Dipyrrylmetheneboron Difluorides as Labels in Two-Photon Excited Fluorometry. Part II–Nucleic Acid Hybridization Assays

Five two-photon excitable dipyrrylmetheneboron difluoride labels (dipyrrylmethene-BF₂ labels) with fluorescence emission maximum between 530 and 590 nm, and a frequently used rhodamine label, TAMRA, were conjugated to aminomodified oligonucleotides. The performance of the labeled oligonucleotides was studied in a separation-free nucleic acid hybridization assay using ArcDia^™ TPX bioaffinity assay technology. The results show that oligonucleotide conjugates of dipyrrylmethene-BF₂ labels provide higher two-photon excited fluorescence yield and better assay sensitivity than corresponding TAMRA conjugate. The effect of conjugation on photophysical properties of the labels and performance of the labeled oligonucleotides in separation-free hybridization assay is discussed.     

Non-empirical calculations of NMR indirect carbon-carbon coupling constants. Part 6: propellanes

A full set of carbon-carbon coupling constants have been calculated at the SOPPA level in the series of six most representative propellanes. Special attention was focused on spin-spin couplings involving both bridgehead carbons, and these data were rationalized in terms of the multipath coupling mechanism and hybridization effects. Many unknown couplings in the propellane frameworks were predicted with high reliability.     

Monitoring molecular beacon DNA probe hybridization at the single-molecule level

We have monitored the reaction dynamics of the DNA hybridization process on a liquid/solid interface at the single-molecule level by using a hairpin-type molecular beacon DNA probe. Fluorescence images of single DNA probes were recorded by using total internal reflection fluorescence microscopy. The fluorescence signal of single DNA probes during the hybridization to individual complementary DNA probes was monitored over time. Among 400 molecular beacon DNA probes that we tracked, 349 molecular beacons (87.5 %) were hybridized quickly and showed an abrupt fluorescence increase, while 51 probes (12.5 %) reacted slowly, resulting in a gradual fluorescence increase. This ratio stayed about the same when varying the concentrations of cDNA in MB hybridization on the liquid/surface interface. Statistical data of the 51 single-molecule hybridization images showed that there was a multistep hybridization process. Our results also showed that photostability for the dye molecules associated with the double-stranded hybrids was better than that for those with the single-stranded molecular beacon DNA probes. Our results demonstrate the ability to obtain a better understanding of DNA hybridization processes using single-molecule techniques, which will improve biosensor and biochip development where surface-immobilized molecular beacon DNA probes provide unique advantages in signal transduction.     

超越SNOM探针通光孔径尺寸的金属纳米间隙超分辨测量

采用电磁场有限元方法,数值模拟了孔径型扫描近场光学显微镜(aperture Scanning Near-field Optical Microscopy,a-SNOM)在照明模式下的工作过程.针对金偶极天线结构,改变天线长度和纳米间隙尺寸,计算了a-SNOM探针孔径的远场辐射速率随探针端面中心坐标变化的扫描曲线,实现了超越a-SNOM探针通光孔径尺寸的天线金属纳米间隙的超分辨测量,对于100nm通光孔径的探针,可分辨最小尺寸为10nm(0.016倍波长)的金属间隙.通过对比金属和介质偶极天线的a-SNOM探针远场辐射速率测量的计算结果,表明天线金属纳米间隙的超分辨测量的实现是由于金属间隙表面等离激元的激发.     

Synthesis and RNA-selective hybridization of α-l-ribo- and β-d-lyxo-configured oligonucleotides

