A novel strategy for in situ maskless synthesis of biochips： Self-driving micro-fluid porous type printing （SMPTP）

A novel maskless technique,self-driving micro-fluid porous type printing(SMPTP),was reported to in situ synthesize oligonucleotide arrays on glass slide,which has the merits of low cost,high quality and simple craft.In SMPTP for fabricating gene- chips,porous fiber tubes with a number of nanometric or micron channels functioned as“active letters”and were assembled in designed patterns,which are identical to the distribution of monomers in each layer of the array,and four patterns were needed for each layer.By means of capillarity,the synthesis solution was automatically taken into porous tubes assembled in a printing plate and reached the surface.An oligonucleotide array of 160 features with four different 15-mer probes was in situ synthesized using this technique.The four specific oligonucleotide probes,including the matched and the mismatched by the fluorescent target sequence,gave obviously different hybridization fluorescent signals.     

Electrochemical detection of a Vibrio parahaemolyticus sequence-specific gene based on a gold electrode modified with a single stranded probe

An electrochemical DNA biosensor for specific-sequences detection of Vibrio parahaemolyticus (VP) was fabricated. A single-stranded 20-mer oligonucleotide (ssDNA) and 6-mercapto-1-hexanol (MCH) were immobilized via a thiol linker on gold disk electrodes by self-assembling. The ssDNA underwent hybridization in a hybridization solution containing complementary or non-complementary or single base pair mismatched DNA sequences of VP. Examination of changes in response to these three target DNAs showed that the developed biosensor had a high selectivity and sensitivity.     

In situ synthesis of DNA micro-arrays using typography technique

A novel typography technique was developed to in situ synthesize oligonucleotide arrays on glass slide,which has the celerity,high spatial resolution,lower cost,reliable operation,and high synthetic efficiency.The principle and process of the typography technique for fabricating gene-chips have been described in detail.A suit of poly(terafluoroethylene)devices for synthesizing oligonucleotide arrays were designed and prepared,and the fiber tubes with a number of nano-or micron-channels were em- ployed.The oligonucleotide arrays of 16 and 160 features with four different probes were synthesized using the typography technique.The four specific oligonucleotide probes including the matched and the mismatched by the fluorescent target sequence gave obviously different hybridization fluorescent signals.It was indicated that the gene-chip fabricated by the typography method could be used to rapidly screen single-nucleotide polymorphisms(SNP)and to detect mutations.     

A New Trace Analytic Method for the Determination of Sequence-Specific DNA with Fluorescent Probes

A new method of fluorescence spectrometry detection of single-strand DNA (ssDNA) was established by hybridizing the ssDNA with its complementary ssDNA to form double-stranded DNA (dsDNA). Our results show that the fluorescence intensity increased significantly when the nucleic acid molecular “light switch"(Ru(phen)₂dppx²⁺) or Hoechst 33258 dye interacted with dsDNA, and the fluorescence intensity also increased as the DNA concentration increased. The changing law was also studied about how the fluorescence intensity changed when the two kinds of fluorescent probes interacted with oligonucleotide of different lengths and different sequences, as well as DNA-DNA′ hybridization products. Then, the effect of the bases mismatch, varying length of DNA chain, and different DNA sequences on the fluorescence intensity were explored at the same time, by detecting the specific DNA sequence of avian influenza H1N1 virus, cauliflower mosaic virus, and hepatitis C virus. Additionally, the selectivity, linear range, and sensitivity of the two probes were compared.     

Mispair-aligned N3T-alkyl-N3T interstrand cross-linked DNA: synthesis and characterization of duplexes with interstrand cross-links of variable lengths

Therapeutic bifunctional alkylating agents generate interstrand cross-links in duplex DNA. As part of our continuing studies on DNA duplexes that contain alkyl interstrand cross-links, we have synthesized a cross-link that bridges the N(3) positions of a mismatched thymidine base pair. This cross-link, which is similar to the N(3)C-alkyl-N(3)C cross-link that has been observed between mismatched cytosine base pairs, was introduced by first incorporating a cross-linked phosphoramidite unit at the 5'-end of an oligonucleotide chain. Fully cross-linked duplexes were then synthesized using an orthogonal approach to selectively remove protecting groups, thus allowing construction of the cross-linked duplex via conventional solid-phase oligonucleotide synthesis. Short DNA duplexes with alkyl cross-links of various lengths (two, four, and seven methylene units) were prepared, and their physical properties were studied via UV thermal denaturation and circular dichroism spectroscopy. These linkers were found to stabilize the duplexes by 37, 31, and 16 degrees C for the two-, four-, and seven-carbon linkers, respectively, relative to a non-cross-linked duplex. Circular dichroism spectra suggested that these lesions induce very little deviation in the global structure relative to the non-cross-linked duplex DNA control. Molecular models show that the two-carbon cross-link spans the distance between the N(3) atoms of the T-T mismatch without perturbing the helix structure, whereas the longer linkers, particularly the seven-carbon linker, tend to push the thymines apart, creating a local distortion. This perturbation may account for the lower thermal stability of the seven-carbon versus two-carbon cross-linked duplex.     

