Accurate Zygote‐Specific Discrimination of Single‐Nucleotide Polymorphisms Using Microfluidic Electrochemical DNA Melting Curves

We report the first electrochemical system for the detection of single‐nucleotide polymorphisms (SNPs) that can accurately discriminate homozygous and heterozygous genotypes using microfluidics technology. To achieve this, our system performs real‐time melting‐curve analysis of surface‐immobilized hybridization probes. As an example, we used our sensor to analyze two SNPs in the apolipoprotein E (ApoE) gene, where homozygous and heterozygous mutations greatly affect the risk of late‐onset Alzheimer’s disease. Using probes specific for each SNP, we simultaneously acquired melting curves for probe–target duplexes at two different loci and thereby accurately distinguish all six possible ApoE allele combinations. Since the design of our device and probes can be readily adapted for targeting other loci, we believe that our method offers a modular platform for the diagnosis of SNP‐based diseases and personalized medicine.     

Tailor‐Made Molecularly Imprinted Polymer for Selective Recognition of the Urinary Tumor Marker Pseudouridine

Pseudouridine (Ψ) is an important urinary cancer biomarker, especially in human colorectal cancer (CRC). Disclosed herein is the first Ψ molecularly imprinted polymer (Ψ‐MIP) material obtained from tailor‐engineered functional monomers. The resulting MIP imprint exhibits a remarkable imprinting factor greater than 70. It is successfully used for the selective recognition of Ψ in spiked human urine. This selective functionalized material opens the route to the development of inexpensive disposable chemosensors for noninvasive CRC diagnosis and prognosis.     

Double‐Stranded RNA‐Specific Templated Reaction with Triplex Forming PNA

RNA, originally perceived as a simple information transfer biopolymer, is emerging as an important regulator in cellular processes. A number of non‐coding RNAs are double‐stranded and there is a need for technologies to reliably detect and image such RNAs for biological and biomedical research. Herein we report double‐stranded RNA‐specific templated reaction resulting from PNA‐reagent conjugates that are brought within reactive distance through the formation of sequence‐specific triplexes onto double‐stranded RNA. The reaction makes use of a ruthenium‐based photocatalyst that reduces a pyridinium‐based immolative linker, unmasking a profluorophore. The reaction was shown to proceed with signal amplification and to be selective for double‐stranded RNA over DNA as well as single‐stranded RNA. The generality of the triplex formation was enabled by non‐canonical nucleobases that extend the Hoogsteen base‐pairing repertoire. The technology was applied to a templated reaction using pre‐microRNA 31.     

The Split Primer Ligation‐triggered 8‐17 DNAzyme Assisted Cascade Rolling Circle Amplification for High Specific Detection of Liver Cancer‐involved mRNAs: TK1 and c‐myc

Simultaneous detection of various intracellular biomarkers is promising for early diagnosis and treatment of cancer. Herein, we develop a novel method for high specific and ultrasensitive detection of liver cancer cell‐involved mRNAs: TK1 and c‐myc based on the split primer ligation‐triggered 8‐17 DNAzyme assisted cascade rolling circle amplification. Only two targets exist simultaneously, can trigger the rolling circle amplification to improve the accuracy and sensitivity. Meanwhile, an electrochemical molecular beacon, based on the host‐guest recognition between ferrocene groups and cucurbit urils [7] (CB[7]/Fc‐MB), is used to cause a “turn‐off” electrochemical signal which is decreased by disrupting its hairpin structure. Under the optimal conditions, the detection limit of TK1 and c‐myc mRNA is as low as 0.06 nM. Moreover, this method can be used to detect the TK1 and c‐myc mRNA in HepG2 cells and distinguish between cancer cells and their normal cells, proving that the method has the potential to detect the variation of biomarkers in vivo.     