Three α-l-ribofuranosyl analogues of RNA nucleotides (α-l-RNA analogues) have been synthesized and incorporated into oligonucleotides using the phosphoramide approach on an automated DNA synthesizer. The 4′-C-hydroxymethyl-α-l-ribofuranosyl thymine monomer was furthermore synthesized. Relative to the unmodified duplexes, incorporation of a single α-l-RNA monomer into a DNA strand leads to reduced thermal stability of duplexes with DNA complements but unchanged thermal stability of duplexes with RNA complements, whereas incorporation of more than one α-l-RNA monomer lead to moderately decreased thermal stability also of duplexes with RNA complements. Efficient hybridization with an RNA complement and no melting transition with a DNA complement were observed with stereoregular chimeric oligonucleotides composed of a mixture of α-l-RNA and affinity enhancing α-l-LNA monomers (α-l-ribo-configured locked nucleic acid). Furthermore, duplexes formed between oligodeoxynucleotides containing an α-l-RNA monomer and complementary RNA were good substrates for Escherichia coli RNase H. RNA-selective hybridization was also achieved by the incorporation of 1-(4-C-hydroxymethyl-β-d-lyxofuranosyl)thymine monomers into a DNA strand, whereas stable duplexes were formed with both complementary DNA and RNA when these monomers were incorporated into an RNA strand.     

Development of a Novel Electrochemical Biosensor for Detection and Discrimination of DNA Sequence and Single Base Mutation in dsDNA Samples Based on PNA‐dsDNA Hybridization – a new Platform Technology

In spite of the extensive attention paid on the development of various DNA detection strategies, very few studies have been reported regarding direct detection of DNA sequence and mutation in dsDNA. Here, we describe the feasibility of detection and discrimination of target DNA sequences and single base mutations (SBM) directly in double‐stranded oligonucleotides and PCR products without the need for denaturation of the target dsDNA samples. This goal was achieved by employing a peptide nucleic acid (PNA) chain, self‐assembled on the gold electrode as a probe, which binds to dsDNA and forms PNA‐dsDNA hybrid.     

High Sensitive Electrochemical Detection of Sequence‐Specific DNA Using Low Current Voltammetry

In this article, we report on efforts to construct a high sensitive electrochemical sensor with immobilized sandwich‐type DNA borne ferrocene (Fc) head for sequence‐specific DNA detection using ultramicroelectrode and low current voltammetry. Based on the difference in deformability between the bending rigid complementary DNA double helix and its anomalous flexile mismatches, the fully complementary target can be distinguished from mismatched targets including the single‐base mismatched target. Detection limit estimated as the amount of DNA is observed to be 100 fM via low current voltammetry. The method offers great promise of high sensitivity and selectivity simultaneously for effective gene identification.     

Establishment of hybrid-derived offspring populations in the Ohomopterus ground beetles through unidirectional hybridization

An approach to deduce the mechanism of stabilization of the hybrid-derived populations in the Ohomopterus ground beetles has been made by comparative studies on the phylogenetic trees of the mitochondrial and nuclear DNA. A phylogenetic tree based on the internal transcribed spacer (ITS) of nuclear ribosomal gene roughly reflects the relations of morphological species group, while mitochondrial NADH dehydrogenase subunit 5 (ND5) gene shows a considerable different topology on the tree; there exist several geographically-linked lineages, most of which consist of more than one species. These results suggest that the replacement of mitochondria has occurred widely in the Ohomopterus species. In most cases, hybridization is unidirectional, i.e., the species A (♂) hybridized with another species B (♀) and not vice versa, with accompanied replacement of mitochondria of A by those of B. The results also suggest that partial or complete occupation of the distribution territory by a hybrid-derived morphological species. The morphological appearance of the resultant hybrid-derivatives are recognized as that of the original species A. Emergence of a morphological new species from a hybrid-derived population has been exemplified.     

无标记DNA在氨基改性导电聚吡咯表面的固定/杂交

通过吡咯(Py)与其衍生物——6-吡咯己胺(PyHA)的共聚物聚(吡咯-co-6-吡咯己胺)[poly(Py-co-PyHA)]的合成研究,并采用电化学循环伏安法来考察体系的电化学活性.在缓冲溶液中,由于探针DNA链上的负电荷与共聚物分子链上的正电荷之间存在强烈的静电吸引力,使得DNA能够固定在导电聚合物膜上.实验结果证明,目标DNA和聚吡咯薄膜之间不存在非特异性吸附,而能和探针DNA进行顺利杂交.此结果为以后研究更为敏感的DNA固定及导电聚合物敏感膜提供了实验基础.