β‐Peptidic Secondary Structures Fortified and Enforced by Zn2+ Complexation – On the Way to β‐Peptidic Zinc Fingers?

The correlation between β²‐, β³‐, and β^2,3‐amino acid‐residue configuration and stability of helix and hairpin‐turn secondary structures of peptides consisting of homologated proteinogenic amino acids is analyzed (Figs. 1–3). To test the power of Zn²⁺ ions in fortifying and/or enforcing secondary structures of β‐peptides, a β‐decapeptide, 1 , four β‐octapeptides, 2 – 5 , and a β‐hexadecapeptide, 10 , have been devised and synthesized. The design was such that the peptides would a) fold to a 14‐helix ( 1 and 3 ) or a hairpin turn ( 2 and 4 ), or form neither of these two secondary structures (i.e., 5 ), and b) carry the side chains of cysteine and histidine in positions, which will allow Zn²⁺ ions to use their extraordinary affinity for RS^? and the imidazole N‐atoms for stabilizing or destabilizing the intrinsic secondary structures of the peptides. The β‐hexadecapeptide 10 was designed to a) fold to a turn, to which a 14‐helical structure is attached through a β‐dipeptide spacer, and b) contain two cysteine and two histidine side chains for Zn complexation, in order to possibly mimic a Zn‐finger motif. While CD spectra (Figs. 6–8 and 17) and ESI mass spectra (Figs. 9 and 18) are compatible with the expected effects of Zn²⁺ ions in all cases, it was shown by detailed NMR analyses of three of the peptides, i.e., 2, 3, 5 , in the absence and presence of ZnCl₂, that i) β‐peptide 2 forms a hairpin turn in H₂O, even without Zn complexation to the terminal β³hHis and β³hCys side chains (Fig. 11), ii) β‐peptide 3 , which is present as a 14‐helix in MeOH, is forced to a hairpin‐turn structure by Zn complexation in H₂O (Fig. 12), and iii) β‐peptide 5 is poorly ordered in CD₃OH (Fig. 13) and in H₂O (Fig. 14), with far‐remote β³hCys and β³hHis residues, and has a distorted turn structure in the presence of Zn²⁺ ions in H₂O, with proximate terminal Cys and His side chains (Fig. 15).     

Direct numerical simulation of particle transport by hairpin vortices in a laminar boundary layer

The transport of solid particles by coherent wall structures is studied here. This phenomenon is present in numerous environmental and engineering flows. The flow above a wall-mounted hemisphere is used for generating hairpin vortices in a laminar boundary layer in a controlled way. By means of direct numerical simulation (DNS) of the fluid flow and simultaneous Lagrangian tracking of particles, the influence of hairpin vortices on solid particles released in the wake of the obstacle is analyzed.     

The Effect of Fluoro Substitution upon the β‐Hairpin Fold of a β‐Tetrapeptide in Methanol

The importance of β‐peptides lies in their ability to mimic the conformational behavior of α‐peptides, even with a much shorter chain length, and in their resistance to proteases. To investigate the effect of substitution of β‐peptides on their dominant fold, we have carried out a molecular‐dynamics (MD) simulation study of two tetrapeptides, Ac‐(2R,3S)‐β^2,3hVal(αMe)‐(2S)‐β²hPhe‐(R)‐β³hLys‐(2R,3S)‐β^2,3‐Ala(αMe)‐NH₂, differing in the substitution at the C_α of Phe2 (pepF with F, and pepH with H). Three simulations, unrestrained (UNRES), using ³J‐coupling biasing with local elevation in combination with either instantaneous (INS) or time‐averaging (AVE) NOE distance restraining, were carried out for each peptide. In the unrestrained simulations, we find three (pepF) and two (pepH) NOE distance bound violations of maximally 0.22 nm that involve the terminal residues. The restrained simulations match both the NOE distance bounds and ³J‐values derived from experiment. The fluorinated peptide shows a slightly larger conformational variability than the non‐fluorinated one.     

Characteristics and structure of turbulent 3D offset jets

Three-dimensional turbulent offset jets were investigated using a particle image velocimetry technique. The measurements were performed at three different exit Reynolds numbers and for four offset heights. The results in the early region of flow development clearly show significant effects of Reynolds number and offset height on the decay of maximum mean velocity and growth of the shear layer. On the contrary, the decay and spread rates were found to be nearly independent of offset height at larger downstream distances. The decay rates of 1.18 ± 0.03 as well as the spread rates of 0.055 ± 0.001 and 0.250 ± 0.005 obtained, respectively, in the wall-normal and lateral directions fall in the range of values reported in previous studies. The locations of the maximum mean velocities increased nearly linearly with streamwise distance in the self-similar region. Analysis from two-point velocity correlations revealed substantially larger structures in the outer layer and self-similar region than in the inner layer and developing region. It was also observed that the hairpin vortices in the inner regions of the wall jets are inclined at angles of 11.2° ± 0.6°, which are in good agreement with reported values in boundary layer studies.     

