

http://absimage.aps.org/image/MAR08/MWS_MAR08-2008-020581.pdf

The Genomic Code for Nucleosome Positioning

Soft robots are primarily composed of easily deformable matter such as fluids, gels, and elastomers that match the elastic and rheological properties of biological tissue and organs. Like an octopus squeezing through a narrow opening or a caterpillar rolling through uneven terrain, a soft robot must adapt its shape and locomotion strategy for a broad range of tasks, obstacles, and environmental conditions. This emerging class of elastically soft, versatile, and biologically inspired machines represents an exciting and highly interdisciplinary paradigm in engineering that could revolutionize the role of robotics in healthcare, field exploration, and cooperative human assistance.

Soft Robotics: A Perspective—Current Trends and Prospects for the Future

This review comprises a detailed survey of ongoing methodologies for soft actuators, highlighting approaches suitable for nanometer- to centimeter-scale robotic applications. Soft robots present a special design challenge in that their actuation and sensing mechanisms are often highly integrated with the robot body and overall functionality. When less than a centimeter, they belong to an even more special subcategory of robots or devices, in that they often lack on-board power, sensing, computation, and control. Soft, active materials are particularly well suited for this task, with a wide range of stimulants and a number of impressive examples, demonstrating large deformations, high motion complexities, and varied multifunctionality. Recent research includes both the development of new materials and composites, as well as novel implementations leveraging the unique properties of soft materials.

Soft Actuators for Small-Scale Robotics.

Fluorescent nanodiamond is a new nanomaterial that possesses several useful properties, including good biocompatibility1, excellent photostability1,2 and facile surface functionalizability2,3. Moreover, when excited by a laser, defect centres within the nanodiamond emit photons that are capable of penetrating tissue, making them well suited for biological imaging applications1,2,4. Here, we show that bright fluorescent nanodiamonds can be produced in large quantities by irradiating synthetic diamond nanocrystallites with helium ions. The fluorescence is sufficiently bright and stable to allow three-dimensional tracking of a single particle within the cell by means of either one- or two-photon-excited fluorescence microscopy. The excellent photophysical characteristics are maintained for particles as small as 25 nm, suggesting that fluorescent nanodiamond is an ideal probe for long-term tracking and imaging in vivo, with good temporal and spatial resolution.

Mass production and dynamic imaging of fluorescent nanodiamonds

Directional arrays of branched microscopic setae constitute a dry adhesive on the toes of pad-bearing geckos, nature's supreme climbers. Geckos are easily and rapidly able to detach their toes as they climb. There are two known mechanisms of detachment: (1) on the microscale, the seta detaches when the shaft reaches a critical angle with the substrate, and (2) on the macroscale, geckos hyperextend their toes, apparently peeling like tape. This raises the question of how geckos prevent detachment while inverted on the ceiling, where body weight should cause toes to peel and setal angles to increase. Geckos use opposing feet and toes while inverted, possibly to maintain shear forces that prevent detachment of setae or peeling of toes. If detachment occurs by macroscale peeling of toes, the peel angle should monotonically decrease with applied force. In contrast, if adhesive force is limited by microscale detachment of setae at a critical angle, the toe detachment angle should be independent of applied force. We tested the hypothesis that adhesion is increased by shear force in isolated setal arrays and live gecko toes. We also tested the corollary hypotheses that (1) adhesion in toes and arrays is limited as on the microscale by a critical angle, or (2) on the macroscale by adhesive strength as predicted for adhesive tapes. We found that adhesion depended directly on shear force, and was independent of detachment angle. Therefore we reject the hypothesis that gecko toes peel like tape. The linear relation between adhesion and shear force is consistent with a critical angle of release in live gecko toes and isolated setal arrays, and also with our prior observations of single setae. We introduced a new model, frictional adhesion, for gecko pad attachment and compared it to existing models of adhesive contacts. In an analysis of clinging stability of a gecko on an inclined plane each adhesive model predicted a different force control strategy. The frictional adhesion model provides an explanation for the very low detachment forces observed in climbing geckos that does not depend on toe peeling.

/pdf/frictional-adhesion-a-new-angle-on-gecko-attachment-4kaek4feu2.pdf

Frictional adhesion: A new angle on gecko attachment.