An ultrasensitive immunosensor array for determination of staphylococcal enterotoxin B

Staphylococcal enterotoxin B (SEB) is a potent gastrointestinal toxin and is heat resistant. SEB is also a potential bioterrorism agent. The ability to measure accurately very low amounts of staphylococcal enterotoxin B in food and other samples is very important. A highly sensitive and stable sandwich fluorescence immunoassay based on a pair of monoclonal antibodies against SEB which were produced by us was developed. Classical sandwich immunoassay was adopted and the glass slides were used as the base of the immunologic reaction. The functionalized fluorescent core-shell silica nanoparticles were used as labels. The fluorescence issued from the labels was detected by a laser-induced fluorescence millimeter sensor array detection platform. The fluorescence intensity has a linear relationship with the amount of SEB in the range of 50 pg/mL-5 ng/mL, and the detection limit of SEB was 20 pg/mL (the absolute detection limit was 0.02 pg). The relative standard deviation (RSD) for 5 parallel measurements of SEB (1 ng/mL) was 9.2%.     

Sunna 535-nm photo-fluorescent film dosimeter response to different environmental conditions

Evaluations on the influence of environmental variabilities on the red fluorescence component of the Sunna Model γ photo-fluorescent dosimeter^TM have previously been reported. This present paper describes the environmental effects on the response of the green fluorescence component of the same dosimeter, which is manufactured using the injection molding technique. The results presented include temperature, relative humidity, and light influences both during and after irradiation. The green fluorescence signal shows a significant dependence on irradiation temperature below room temperature at 1%/°C. Above room temperature (approximately 24–60°C), the irradiation temperature effect varies from −0.1%/°C to 1.0%/°C, depending on the absorbed dose level. For facilities with irradiation temperatures between 30°C and 60°C and absorbed dose levels above 10 kGy, irradiation temperature effects are minimal. Light-effects results indicate that the dosimeter is influenced by ultraviolet and blue wavelengths during irradiation as well as during the post-irradiation stabilization period (approximately 22 h), requiring the use of light-tight packaging. Results also show that the dosimeter exhibits negligible effects from ambient moisture during and after irradiation when in the range of 33–95% relative humidity.     

Single-mismatch detection using nucleic acid molecular 'light switch'

A novel nucleic acid molecular ‘light switch’ method is developed for the sensitive recognition and detection of a single-base mismatched oligonucleotides. The detection limit of oligonucleotide of perfect double stranded and that with single-base, two-base and three-base mismatched are 0.11, 0.17, 0.34 and 1.5 ng ml⁻¹, respectively. It was found that Ru(phen)₂(dppx)²⁺ (phen=1,10-phenanthroline, dppx=7,8-dimethyl-dipyridophenazine) can be used to detect and recognize the perfect double stranded oligonucleotides from mismatched and random targets by the intensity of fluorescence and temperature. This method can be used to recognize and quantitatively detect target DNA with specific sequence. The advantage of this method is that no requisites are needed to separate the coexisting random targets in the case of a mixed solution containing perfect, mismatched and random targets, which make the recognition analysis of oligonucleotide simple and fast. Moreover, it has potential in the study of dynamic process of DNA hybridization.     

Stable and selective formation of hoogsteen-type triplexes and duplexes using twisted intercalating nucleic acids (TINA) prepared via postsynthetic Sonogashira solid-phase coupling reactions