Multiplex identification of drug‐resistant Gram‐positive pathogens using stuffer‐free MLPA system

Early detection of pathogens from blood and identification of their drug resistance are essential for sepsis management. However, conventional culture‐based methods require relatively longer time to identify drug‐resistant pathogens, which delays therapeutic decisions. For precise multiplex detection of drug‐resistant Gram‐positive pathogens, we developed a method by using stuffer‐free multiplex ligation‐dependent probe amplification (MLPA) coupled with high‐resolution CE single‐strand conformation polymorphisms (CE‐SSCP) system. We designed three probe sets for genes specific to Gram‐positive species (Staphylococcus aureus: nuc, Enterococcus faecium: sodA, and Streptococcus pneumoniae: lytA) and two sets for genes associated with drug resistance (mecA and vanA) to discriminate major Gram‐positive pathogens with the resistance. A total of 94 different strains (34 reference strains and 60 clinical isolates) were used to validate this method and strain‐specific peaks were successfully observed for all the strains. To improve sensitivity of the method, a target‐specific preamplification step was introduced and, consequently, the sensitivity increased from 10 pg to 100 fg. We also reduced a total assay time to 8 h by optimizing hybridization time without compromising test sensitivity. Taken together, our multiplex detection system can improve detection of drug‐resistant Gram‐positive pathogens from sepsis patients’ blood.     

Identification of Flavin Mononucleotide as a Cell‐Active Artificial N6‐Methyladenosine RNA Demethylase

N⁶‐Methyladenosine (m⁶A) represents a common and highly dynamic modification in eukaryotic RNA that affects various cellular pathways. Natural dioxygenases such as FTO and ALKBH5 are enzymes that demethylate m⁶A residues in mRNA. Herein, the first identification of a small‐molecule modulator that functions as an artificial m⁶A demethylase is reported. Flavin mononucleotide (FMN), the metabolite produced by riboflavin kinase, mediates substantial photochemical demethylation of m⁶A residues of RNA in live cells. This study provides a new perspective to the understanding of demethylation of m⁶A residues in mRNA and sheds light on the development of powerful small molecules as RNA demethylases and new probes for use in RNA biology.     

Nonisothermal crystallization and melting behavior of a luminescent conjugated polymer,poly(9,9‐dihexylfluorene‐alt‐co‐2,5‐didecyloxy‐1,4‐phenylene)

The nonisothermal crystallization kinetics of a luminescent conjugated polymer, poly(9,9‐dihexylfluorene‐alt‐co‐2,5‐didecyloxy‐1,4‐phenylene) (PF6OC10) with three different molecular weights was investigated by differential scanning calorimetry under different cooling rates from the melt. With increasing molecular weight of PF6OC10, the temperature range of crystallization peak steadily became narrower and shifted to higher temperature region and the crystallization rate increased. It was found that the Ozawa method failed to describe the nonisothermal crystallization behavior of PF6OC10. Although the Avrami method did not effectively describe the nonisothermal crystallization kinetics of PF6OC10 for overall process, it was valid for describing the early stage of crystallization with an Avrami exponent n of about 3. The combined method proposed in our previous report was able to satisfactorily describe the nonisothermal crystallization behavior of PF6OC10. The crystallization activation energies determined by Kissinger, Takhor, and Augis‐Bennett models were comparable. The melting temperature of PF6OC10 increased with increasing molecular weight. For low‐molecular‐weight sample, PF6OC10 showed the characteristic of double melting phenomenon. The interval between the two melting peaks decreased with increasing molecular weight, and only one melting peak was observed for the high‐molecular‐weight sample. © 2007 Wiley Periodicals, Inc. J Polym Sci Part B: Polym Phys 45: 976–987, 2007     

Application of thin‐layer chromatography/infrared matrix‐assisted laser desorption/ionization orthogonal time‐of‐flight mass spectrometry to structural analysis of bacteria‐binding glycosphingolipids selected by affinity detection

Glycosphingolipids (GSLs) play key roles in the manifestation of infectious diseases as attachment sites for pathogens. The thin‐layer chromatography (TLC) overlay assay represents one of the most powerful approaches for the detection of GSL receptors of microorganisms. Here we report on the direct structural characterization of microbial GSL receptors by employment of the TLC overlay assay combined with infrared matrix‐assisted laser desorption/ionization orthogonal time‐of‐flight mass spectrometry (IR‐MALDI‐o‐TOF‐MS). The procedure includes TLC separation of GSL mixtures, overlay of the chromatogram with GSL‐specific bacteria, detection of bound microbes with primary antibodies against bacterial surface proteins and appropriate alkaline phosphatase labeled secondary antibodies, and in situ MS analysis of bacteria‐specific GSL receptors. The combined method works on microgram scale of GSL mixtures and is advantageous in that it omits laborious and time‐consuming GSL extraction from the silica gel layer. This technique was successfully applied to the compositional analysis of globo‐series neutral GSLs recognized by P‐fimbriated Escherichia coli bacteria, which were used as model microorganisms for infection of the human urinary tract. Thus, direct TLC/IR‐MALDI‐o‐TOF‐MS adds a novel facet to this fast and sensitive method offering a wide range of applications for the investigation of carbohydrate‐specific pathogens involved in human infectious diseases. Copyright © 2010 John Wiley & Sons, Ltd.     

