The development of a real-time 5' nuclease RT-PCR assay for the detection of apple chlorotic leaf spot virus (ACLSV) from infected plant material is described. A short fluorogenic 3' minor groove binder-DNA hydrolysis probe was used to circumvent genome variability between isolates and target a short conserved sequence. The covalent attachment of the minor groove binder moiety at the 3' end of the probe increased the probe/target duplex stability and raised the melting temperature to a range suitable for real-time analysis. The method is rapid, sensitive and takes place within a single tube without post-PCR handling of the amplification products.
Download full-text PDF |
Source |
|---|---|
| http://dx.doi.org/10.1016/s0166-0934(02)00035-6 | DOI Listing |
Publication Analysis
Top Keywords
Similar Publications
Carbonless DNA.
Phys Chem Chem Phys
January 2025
Faculty of Chemistry, University of Gdańsk, Wita Stwosza 63, 80-308 Gdańsk, Poland.
Carbonless DNA was designed by replacing all carbon atoms in the standard DNA building blocks with boron and nitrogen, ensuring isoelectronicity. Electronic structure quantum chemistry methods (DFT(ωB97XD)/aug-cc-pVDZ) were employed to study both the individual building blocks and the larger carbon-free DNA fragments. The reliability of the results was validated by comparing selected structures and binding energies using more accurate methods such as MP2, CCSD, and SAPT2+3(CCD)δ.
View Article and Find Full Text PDFSatellite DNA shapes dictate pericentromere packaging in female meiosis.
Nature
January 2025
Department of Biochemistry and Biophysics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA.
The abundance and sequence of satellite DNA at and around centromeres is evolving rapidly despite the highly conserved and essential process through which the centromere directs chromosome inheritance. The impact of such rapid evolution is unclear. Here we find that sequence-dependent DNA shape dictates packaging of pericentromeric satellites in female meiosis through a conserved DNA-shape-recognizing chromatin architectural protein, high mobility group AT-hook 1 (HMGA1).
View Article and Find Full Text PDFDivergent evolution of opposite base specificity and single-stranded DNA activity in animal and plant AP endonucleases.
Nucleic Acids Res
January 2025
Maimónides Biomedical Research Institute of Córdoba (IMIBIC), Avda. Menéndez Pidal s/n, Córdoba 14004, Spain.
Apurinic/apyrimidinic (AP) endonucleases are key enzymes responsible for the repair of base-less nucleotides generated by spontaneous hydrolysis or as DNA repair intermediates. APE1, the major human AP endonuclease, is a druggable target in cancer and its biological function has been extensively studied. However, the molecular features responsible for its substrate specificity are poorly understood.
View Article and Find Full Text PDFComprehensive Investigations About the Binding Interactions of Sudan Dyes with DNA by Spectroscopy and Docking Methods.
J Fluoresc
January 2025
School of Chemical and Environmental Engineering, Yancheng Teachers University, Yancheng City, Jiangsu Province, 224007, People's Republic of China.
Sudan dyes are recognized as carcinogens, which are strictly determined whether there are them in food for food safety. Hence, in order to understand the mechanism at the molecular level, this work investigated the binding interactions of Sudan I-IV with calfthy mus DNA. The synchronous fluorescence and UV-vis spectral results suggested the complex formation between Sudan I-IV and ct-DNA.
View Article and Find Full Text PDFBLV-CoCoMo Dual qPCR Assay Targeting LTR Region for Quantifying Bovine Leukemia Virus: Comparison with Multiplex Real-Time qPCR Assay Targeting Region.
Pathogens
December 2024
Laboratory of Global Infectious Diseases Control Science, Graduate School of Agricultural and Life Sciences, The University of Tokyo, 1-1-1 Yayoi, Bunkyo-ku, Tokyo 113-8657, Japan.
The proviral load (PVL) of the bovine leukemia virus (BLV) is a useful index for estimating disease progression and transmission risk. Real-time quantitative PCR techniques are widely used for PVL quantification. We previously developed a dual-target detection method, the "Liquid Dual-CoCoMo assay", that uses the coordination of common motif (CoCoMo) degenerate primers.
View Article and Find Full Text PDFWant AI Summaries of new PubMed Abstracts delivered to your In-box?
Enter search terms and have AI summaries delivered each week - change queries or unsubscribe any time!