Bulge insertions of (R)-1-O-[4-(1-pyrenylethynyl)phenylmethyl]glycerol (5) into the middle of homopyrimidine oligodeoxynucleotides (twisted intercalating nucleic acids, TINA) obtained via postsynthetic Sonogashira coupling reaction led to extraordinary high thermal stability of Hoogsteen-type triplexes and duplexes, whereas Watson-Crick-type duplexes of the same nucleotide content were destabilized. Modified oligonucleotides were synthesized using the phosphoramidite of (S)-1-(4,4'-dimethoxytriphenylmethyloxy)-3-(4-iodo-benzyloxy)-propan-2-ol followed by treatment of the oligonucleotide on a CPG-support with the Sonogashira-coupling reaction mixture containing different ethynylaryls. Bulged insertion of the pyrene derivative 5 into oligonucleotides was found to be the best among the tested modifications for binding to the Hoogsteen-type triplexes and duplexes. Thus, at pH 7.2 an oligonucleotide with cytidine content of 36% possessing two bulged insertions of 5 separated by three bases formed a stable triplex (T(m) = 43.0 degrees C), whereas the native oligonucleotide was unable to bind to the target duplex. The corresponding Watson-Crick-type duplex with the same oligonucleotide had T(m) of 38.0 degrees C at pH 7.2, while the T(m) of unmodified dsDNA was 47.0 degrees C. Experiments with mismatched oligonucleotides, luminescent properties, and potential applications of TINA technology is discussed.     

Thermoluminescence characteristics of minerals from irradiated potatoes of different origins of production

Thermoluminescence (TL) characteristics were investigated for minerals, which were separated from potatoes irradiated at 0–1 kGy of different origins of production in Korea. The polyminerals analyzed by X-ray diffractometer were mainly composed of quartz and feldspar, and showed varied contents with producing origins, that contributed to typical TL responses to irradiation. The glow curve of irradiated samples at 0.05–1 kGy peaked at approximately 200°C with high intensity, but that of non-irradiated potatoes was observed at approximately 300°C with low intensity. Discrimination between irradiated (more than 0.05 kGy) and non-irradiated samples was possible just on the basis of the first glow curve, however, normalization of results through a re-irradiation step greatly improved their reliability. The signal intensity of TL decreased with the lapse of post-irradiation time under different storage conditions (0±0.5°C/dark room, 25±5°C/dark room and 25±5°C/naturally lighted room) but was still distinguishable from that of the non-irradiated sample even after one year.     

Combinatorial decoding: an approach for universal DNA array fabrication

A fiber optic microsphere-based oligonucleotide array is described that employs the sequence of the oligonucleotide probe attached to each microsphere as positional identifiers. Each microsphere serves as an immobilized array feature, functionalized with a unique single-stranded oligonucleotide sequence and randomly distributed into an array of microwells. To determine the sequences attached to individual microspheres, a series of fluorescently labeled combinatorial-pooled oligonucleotide target solutions was designed. Each combinatorial decoding solution is intended to identify the nucleotide at a particular position on every microsphere in the array. The combinatorial target solutions were synthesized by linking the four possible nucleotides at each position to four different fluorescent reporter dyes. As such, when the solutions were hybridized to the array, one of four possible fluorescent responses was generated for each position on a microsphere probe sequence. Adjusting the stringency of hybridization enabled single-base mismatch discrimination, and the signal with the highest intensity corresponded to the perfect nucleotide match. By consecutively exposing the array to a series of combinatorial decoding pool solutions, it was possible to simultaneously determine the sequence of every randomly positioned oligonucleotide-functionalized microsphere in the array. Once mapped, the microsphere array can be used for any typical genomic microarray experiment.     

Fluorescence quenching of conjugated polymer by coupling plasmonic silver nanocap array

The optical properties of poly(2,5-dioctyloxy-p-phenylene) (DOO-PPP) coupled to a silver nanocap array are investigated by Raman and photoluminescence spectra. The emission intensity of the DOO-PPP coupled to the silver nanocap array is much weaker than that of the DOO-PPP film due to the fluorescence quenching of the silver nanocap array. In contrast with the freshly prepared sample, the fluorescence quenching efficiency of the silver nanocap array is obviously decreased for the sample exposed in air; correspondingly, the Raman intensity at 1609 cm⁻¹ is markedly decreased, which is characteristic Raman peak of the inter-ring CC stretching vibration in the conjugated polymer. The experimental results indicate that the inter-ring CC stretching vibration plays an important role for the fluorescence quenching in the DOO-PPP coupled to the silver nanocap array.     

