A graphical method to construct a phylogenetic tree

A 3D graphical representation of DNA sequences, which has no circuit or degeneracy, is derived for mathematical denotation of DNA sequence. Based on this graphical representation, we propose a new sequence distance measure. We make use of the corresponding similarity matrix to construct a phylogenic tree by virtue of the fuzzy theory. The examination of phylogenic tree belong to eight species illustrates the utility of our approach. © 2006 Wiley Periodicals, Inc. Int J Quantum Chem, 2006     

Chemiluminescence determination of ultramicro DNA with a flow-injection method

A high sensitive flow-injection chemiluminescence method for determination of calf thymus DNA and herring sperm DNA has been developed. The method is based on the chemiluminescence reaction of Rhodamine B-cerium(IV)-thermally denatured DNAs in sulfuric acid media. The proposed procedure allows quantitation of DNAs in the range 2.6×10⁻⁵ to 0.26 μg ml⁻¹ for calf thymus DNA and 5.0×10⁻⁸ to 5.0×10⁻⁵ μg ml⁻¹ for herring sperm DNA with correlation coefficients 0.9998 and 0.9996 (both n=11), respectively. The detection limits (3σ) are 6.5×10⁻⁶ μg ml⁻¹ for calf thymus DNA and 4.3×10⁻⁸ μg ml⁻¹ for herring sperm DNA. The possible mechanism of chemiluminescence in the system is discussed.     

共振光散射成像检测5,10,15,20-四(对三甲基氨基苯)卟吩诱导的DNA超螺旋聚集体

A resonance light scattering （RLS） imaging method was proposed based on imaging and measuring the RLS features of single suprahelical species of DNA, and its appfication to DNA assay was also investigated. In acidic medium, porphine-5,10,15,20-tetrakis（p-phenyltlimethylaminium） （PTPTMA）, could stack along the molecular surface of DNA with the mode of long-range assembly to induce the formation of suprahelical species of DNA, resulting in strong RLS signals in the range of 450-510 nm. Under the excitation of 488 nm fight beam of argon ion laser source, single suprahelical species could be observed with the aid of a common microscope due to the strong scattered fight emitted by the suprahelical species. By capturing the RLS images of the single suprahelical species with a cooled charge coupled device （CCD） camera, and analyzing the RLS data, herein an RLS imaging method of DNA was proposed based on the linear relationship between the counts of suprahelical species in the detection focus plane and the concentration of DNA in nanograms. When 1.8 μmol/L PTPTMA was employed, both calf thymus DNA （ct DNA） and fish sperm DNA （fs DNA） in the range of 25-1100 ng/mL could be detected with the limits of detection lower than 25 ng/mL （3a）. Four synthetic samples were detected satisfactorily with relative standard deviations less than 5.1%.     

New 2D graphical representation of DNA sequences

We consider a 2D graphical representations of DNA sequences, which avoids loss of information associated with crossing and overlapping of the corresponding curve. We outline an approach, which is based on the construction of a three-component vector whose components are the normalized leading eigenvalues of the L/L matrices associated with DNA. The examination of similarities/dissimilarities among the coding sequences of the first exon of beta-globin gene of different species illustrates the utility of the approach.     

一种含芴基的钌(II)配合物的合成及DNA键合性质

合成了一种新的钌(II)配合物[Ru(bpy)2(Hfip)](ClO4)2, 其中bpy代表2,2′-联吡啶, Hfip代表2-(9H-芴-2-基)-1H-咪唑-[4,5-f]-[1,10]-邻菲啰啉. 通过紫外可见光谱、荧光光谱、稳态荧光淬灭、与溴化乙锭的竞争实验、粘度测量和DNA热变性研究了该配合物与小牛胸腺DNA的键合性质. 结果表明, 该配合物能嵌入键合DNA, 键合常数Kb=8.6×105 L·mol-1 (50 mmol·L-1 NaCl).     

A Novel Method for Quantification of Circulating DNA in Serum by Capillary Zone Electrophoresis

In this paper, we first presented a novel method for quantification of circulating DNA in human serum based on capillary zone electrophoresis with laser-induced fluorescence detection (CZE-LIF). The serum was digested by proteinase to release free DNA, and then CZE-LIF system was used for the quantification of total circulating DNA. This method was successfully used to quantify the circulating DNA levels in sera from healthy individuals and certain cancer patients.We found the significantly elevated circulating DNA levels in certain prostate cancer patients. Our results demonstrated that CZE-LIF system has good linearity, excellent sensitivity (0.5 ng/mL DNA),satisfactory reproducibility (RSDs in one day and between days were both less than 5%) and reliability, and is well suitable to the quantification of the circulating DNA in human serum or plasma.