Huanhuan Shi

A review: Fabrications, detections and applications of peptide nucleic acids (PNAs) microarray

Peptide nucleic acid (PNA) is a mimic of DNA that shows a high chemical stability and can survive the enzymatic degradation of nucleases and proteases. The superior binding properties of PNA enable the formation of PNA/DNA or PNA/RNA duplex with excellent thermal stability and unique ionic strength effect. The introduction of microarray makes it possible to achieve accurate, high throughput parallel analysis of DNA or RNA with a highly integrated and low reagents consuming device. This powerful tool expands the applications of PNA in genotyping based on single nucleotide polymorphism (SNP) detection, the monitoring of disease-related miRNA expression and pathogen detection. This review paper discusses the fabrications of PNA microarrays through in situ synthesis strategy or spotting method by automatic devices, the various detection methods for the microarray-based hybridization and the current applications of PNA microarrays.

Diketopyrrolopyrrole Amphiphile-Based Micelle-Like Fluorescent Nanoparticles for Selective and Sensitive Detection of Mercury(II) Ions in Water

A technique for encapsulating fluorescent organic probes in a micelle system offers an important alternative method to manufacture water-soluble organic nanoparticles (ONPs) for use in sensing Hg2+. This article reports on a study of a surfactant-free micelle-like ONPs based on a 3,6-di(2-thienyl)-2,5-dihydropyrrolo[3,4-c]pyrrole-1,4-dione (TDPP) amphiphile, (2-(2-(2-methoxyethoxy)ethyl)-3,6-di(2-thiophyl)-2,5-dihydropyrrolo[3,4-c]pyrrole-1,4-dione (NDPP) fabricated to monitor Hg2+ in water. NDPP was synthesized through a simple one-step modification of a commercially available dye TDPP with a flexible and hydrophilic alkoxy. This study reports, for the first time, that TDPP dyes can respond reversibly, sensitively, and selectively to Hg2+ through TDPP-Hg-TDPP complexation, similar to the well-known thymine(T)-Hg-thymine(T) model and the accompanying molecular aggregation. Interestingly, transmission electron microscopy (TEM) and dynamic light scattering (DLS) confirmed that, in water, NDPP forms loose micelle-like fluorescent ONPs with a hydrohobic TDPP portion encapsulated inside. These micelle-like nanoparticles offer an ideal location for TDPP-Hg complexation with a modest molecular aggregation, thereby providing both clear visual and spectroscopic signals for Hg2+ sensing. An estimated detection limit of 11 nM for Hg2+ sensing with this NDPP nanoparticle was obtained. In addition, NDPP ONPs show good water solubility and high selectivity to Hg2+ in neutral or alkalescent water. It was superior to most micelle-based nanosensors, which require a complicated process in the selection or synthesis of suitable surfactants. The determinations in real samples (river water) were made and satisfactory results were achieved. This study provides a low-cost strategy for fabricating small molecule-based fluorescent nanomaterials for use in sensing Hg2+. Moreover, the NDPP nanoparticles show potential ability in Hg2+ ion adsorption and recognization of cysteine using NDPP-Hg composite particle.

Light-Directed Synthesis of High-Density Peptide Nucleic Acid Microarrays.

Peptide nucleic acids (PNAs) are a class of nucleic acid mimics that can bind to the complementary DNA or RNA with high specificity and sensitivity. PNA-based microarrays have distinct characteristics and have improved performance in many aspects compared to DNA microarrays. A new set of PNA monomers has been synthesized and used as the building blocks for the preparation of high density PNA microarrays. These monomers have their backbones protected by the photolabile group 2-(2-nitrophenyl)propyloxy carbonyl (NPPOC), and their exocyclic amino groups protected by amide carbonyl groups. A light-directed synthesis system was designed and applied to the in situ synthesis of a PNA microarray with a density of over 10,000 probes per square centimeter. This PNA microarray was able to detect single and multiple base-mismatches correctly with a high discrimination ratio.

Recognition Mechanisms and Applications of Peptide Nucleic Acids Targeting Double-stranded DNA.

Targeting double-stranded DNA (dsDNA) with high affinity and specificity has become a hot topic in biochemistry and molecular biology research. Gene diagnosis and therapy, DNA manipulation, and gene expression regulation could be achieved based on certain recognition principles through specific interactions between dsDNA and natural nucleotides or synthesized ligands. Some ligands (e.g., peptide nucleic acids (PNAs), triple helix-forming oligonucleotides (TFOs), oligopolyamides, and zinc-finger peptides) show sufficient affinity and specificity for targeting dsDNA sequences. PNA can simply synthesize and recognize dsDNA without sequence limitation under physiological conditions. This paper provides a review on the recognition mechanisms, influencing factors, and applications of the four recognition modes of PNA targeting dsDNA. These modes include triplex invasion, triplex binding, duplex invasion, and double duplex invasion. This paper also discusses the challenges to be addressed by future research to fully explore the potential of PNA probe design for specific dsDNA recognition.

Design and Simulation of a Passive Micromixer with Gourd-Shaped Channel

A gourd-shaped contraction-expansion design is proposed for a passive planar micromixer in this study. The mixing performance of the micromixer is analyzed numerically and compared with a T-shaped planar micromixer. The gourd-shaped contraction-expansion structure can enhance the vortex-formation and mixing abilities of the micromixer. The numerical simulation reveals that the gourd-shaped structure can improved vortex generation and mixing efficiency within a high Reynolds number range. The micromixer with an optimized waist width of 50 μm reaches a mixing efficiency of approximately 83.25% and maintains a moderate pressure drop of 4860 Pa at Re = 100. This study can shed light on the design of new 2D micromixers from the point view of bionics.

Fluorescent Pyrene Assisted Photodeprotection of 2-(2-nitrophenyl)Propyloxycarbonyl Groups on Self-Assembled Monolayers.

Accelerating the photodeprotection rate of photolabile protecting group is conducive to a light-directed chemical reaction, especially for the in situ synthesis of a biochip. Herein, a photosensitizer pyrene was applied to the photodeprotection of 2-(2-nitrophenyl)propyloxycarbony (NPPOC) groups on self-assembled monolayers (SAMs). It was found that the addition of pyrene could largely improve photodeprotection rate, and effectively prevent molecule damage that are often encountered by the photosensitizer 2-isopropyl thioxanthone (ITX). The most likely explanation for this result is that the whole photodeprotection process involves three joint actions, including ultraviolet light irradiation, triplet energy transfer by pyrene, and singlet fluorescence irradiation from pyrene. The joint actions enable the transfer of over-absorbed energy from pyrene to protecting groups in terms of fluorescence rather than free radicals produced by ITX that are detrimental to the molecules modified on glass substrates. Pyrene dissolved in an optimized combination of mixed solvent of dimethylacetamide (DMAC), ethanol, and dioxane with a volume ratio of 1:1:1 was tested to produce a complete photodeprotection of NPPOC groups within 6 min under 365 nm ultraviolet with an intensity of 10.8 mW/cm2. Meanwhile, tens to hundreds of cycles of photodeprotection could be conducted at a high efficiency. This research will shed light on the deprotection of photolabile groups with weak ultraviolet using a fluorescent sensitizer.