Water‐soluble cationic polypyrrole based probe for fluorometric and voltammetric detection of base pair mismatched oligonucleotides

Water‐soluble cationic polypyrrole, poly(N‐(4‐butyl‐(1‐methylimidazole)) pyrrole bromide) (PNBMIP‐Br), was synthesized and applied for base pair mismatched oligonucleotides detection. Interactions between PNBMIP‐Br and a series of oligonucleotides, including ss‐DNA and base pair mismatched ds‐DNA were studied by fluorometric spectra, circular dichroism spectra and voltammetric detection. The results showed that the electrostatic attraction and fluorescence resonance energy transfer of PNBMIP‐Br/DNA complexes resulted in an amplification and effective recognition of the fluorescence signals. The results of cyclic voltammograms indicate that voltammetric detection is an effective method to distinguish ss‐DNA and ds‐DNA. © 2015 Wiley Periodicals, Inc. J. Polym. Sci., Part A: Polym. Chem. 2015 , 53, 1600–1605     

Genotyping by alkaline dehybridization using graphically encoded particles

This work describes a nonenzymatic, isothermal genotyping method based on the kinetic differences exhibited in the dehybridization of perfectly matched (PM) and single-base mismatched (MM) DNA duplexes in an alkaline solution. Multifunctional encoded hydrogel particles incorporating allele-specific oligonucleotide (ASO) probes in two distinct regions were fabricated by using microfluidic-based stop-flow lithography. Each particle contained two distinct ASO probe sequences differing at a single base position, and thus each particle was capable of simultaneously probing two distinct target alleles. Fluorescently labeled target alleles were annealed to both probe regions of a particle, and the rate of duplex dehybridization was monitored by using fluorescence microscopy. Duplex dehybridization was achieved through an alkaline stimulus using either a pH step function or a temporal pH gradient. When a single target probe sequence was used, the rate of mismatch duplex dehybridization could be discriminated from the rate of perfect match duplex dehybridization. In a more demanding application in which two distinct probe sequences were used, we found that the rate profiles provided a means to discriminate probe dehybridizations from both of the two mismatched duplexes as well as to distinguish at high certainty the dehybridization of the two perfectly matched duplexes. These results demonstrate an ability of alkaline dehybridization to correctly discriminate the rank hierarchy of thermodynamic stability among four sets of perfect match and single-base mismatch duplexes. We further demonstrate that these rate profiles are strongly temperature dependent and illustrate how the sensitivity can be compensated beneficially by the use of an actuating gradient pH field.     

1,3,6,8-Tetraethynylpyrene and 1,3,6,8-tetrakis (trimethylsilylethynyl) pyrene: Photophysical properties in homogeneous media

The photophysical properties of two new tetra substituted derivatives of pyrene: 1,3,6,8-tetraethynylpyrene (TEP) and 1,3,6,8-tetrakis(trimethylsilylethynyl)pyrene (TEP-TMS) have been studied. Studies were done with respect to mirror image symmetry in the absorption and emission spectra and permissive or forbidden nature of S₀–S₁ transition, solvent sensitivity of the first and third vibronic bands and fluorescence anisotropy. Both the derivatives exhibited a strongly allowed S₀–S₁ transition, high fluorescence quantum yield, shorter fluorescence lifetime compared to pyrene and invariance of the vibronic band intensity ratio to solvent polarity. The behavior of the two pyrene derivatives validates the hypothesis “solvent polarity mediates vibronic coupling and therefore the emission band intensities, for forbidden S₀–S₁ transitions”. The trimethylsilyl derivative (TEP-TMS) was characterized by a strong fluorescence in solid state. The tetraethynyl derivative (TEP) showed high fluorescence anisotropy comparable to the well-known anisotropy probe DPH in glycerol at 0 °C. The fluorescence intensities of TEP and TEP-TMS did not show any significant change in the temperature ranger 0–40 °C for a low viscous solvent like ethanol and in the range 0–60 °C in glycerol. Unlike pyrene, no excimer emission was observed even up to 10⁻³ M for TEP and TEP-TMS.     

Photo-luminescence of Risø B3 and PVB films for application in radiation dosimetry

Risø B3 film dosimeters (23 μm) prepared from poly(vinyl butyral) (PVB) incorporating pararosaniline cyanide, as the radiation-sensitive element and PVB films (25 μm) prepared from PVB without any additives are investigated for γ-radiation measurement using spectrofluorimetry based on their emission properties. The unirradiated Risø B3 film when excited at 554 nm shows an emission band at 602 nm while PVB film shows an emission band at 305 nm when excited at 235 nm wavelength. The fluorescence intensity of both emission bands decreases with the increase of absorbed dose due to the damage caused by ionizing radiation. The useful dose range of Risø B3 film extends up to 120 kGy while that of PVB film extends up to 60 kGy. The response of Risø B3 film increases with the increase of relative humidity during irradiation while that of PVB has less effect in the humidity range of 20–70%. The percent uncertainty associated with the measurement of the dose response was found to be ±3% (1σ) for both films. Risø B3 and PVB films show good post-irradiation stability in dark and indirect daylight where the deviation in the response overall a 2-month storage period was found to be ±5% for Risø B3 and ±2% for PVB.     