A Quadruplex‐Based,Label‐Free,and Real‐Time Fluorescence Assay for RNase H Activity and Inhibition

We demonstrate a unique quadruplex‐based fluorescence assay for sensitive, facile, real‐time, and label‐free detection of RNase H activity and inhibition by using a G‐quadruplex formation strategy. In our approach, a RNA–DNA substrate was prepared, with the DNA strand designed as a quadruplex‐forming oligomer. Upon cleavage of the RNA strand by RNase H, the released G‐rich DNA strand folds into a quadruplex in the presence of monovalent ions and interacts with a specific G‐quadruplex binder, N‐methyl mesoporphyrin IX (NMM); this gives a dramatic increase in fluorescence and serves as a reporter of the reaction. This novel assay is simple in design, fast in operation, and is more convenient and promising than other methods. It takes less than 30 min to finish and the detection limit is much better or at least comparable to previous reports. No sophisticated experimental techniques or chemical modification for either RNA or DNA are required. The assay can be accomplished by using a common spectrophotometer and obviates possible interference with the kinetic behavior of the catalysts. Our approach offers an ideal system for high‐throughput screening of enzyme inhibitors and demonstrates that the structure of the G‐quadruplex can be used as a functional tool in specific fields in the future.     

Reversible Photoswitching of RNA Hybridization at Room Temperature with an Azobenzene C‐Nucleoside

Photoregulation of RNA remains a challenging task as the introduction of a photoswitch entails changes in the shape and the stability of the duplex that strongly depend on the chosen linker strategy. Herein, the influence of a novel nucleosidic linker moiety on the photoregulation efficiency of azobenzene is investigated. To this purpose, two azobenzene C‐nucleosides were stereoselectively synthesized, characterized, and incorporated into RNA oligonucleotides. Spectroscopic characterization revealed a reversible and fast switching process, even at 20 °C, and a high thermal stability of the respective cis isomers. The photoregulation efficiency of RNA duplexes upon trans‐to‐cis isomerization was investigated by using melting point studies and compared with the known D ‐threoninol‐based azobenzene system, revealing a photoswitching amplitude of the new residues exceeding 90 % even at room temperature. Structural changes in the duplexes upon photoisomerization were investigated by using MM/MD calculations. The excellent photoswitching performance at room temperature and the high thermal stability make these new azobenzene residues promising candidates for in‐vivo and nanoarchitecture photoregulation applications of RNA.     

Magnetic solid‐phase extraction of tobacco‐specific N‐nitrosamines using magnetic graphene composite as sorbent

Tobacco‐specific N‐nitrosamines are carcinogenic components in mainstream cigarette smoke. To explore tobacco‐specific N‐nitrosamine release levels in cigarettes, a magnetic solid‐phase extraction procedure using magnetic graphene composite as sorbent for fast enrichment of tobacco‐specific N‐nitrosamine was developed. Under optimal conditions, a tobacco‐specific N‐nitrosamine determination method was successfully proposed by combining magnetic solid‐phase extraction procedure and high‐performance liquid chromatography coupled with tandem mass spectrometry. The method's limit of detection for tobacco‐specific N‐nitrosamines in mainstream cigarette smoke ranged from 0.018 to 0.057 ng/cigarette. Good linearities were obtained with correlation coefficients above 0.9992. The accuracies of tobacco‐specific N‐nitrosamines in a spiked mainstream cigarette smoke sample were from 89.3 to 109.4%, with a relative standard deviation of less than 11.2%. The proposed method has the merits of rapidity and high sensitivity. Finally, the method was successfully applied to tobacco‐specific N‐nitrosamine analysis in real samples.     