Toehold-mediated nonenzymatic amplification circuit on graphene oxide fluorescence switching platform for sensitive and homogeneous microRNA detection

A novel graphene oxide (GO) fluorescence switch-based homogenous system has been developed to solve two problems that are commonly encountered in conventional GO-based biosensors. First, with the assistance of toehold-mediated nonenzymatic amplification (TMNA), the sensitivity of this system greatly surpasses that of previously described GO-based biosensors, which are always limited to the nM range due to the lack of efficient signal amplification. Second, without enzymatic participation in amplification, the unreliability of detection resulting from nonspecific desorption of DNA probes on the GO surface by enzymatic protein can be avoided. Moreover, the interaction mechanism of the double-stranded TMNA products contains several single-stranded toeholds at two ends and GO has also been explored with combinations of atomic force microscopy imaging, zeta potential detection, and fluorescence assays. It has been shown that the hybrids can be anchored to the surface of GO through the end with more unpaired bases, and that the other end, which has weaker interaction with GO, can escape GO adsorption due to the robustness of the central dsDNA structures. We verified this GO fluorescence switch-based detection system by detecting microRNA 21, an overexpressed non-encoding gene in a variety of malignant cells. Rational design of the probes allowed the isothermal nonenzymatic reaction to achieve more than 100-fold amplification efficiency. The detection results showed that our strategy has a detection limit of 10 pM and a detection range of four orders of magnitude.     

A Novel Electrochemical Aptasensor for Carcinoembryonic Antigen Detection Based on Target‐induced Bridge Assembly

The present study describes a novel electrochemical aptasensor for detection of carcinoembryonic antigen (CEA), a key cancer biomarker. The sensing strategy relied on the CEA‐induced bridge assembly, as a physical barrier, on the surface of gold electrode, resulting in a significant increase of the sensor sensitivity. Under optimal conditions, the aptasensing platform showed a wide linear range (3 pg/mL to 40 ng/mL) and a low detection limit (0.9 pg/mL). Some possible interfering materials were also assessed and the results indicated that the designed aptasensor had good specificity toward CEA. The quantitation of CEA in the spiked human serum samples confirmed the reliability and applicability of the electrochemical aptasensor. So, the developed sensing method has a potential application in the clinical diagnosis.     

Contributions of a Surface Hydrophobic Cluster to the Folding and Structural Stability of Ubiquitin

The role of the small exterior hydrophobic cluster (SEHC) in the strand region of the N‐terminal β‐hairpin of ubiquitin on the structural stability and the folding/unfolding kinetics of the protein have been examined. We introduce a Phe→Ala substitution at residue 4 in the strand region of the N‐terminal β‐hairpin of the ubiquitin. A peptide with the same amino acid sequence as the first 21 residues of the mutated ubiquitin has also been synthesized. The F4A mutation unfolds the hairpin structure of the peptide segment without disruption of the turn. The same mutation does not seem to affect the overall structure, but the stability of the mutated full‐length protein decreases by approx. 2 kcal/mol. Kinetically, the entire hairpin structure is implicated in the transition state during folding of the wild type protein. The rate of refolding is retarded by the F4A mutation in ～80% of the protein molecules. The F4A substitution also increases the unfolding rate of the protein by 10 fold. Thus the hydrophobic side‐chain of Phe‐4 not only contributes to the stability of the hairpin, but also to the stability of the entire protein by forming a cluster together with the hydrophobic residues on the C‐terminal strand.     

Hairpin Probe for Sequence-specific Recognition of Double-stranded DNA on Simian Virus 40

Simian virus 40(SV40) is a polyomavirus and can induce a series of different tumors. The recognition of SV40 genome is crucial to tumor diagnosis and gene therapy. Herein, a sensitive and selective colorimetric method for sequence-specific recognition of homopyrimidine·homopurine duplex DNA(dsDNA) of SV40(4424—4440, gp6) was established with a hairpin probe based upon the formation of triplex DNA. Hairpin probe 5'-CCC TAC CCA TTT TTT CTT CTC TTT CCT GGG TAG GGC GGG TTG GG-3'(HP) containing G-rich sequence and 17-bp triplex-forming sequence was used as the signal probe, which was stem-loop structure alone and exhibited low catalytic activity. Upon its binding to the target duplex of SV40, hairpin probe transferred from stem-loop structure to parallel triplex DNA, accompanied by the recovery of catalytic activity of DNAzyme and a sharp increase of absorbance. Under optimum conditions, the absorbance was increased proportionally to the concentration of dsDNA over the range from 500 pmol/L to 40.0 nmol/L with a detection limit of 433 pmol/L. Moreover, satisfied results were obtained when the assay was used to recognize the mismatched sequences.     

Turbulent boundary layer flow with a step change from smooth to rough surface

A direct numerical simulation (DNS) dataset of a turbulent boundary layer (TBL) with a step change from a smooth to a rough surface is analyzed to examine the characteristics of a spatially developing flow. The roughness elements are periodically arranged two-dimensional (2-D) spanwise rods, with the first rod placed 80θ_in downstream from the inlet, where θ_in denotes the inlet momentum thickness. Based on an accurate estimation of relevant parameters, clear evidence for mean flow universality is provided when scaled properly, even for the present roughness configuration, which is believed to have one of the strongest impacts on the flow. Compared to previous studies, it is shown that overshooting behavior is present in the first- and second-order statistics and is locally created either within the cavity or at the leading edge of the roughness depending on the type of statistics and the wall-normal measurement location. Inspection of spatial two-point correlations of the streamwise velocity fluctuations shows a continuous increase of spanwise length scales of structures over the rough wall after the step change at a greater growth rate than that over smooth wall TBL flow. This is expected because spanwise energy spectrum shows presence of much energetic wider structures over the rough wall. Full images of the DNS data are presented to describe not only predominance of hairpin vortices but also a possible spanwise scale growth mechanism via merging over the rough wall.