Studies of the Interaction of Platinum Drugs with DNA Using Oligonucleotide Microarrays

Summary: A novel method for the study of the interaction of the platinum drug cis-diamminedichloroplatinum(II) (cis-DDP or cisplatin) with 50-mer oligonucleotides that were printed in high throughput microarray format is introduced. Our aim has been to identify sequence level differences in the interaction of various drug candidates that may serve to enable rational targeting of drugs to specific genes. A microarray of 26 control genes commonly used in oligonucleotide, Affymetrix and c-DNA microarray platforms were microcontact spotted as amine-terminated 50-mer oligonucleotides onto glycidoxypropyltimethoxy silane (GPMS)-modified glass slides. The generalized study format involved hybridization of probes with 10 fluorescently labeled complements as target followed by confocal imaging to reveal original spot intensities. Microarrays were then incubated at 37 °C with hydrolysed cisplatin while in hybridization cassettes, washed in buffer and then scanned again to reveal secondary intensities. We have investigated the influence of cisplatin to stabilize the relative fluorescence intensity via intrastrand crosslinking by studying the impact of varying drug:probe-DNA mole ratio (0:1 (blank), 1:1, 25:1 and 50:1) and annealing temperatures (36, 46, or 56 °C) on retained intensity. ANOVA revealed that 4 of the 10 genes demonstrated (p < 0.0001) the expected result of increased signal retention with decreased temperature and increased drug concentration.     

A mismatch-selective bifunctional rhodium-Oregon Green conjugate: a fluorescent probe for mismatched DNA

A fluorescent metallointercalator conjugate that selectively targets DNA base mismatches has been synthesized by coupling an organic fluorophore to a bulky Rh intercalator containing the chrysenequinone diimine ligand. Ion pairing between the cationic Rh and anionic fluorophore moieties dramatically quenches the fluorescence of the conjugate in solution and in the presence of matched DNA. However, in the presence of mismatched DNA, the fluorescence of the conjugate is increased >300%. This increase in fluorescence is attributed to the loss in intramolecular quenching associated with DNA binding; intercalation of the Rh moiety into the mismatched site can lead to electrostatic repulsion of the anionic fluorophore away from the DNA phosphate backbone and Rh. Denaturing PAGE experiments with 32P-labeled oligonucleotides indicate that the conjugate selectively binds the mismatched DNA with a binding affinity of 6 x 105 M-1 and, upon irradiation, cleaves the DNA backbone neighboring the mismatched site.     

新型尾式组氨酸卟啉的合成及性质

设计并合成了新型尾式氨基酸卟啉5-(Trt-组氨酸酰胺基苯基)-10,15,20-三苯基卟啉(Trt-His-NH2-TPP,1)及其金属卟啉配合物(Zn,Co,Fe,Mn,分别标记为2～5).通过元素分析、核磁共振氨谱、质谱、紫外-可见光谱和红外光谱等对化合物进行了表征,研究了它们的荧光性质,并通过理论模拟研究了其最...     

Immobilization enzyme fluorescence capillary analysis for determination of lactic acid

A new method for the determination of lactic acid based on the immobilization enzyme fluorescence capillary analysis (IE-FCA) was proposed. Lactic dehydrogenase (LDH) was immobilized on inner surface of a capillary with glutaraldehyde, and an immobilized enzyme lactate capillary bioreactor (IE-LCBR) was formed for the determination of lactic acid. After nicotinamide adenine dinucleotide (NAD⁺) is mixed with lactic acid solution, it was sucked into the IE-LCBR and was detected at λ_ex 353 nm/λ_em 466 nm. Optimized conditions are as follows: the temperature is 38 °C; the reaction time is 15 min; the concentrations of Tris buffer (pH 8.8) and NAD⁺ are 0.1 mol L⁻¹ and 4 mmol L⁻¹, respectively; the concentration of LDH used for immobilization is 15 kU L⁻¹. The concentration of lactic acid is directly proportional to the fluorescence intensity measured from 0.50 to 2.0 mmol L⁻¹; and the analytical recovery of added lactic acid was 99–105%. The minimum detection limit of the method is 0.40 mmol L⁻¹ and sensitivity of the IE-CBR is 4.6 F mmol⁻¹ L⁻¹ lactate. Its relative standard deviation (R.S.D.) is ≤2.0%. This IE-FCA method was employed for determination of lactate in milk drink.