Reconstructing interference fringes in slit experiments by complex quantum trajectories

There are external and internal representations for a quantum state Ψ. External representation is commonly adopted in the standard quantum mechanics by exploiting probability density function Ψ*Ψ to explain the observed interference fringes in slit experiments. On the other hand, in quantum Hamilton mechanics, the quantum state Ψ has a dynamical representation that reveals the internal mechanism underlying the externally observed interference fringes. The internal representation of Ψ is described by a set of Hamilton equations of motion, by which quantum trajectories of a particle moving in Ψ can be solved. In this article, millions of complex quantum trajectory connecting slits to a screen are solved from the Hamilton equations, and the statistical distribution of their arrivals on the screen is shown to reproduce the observed interference fringes. This appears to be the first quantitative verification of the equivalence between the trajectory‐based statistics and the wavefunction‐based statistics on slit experiments. © 2012 Wiley Periodicals, Inc.     

Characterization of G‐Quadruplex/Hairpin Transitions of RNAs by 19F NMR Spectroscopy

2′‐O‐[(4‐Trifluoromethyl‐triazol‐1‐yl)methyl] reporter groups have been incorporated into guanosine‐rich RNA models (including a known bistable Qd/Hp RNA and two G‐rich regions of mRNA of human prion protein, PrP) and applied for the ¹⁹F NMR spectroscopic characterization of plausible G‐quadruplex/hairpin (Qd/Hp) transitions in these RNA structures. For the synthesis of the CF₃‐labeled RNAs, phosphoramidite building blocks of 2′‐O‐[(4‐CF₃‐triazol‐1‐yl)methyl] nucleosides (cytidine, adenosine, and guanosine) were prepared and used as an integral part of the standard solid‐phase RNA synthesis. The obtained ¹⁹F NMR spectra supported the usual characterization data (obtained by UV‐ and CD‐melting profiles and by ¹H NMR spectra of the imino regions) and additionally gave more detailed information on the Qd/Hp transitions. The molar fractions of the secondary structural species (Qd, Hp) upon thermal denaturation and under varying ionic conditions could be determined from the intensities and shifts of the ¹⁹F NMR signals. For a well‐behaved Qd/Hp transition, thermodynamic parameters could be extracted.     

Specific Binding of a d‐RNA G‐Quadruplex Structure with an l‐RNA Aptamer

G‐quadruplex (G4) structures are of general importance in chemistry and biology, such as in biosensing, gene regulation, and cancers. Although a large repertoire of G4‐binding tools has been developed, no aptamer has been developed to interact with G4. Moreover, the G4 selectivity of current toolkits is very limited. Herein, we report the first l ‐RNA aptamer that targets a d ‐RNA G‐quadruplex (rG4). Using TERRA rG4 as an example, our results reveal that this l ‐RNA aptamer, Ap3‐7, folds into a unique secondary structure, exhibits high G4 selectivity and effectively interferes with TERRA‐rG4–RHAU53 binding. Our approach and findings open a new door in further developing G4‐specific tools for diverse applications.     

Multiplex identification of sepsis‐causing Gram‐negative pathogens from the plasma of infected blood

Early and accurate detection of bacterial pathogens in the blood is the most crucial step for sepsis management. Gram‐negative bacteria are the most common organisms causing severe sepsis and responsible for high morbidity and mortality. We aimed to develop a method for rapid multiplex identification of clinically important Gram‐negative pathogens and also validated whether our system can identify Gram‐negative pathogens with the cell‐free plasm DNA from infected blood. We designed five MLPA probe sets targeting the genes specific to major Gram‐negative pathogens (uidA and lacY for E. coli, ompA for A. baumannii, phoE for K. pneumoniae, and ecfX for P. aeruginosa) and one set targeting the CTX‐M group 1 to identify the ESBL producing Gram‐negative pathogens. All six target‐specific peaks were clearly separated without any non‐specific peaks in a multiplex reaction condition. The minimum detection limit was 100 fg of pathogen DNA. When we tested 28 Gram‐negative clinical isolates, all of them were successfully identified without any non‐specific peaks. To evaluate the clinical applicability, we tested seven blood samples from febrile patients. Three blood culture positive cases showed E. coli specific peaks, while no peak was detected in the other four culture negative samples. This technology can be useful for detection of major sepsis‐causing, drug‐resistant Gram‐negative pathogens and also the major ESBL producing Gram‐negatives from the blood of sepsis patients in a clinical setting. This system can help early initiation of effective antimicrobial treatment against Gram‐negative pathogens for sepsis patients, which is very crucial for better treatment outcomes.