T-hairpin structure found in the RNA element involved in piRNA biogenesis

PIWI-interacting RNAs (piRNAs) repress transposons to protect the germline genome from DNA damage caused by transposon transposition. In Drosophila, the Traffic jam (Tj) mRNA is consumed to produce piRNA in its 3′ UTR. A cis element located within the 3′-UTR, Tj-cis, is necessary for piRNA biogenesis. In this study, we analyzed the structure of the Tj-cis RNA, a 100 nt RNA corresponding to the Tj-cis element, by the SHAPE and NMR analyses and found that a stable hairpin structure formed in the 5′ half of the Tj-cis RNA. The tertiary structure of the 16 nt stable hairpin was analyzed by NMR, and a novel stem-loop structure, the T-hairpin, was found. In the T-hairpin, four uridine residues are exposed to the solvent, suggesting that this stem loop is the target of Yb protein, a Tudor domain-containing piRNA biogenesis factor. The piRNA biogenesis assay showed that both the T-hairpin and the 3′ half are required for the function of the Tj-cis element, suggesting that both the T-hairpin and the 3′ half are recognized by Yb protein.

A Ratiometric Fluorescent Aptamer Homogeneous Biosensor Based on Hairpin Structure Aptamer for AFB1 Detection

On the basis of aptamer (Apt) with hairpin structure and fluorescence resonance energy transfer (FRET), a ratio fluorescent aptamer homogeneous sensor was prepared for the determination of Aflatoxin B1 (AFB1). Initially, the Apt labeled simultaneously with Cy5, BHQ2, and cDNA labeled with Cy3 were formed a double-stranded DNA through complementary base pairing. The fluorescent aptamer sensor demonstrates a weak fluorescence emission of Cy3 and a high fluorescence emission of Cy5 due to the quenching effect of BHQ2. The double-stranded DNA structure will be disintegrated in the presence of AFB1, resulting the removal of Cy3 and the close of Cy5 with BHQ2. The fluorescence signal of Cy3 and Cy5 were restored and quenched respectively. Thus, the ratio change of FCy3 to FCy5 was used to realized the detection of AFB1 with wider detection range and lower limit of detection (LOD). The response of the optimized protocol for AFB1 detection was wider linear range from 0.05 ng/mL to 100 ng/mL and the LOD was 12.6 pg/mL. The sensor designed in this strategy has the advantages of simple preparation and fast signal response. It has been used for the detection of AFB1 in labeled corn and wine, indicating it had good application potential in practical samples.

Parametric Analysis of the Defected Ground Structure-Based Hairpin Band Pass Filter for VSAT System on Chip Applications

In this study, a three-pole hairpin structure was fabricated on the top of the substrate material and an open loop microstrip structure at the ground to give a modified triple-band BPF with a unique design. A Rogers (RT5880) material with εr = 2.2 and thickness of 1.27mm was used to fabricate the proposed structure. The space between two consecutive hairpin resonators has different distances d1 and d2 with values of 0.2mm and 0.4mm respectively. The proposed filter offers a compact size with low return loss. The equivalent LC circuit of the DGS and hairpin structure is obtained with the Ansys electronic desktop and by using simple circuit analysis. The desired microstrip triple-band BPF operates at the Ku band, resonates at 10.28GHz, 12GHz, and 14.62GHz, while the simulated and experimental results are almost identical. The proposed wideband BPF satisfies the International Telecommunication Union ((ITU) region 3 spectrum requirements. Direct Broadcast Service (DBS) and Fixed Satellite Service (FSS) in transmit mode respectively employ the frequency band 11.41-12.92GHz and 14-14.5GHz.

Research on DNA Nanostructures Based on the Hybrid Chain Reaction for the Assignment Problem

Nanostructures with information processing play an important role in many fields. It is an excellent approach to the application that DNA nanostructures represented by DNA origami molecules combine with the hybrid chain reaction. In this paper, the assignment problem is mapped to a combinatorial graph on the DNA origami substrate. The graph has several modules corresponding to the time efficiency matrix of the assignment problem. The starting chain of the corresponding module is hybridized with the hairpin structure of the starting point, and the corresponding module is opened to emit light. The feasible solution to the problem can be obtained by observing the light-emitting fluorescent numbers of the opened modules. The fluorescent numbers of all the opened modules are added up on the same origami substrate, then different opening methods in different test tubes are compared, and the optimal solution is obtained.

Fast Detection of Chloramphenicol in Raw Milk Using a Hairpin Aptamer-templated Silver Nanoclusters

In this presented work, a facile and efficient method was established for the detection of chloramphenicol (CAP) based on target-induced structure transformation of aptamer. This aptamer DNA with a hairpin structure can coincidentally serve as a template for the synthesis of bright silver nanoclusters (quantum yield 16.36%). The binding of CAP with aptamer DNA could cause the destruction of the hairpin structure, resulting in the quenching of the fluorescence of silver nanoclusters (AgNCs). It costs less than 10 minutes to complete the assay, and excellent sensitivity was achieved with detection limit of 0.052 nmol/L. The selectivity and recovery experiments also demonstrated satisfactory results of this proposed protocol. The method has potential applicability, and provides a new strategy for the development of label-free sensors based on aptamer and AgNCs.

A β-hairpin epitope as novel structural requirement for protein arginine rhamnosylation

For bacterial arginine rhamnosylation, the rhamnosyltransferase EarP specifically recognizes a β-hairpin structure in the acceptor substrate.