Conventional pressure sensitive adhesives (PSAs) are fabricated from soft viscoelastic materials that satisfy Dahlquist's criterion for tack with a Young's modulus (E) of 100 kPa or less at room temperature and 1 Hz. In contrast, the adhesive on the toes of geckos is made of beta-keratin, a stiff material with E at least four orders of magnitude greater than the upper limit of Dahlquist's criterion. Therefore, one would not expect a beta-keratin structure to function as a PSA by deforming readily to make intimate molecular contact with a variety of surface profiles. However, since the gecko adhesive is a microstructure in the form of an array of millions of high aspect ratio shafts (setae), the effective elastic modulus (E(eff)) is much lower than E of bulk beta-keratin. In the first test of the E(eff) of a gecko setal adhesive, we measured the forces resulting from deformation of isolated arrays of tokay gecko (Gekko gecko) setae during vertical compression, and during tangential compression at angles of +45 degrees and -45 degrees . We tested the hypothesis that E(eff) of gecko setae falls within Dahlquist's criterion for tack, and evaluated the validity of a model of setae as cantilever beams. Highly linear forces of deformation under all compression conditions support the cantilever model. E(eff) of setal arrays during vertical and +45 degrees compression (along the natural path of drag of the setae) were 83+/-4.0 kPa and 86+/-4.4 kPa (means +/- s.e.m.), respectively. Consistent with the predictions of the cantilever model, setae became significantly stiffer when compressed against the natural path of drag: E(eff) during -45 degrees compression was 110+/-4.7 kPa. Unlike synthetic PSAs, setal arrays act as Hookean elastic solids; setal arrays function as a bed of springs with a directional stiffness, assisting alignment of the adhesive spatular tips with the contact surface during shear loading.

/pdf/effective-elastic-modulus-of-isolated-gecko-setal-arrays-349ymnqlpp.pdf

Effective elastic modulus of isolated gecko setal arrays

The magnetic tweezer is a single-molecule instrument that can apply a constant force to a biomolecule over a range of extensions, and is therefore an ideal tool to study biomolecules and their interactions. However, the video-based tracking inherent to most magnetic single-molecule instruments has traditionally limited the instrumental resolution to a few nanometers, above the length scale of single DNA base-pairs. Here we have introduced superluminescent diode illumination and high-speed camera detection to the magnetic tweezer, with graphics processing unit-accelerated particle tracking for high-speed analysis of video files. We have demonstrated the ability of the high-speed magnetic tweezer to resolve particle position to within 1 A at 100 Hz, and to measure the extension of a 1566 bp DNA with 1 nm precision at 100 Hz in the presence of thermal noise.

A high-speed magnetic tweezer beyond 10,000 frames per second

Although bacterial gyrase and topoisomerase IV have critical interactions with positively supercoiled DNA, little is known about the actions of these enzymes on overwound substrates. Therefore, the abilities of Bacillus anthracis and Escherichia coli gyrase and topoisomerase IV to relax and cleave positively supercoiled DNA were analyzed. Gyrase removed positive supercoils ∼10-fold more rapidly and more processively than it introduced negative supercoils into relaxed DNA. In time-resolved single-molecule measurements, gyrase relaxed overwound DNA with burst rates of ∼100 supercoils per second (average burst size was 6.2 supercoils). Efficient positive supercoil removal required the GyrA-box, which is necessary for DNA wrapping. Topoisomerase IV also was able to distinguish DNA geometry during strand passage and relaxed positively supercoiled substrates ∼3-fold faster than negatively supercoiled molecules. Gyrase maintained lower levels of cleavage complexes with positively supercoiled (compared with negatively supercoiled) DNA, whereas topoisomerase IV generated similar levels with both substrates. Results indicate that gyrase is better suited than topoisomerase IV to safely remove positive supercoils that accumulate ahead of replication forks. They also suggest that the wrapping mechanism of gyrase may have evolved to promote rapid removal of positive supercoils, rather than induction of negative supercoils.

/pdf/activities-of-gyrase-and-topoisomerase-iv-on-positively-3h7oecaun8.pdf

Activities of gyrase and topoisomerase IV on positively supercoiled DNA.

Fluorescent nanodiamonds (FNDs) are promising bio-imaging probes compared with other fluorescent nanomaterials such as quantum dots, dye-doped nanoparticles, and metallic nanoclusters, due to their remarkable optical properties and excellent biocompatibility. Nevertheless, they are prone to aggregation in physiological salt solutions, and modifying their surface to conjugate biologically active agents remains challenging. Here, inspired by the adhesive protein of marine mussels, we demonstrate encapsulation of FNDs within a polydopamine (PDA) shell. These PDA surfaces are readily modified via Michael addition or Schiff base reactions with molecules presenting thiol or nitrogen derivatives. We describe modification of PDA shells by thiol terminated poly(ethylene glycol) (PEG-SH) molecules to enhance colloidal stability and biocompatibility of FNDs. We demonstrate their use as fluorescent probes for cell imaging; we find that PEGylated FNDs are taken up by HeLa cells and mouse bone marrow-derived dendritic cells and exhibit reduced nonspecific membrane adhesion. Furthermore, we demonstrate functionalization with biotin-PEG-SH and perform long-term high-resolution single-molecule fluorescence based tracking measurements of FNDs tethered via streptavidin to individual biotinylated DNA molecules. Our robust polydopamine encapsulation and functionalization strategy presents a facile route to develop FNDs as multifunctional labels, drug delivery vehicles, and targeting agents for biomedical applications.

Andrew Dittmore

Papers

Frictional adhesion: A new angle on gecko attachment.

Effective elastic modulus of isolated gecko setal arrays

A high-speed magnetic tweezer beyond 10,000 frames per second

Activities of gyrase and topoisomerase IV on positively supercoiled DNA.

Polydopamine encapsulation of fluorescent nanodiamonds for biomedical applications.