Detection of the covalently closed circular DNA of duck hepatitis B virus by Taq-Man fluorescent quantitative PCR assay

To develop a fluorescent quantitative PCR assay based on Taq-Man chemistry to detect the covalenfly closed circular DNA （eccDNA） of duck hepatitis B virus （DHBV）, a pair of primers was designed from both sides of the nick in the minus strand of DHBV and a Taq-Man probes between the primers, modified with 6-Fam at 5＇ end and Tamra at its 3＇ end was designed to detect the PCR products during PCR cycles. The DHBV DNA fragment was cloned into vector PUCm-T, and the recombinant plasmid was purified and subsequently qualified as the HBV DNA standard. The experimental conditions and reagents used in PCR assay for amplification were sophisticatedly optimized in order to yield a perfect amplification efficacy and reduce the possibility to produce non-specific amplification. It was demonstrated that the detect limit of assay was 10^3 copies/ml, and a linear standard curve was obtained between 10^5 -10^9 copies/ml [ C1 =-2.8361 ln（x） ＋ 41.45, r =-0.9985]. The coefficient of variation was 0.2%-3.14% and 2.22%-4.43% for intra- and inter-assay respectively. After a dynamic survey on the contents of DHBV DNA in serum of ducks, it was found that its peak value appeared at the second week of birth in ducks. It is evident that this method of Taq-Man fluorescent quantitative PCR assay appears to be simple, sensitive and specific.

Detection of Mycoplasma Contamination in Animal Cell Cultures

[ Objective ] To develop a rapid efficient method for detecting mycoplasma contamination in cell cultures. [ Method] A pair of primers was designed according to two highly conserved nucleotide sequences of the 16S RNA from six kinds of mycoplasma that commonly contaminated cells. Then the mycoplasma contamination of 25 cell samples was defected by PCR and DNA fluorescence staining. EResultl When these cell samples were detected by DNA fluorescence staining, the positive rate and probable positive rate were respectively 24% and 16%. And when they were detected by PCR, the positive rate was 36%. [ Condusion] The PCR method is more sensitive and specific than the DNA fluorescence staining, and combining these two methods is the optimal way to detect mycoplasma contamination in cell cultures.

RAPID DETECTION OF ONCOGENE AMPLIFICATION IN PARAFFIN SECTIONS OF BREAST CARCINOMAS USING QUANTITATIVE DIFFERENTIAL PCR AND FLUORESCENT DNA TECHNOLOGY

Gene amplification is a common mechanism of oncogene activation and contributes to tumor progression. Analysis of such genetic alterations are relevant to the understanding of tumor genetics and could provide prognostic information for the individual patient. Standard analytical approaches using Southern blot and slot blot require a large amount of good

GAG-containing nucleotides as mediators of DNA-silver clusters and iron-DNA interplay

New types of fluorescence DNA-based silver nanoclusters（DNAn-Ag NCs, n = 1, 2, 3c, 4c, 5c） were synthesized by C3T-rich nucleotides as templates. It is found that the assembly of DNAn-Ag NCs with nucleotides containing GAG sequences produce silver clusters with an enhanced red emission. Results indicate that GAG is the good enhancer of DNAn-Ag NCs constructed by C3T-rich nucleotides. The fluorescence titration reveals that enhanced red emission is sensitive to Fe（Ⅲ/Ⅱ） ions with the formation of non-emission nanoclusters. Thus, the GAG-containing nucleotide can be an enhancer for the emission of silver clusters with C3T-rich nucleotide and a mediator of the iron-cluster interplay.

Advances in single-particle detection for DNA sensing

Rapid, accurate and sensitive detection of particular DNA sequence is critical in fundamental biomedical research and clinical diagnostics. However, conventional approaches for DNA assay often suffer from cumbersome procedures, long analysis time and insufficient sensitivity. Recently, single-particle detection technology has emerged as a powerful tool in the biosensing area due to its significant advantages of ultrahigh sensitivity, low sample-consumption and rapid analysis time. Especially, the introduction of novel nanomaterials has greatly promoted the development of single-particle detection and its applications for DNA sensing. In this review, we summarize the recent advance in single-particle detection strategies for DNA sensing, and focus mainly on metallic nanoparticle-and semiconductor quantum dot-based single-particle detection. We highlight the emerging trends in this field as well.

Enzyme-free and multiplexed micro RNA detection using micro RNA-initiated DNA molecular motor

In this work,we have developed a sensitive,simple,and enzyme-free assay for detection of micro RNAs(mi RNAs)by means of a DNA molecular motor consisting of two stem-loop DNAs with identical stems and complementary loop domains.In the presence of mi RNA target,it can hybridize with one of the stem-loop DNA to open the stem and to produce a mi RNA/DNA hybrid and a single strand(ss)DNA,the ss DNA will in turn hybridize with another stem-loop DNA and finally form a double strand(ds)DNA to release the mi RNA.One of the stem-loop DNA is double-labeled by a fluorophore/quencher pair with efficiently quenched fluorescence.The formation of ds DNA can produced specific fluorescence signal for mi RNA detection.The released mi RNA will continuously initiate the next hybridization of the two stem-loop DNAs to form a cycle-running DNA molecular motor,which results in great fluorescence amplification.With the efficient signal amplification,as low as 1 pmol/L mi RNA target can be detected and a wide dynamic range from 1 pmol/L to 2 nmol/L is also obtained.Moreover,by designing different stem-loop DNAs specific to different mi RNA targets and labeling them with different fluorophores,multiplexed mi RNAs can be simultaneously detected in one-tube reaction with the synchronous fluorescence spectrum(SFS)technique.

Synthesis and optical behaviors of 6-seleno-deoxyguanosine

We have developed a simple method to synthesize 6-seleno-2′-deoxyguanosine(SedG)by selectively replacing the 6-oxygen atom with selenium.This selenium-atom-specific modification(SAM)alters the optical properties of the naturally occurring2′-deoxyguanosine(dG).Unlike the native dG,the UVabsorption ofSedG is significantly influenced by the pH of the aqueous solution.Moreover,SedG is fluorescent at the physiological pH and exhibits pH-dependent fluorescence in aqueous solutions.Furthermore,SedG has noticeable fluorescence in non-aqueous solutions,indicating its sensitivity to environmental changes.This is the first time a fluorescent nucleoside by single-atom alteration has been observed.Fluorescent nucleosides modified by a single atom have great potential as molecular probes with minimal perturbations to investigate nucleoside interactions with proteins,such as membrane-transporter proteins.