Effects of DNA secondary structure on oligonucleotide probe binding efficiency

Secondary structure motifs in nucleic acid probes generally impair intended hybridization reactions and so efforts to predict and avoid such structures are commonly employed in probe design schemes. Another key facet of probe design that has received much less attention, however, is that secondary structure at targeted probe binding site regions may also impair hybridization. Thus, evaluation of both probe and target site secondary structures together should improve hybridization prediction and design effectiveness. Several challenges confound this goal, including imperfect empirical rules and parameters underlying predictions and the fact that folding algorithms scale poorly with respect to sequence length. Here, we attempt to quantify the consequences of target site structure on predicted hybridization using sequences sampled from the human genome. We also provide a methodology for choosing a reasonable “window size” around target sites that is as small as possible without compromising folding algorithm prediction accuracy.     

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.     

Efficient synthesis of terminal 4-methylumbelliferyl labeled 5-fluoro-2′-deoxyuridine-5′-O-tetraphosphate (Um-PPPP-FdU): a potential probe for homogenous fluorescent assay

Efficient synthesis of 5-fluoro-2′-deoxyuridine-5′-O-tetraphosphate bearing 4-methylumbelliferyl label on the terminal phosphate is reported. This compound has the potential as a promising probe molecule for homogenous fluorescent polymerase assay. This class of compounds will aid in quantification of cellular internalization and DNA incorporation of nucleotide based chemotherapeutic agents to offer mechanistic insights.     

Sequence Dependence of Fluorescent Quenching of Chromophores Covalently Bonded to Oligo-DNAs before and after Duplex Formation

The labeling of oligo- and polynucleotides with fluorescent probes is an important technique for the analysis of DNAs and RNAs. The effect of duplex formation with complementary oligo-DNA on the quenching behavior of two fluorescent chromophores (eosin, Eo and tetramethylrhodamine, TMR) attached to the 5′-terminal of various 10mer oligo-DNAs was investigated and the dependence of the quenching on DNA base sequence is discussed. We found that guanine residues played a major role in the quenching of the fluorescence of the chromophores. Guanine residues on the complementary DNA near the chromophores, in particular, had a significant influence on the quenching.     

A novel kind of dimmer (excimer)-induced-AIE compound 2-phenylisothiazolo[5,4-b]pyridin-3(2H)-one as high selective bisulfite anion probe

An interesting dimmer (excimer)-induced-AIE characteristic of 2-phenylisothiazolo[5,4-b]pyridin-3(2H)-one was observed. By using a ring-opening reaction, we developed a novel fluorescent probe based on sub-micron particles of 2-phenylisothiazolo[5,4-b]pyridin-3(2H)-one in water.     

Sn-Al-β分子筛酸性在葡萄糖转化反应中作用的固体NMR研究

制备了一系列具有不同酸性质的β分子筛催化剂, 通过固体核磁共振(NMR)探针分子技术对其酸性质进行了表征, 并考察了其催化葡萄糖转化为乙酰丙酸甲酯的性能. 吸附三甲基磷的³¹P NMR实验结果表明, 含有骨架Sn以及Al原子的Sn-Al-β催化剂同时具有Br?nsted与Lewis酸性. 通过2-¹³C-丙酮探针分子区分出 3种酸强度的Br?nsted酸位, 其中一种酸强度接近“超强酸”, 可能是由于空间邻近的Br?nsted酸位和Lewis酸位发生协同作用产生的. 葡萄糖转化为乙酰丙酸甲酯的催化反应结果表明, 相比于分别只含有Lewis酸位和Br?nsted酸位的Sn-β和Al-β样品以及两者的物理混合样品, Sn-Al-β分子筛催化剂具有高催化活性与产物选择性, 这主要是由于Br?nsted酸位和Lewis酸位的协同作用产生了强Br?nsted酸位, 这种强Br?nsted酸位进一步导致了更高的催化活性.     

Synthesis of core-shell structured Au@Bi2S3 nanorod and its application as DNA immobilization matrix for electrochemical biosensor construction

The core-shell structured Au@Bi2S3 nanorods have been prepared through direct in-situ growth of Bi2S3 at the surface of pre-synthesized gold nanorods.The product was characterized by X-ray diffraction,transmission electron microscopy and energy-dispersive X-ray spectroscopy.Then the obtained Au@Bi2S3 nanorods were coated onto glassy carbon electrode to act as a scaffold for fabrication of electrochemical DNA biosensor on the basis of the coordination of-NH2 modified on 5’-end of probe DNA and Au@Bi2S3.Electrochemical characterization assays demonstrate that the Au@Bi2S3 nanorods behave as an excellent electronic transport channel to promote the electron transfer kinetics and increase the effective surface area by their nanosize effect.The hybridization experiments reveal that the Au@Bi2S3 matrix-based DNA biosensor is capable of recognizing complementary DNA over a wide concentration ranging from 10 fmol/L to 1 nmol/L.The limit of detection was estimated to be 2 fmol/L(S/N=3).The biosensor also presents remarkable selectivity to distinguish fully complementa ry sequences from basemismatched and non-complementary ones,showing great promising in practical application.     

Optimized Fluorescent Probe for Specific Imaging of Glutathione S‐Transferases in Living Cells and Mice

GSTP1 has been considered to be a marker for malignancy in many tissues. However, the existing GST fluorescent probes are unfavorable for in vivo imaging because of the limited emission wavelength or insufficient fluorescence enhancement (six‐fold). The limited fluorescence enhancement of GST fluorescent probes is mainly ascribed to the high background signals resulting from the spontaneous reaction between GSH and the probes. In this work, a highly specific GST probe with NIR emission has been successfully developed through optimization of the essential unit of the probe to repress the spontaneous reaction. The novel GST probe exhibits over 100‐fold fluorescence enhancement upon incubation with GSTP1/GSH and high selectivity over other potential interference. In addition, the probe has been proved to be capable of tracking endogenous GST in A549 cells. Finally, the in vivo imaging results demonstrate that the probe can be used for effective imaging of endogenous GST activity in subcutaneous tumor mouse with high contrast.