RNase H meets molecular beacons: an ultrasensitive fluorometric assay for nucleic acids. 2018

Shao-Xiang Wang, and Kai-Sheng Liu, and Yi-Fei Lou, and Shao-Qi Wang, and Yong-Bo Peng, and Jian-Ping Chen, and Jia-Hao Huang, and Shou-Xia Xie, and Liang Cui, and Xiao Wang
Guangdong Key Laboratory for Genome Stability & Disease Prevention, School of Pharmaceutical Sciences, Shenzhen University Health Science Center, Shenzhen, 518060, China.

An innovative signal amplification strategy assisted by RNase H is described here for the detection of DNA targets in a universal fashion. A tailor-made RNA molecular beacon (RMB) conjugated with a fluorescence resonance energy transfer (FRET) pair (fluorophore and quencher) was designed, characterized, and combined with the employment of RNase H. Its performance is compared to that of other nucleases including Exonuclease III and T7 exonuclease. Fluorometry, performed best at excitation/emission wavelengths of 490/520 nm, gives an amazingly low detection limit of 23 fM for target DNA. The method was verified by the determination of human hemochromatosis (HFE) gene. It is perceived that the method represents a versatile tool for the detection of a wide range of targets. Graphical Abstract An RNase H-assisted signal amplification (RASA) method for the fluorometric assay of nucleic acids has been developed by using a unique RNA molecular beacon (RNA MB) conjugated with a fluorophore (F) and quencher (Q) pair for signal generation.

UI MeSH Term Description Entries
D009690 Nucleic Acid Conformation The spatial arrangement of the atoms of a nucleic acid or polynucleotide that results in its characteristic 3-dimensional shape. DNA Conformation,RNA Conformation,Conformation, DNA,Conformation, Nucleic Acid,Conformation, RNA,Conformations, DNA,Conformations, Nucleic Acid,Conformations, RNA,DNA Conformations,Nucleic Acid Conformations,RNA Conformations
D004247 DNA A deoxyribonucleotide polymer that is the primary genetic material of all cells. Eukaryotic and prokaryotic organisms normally contain DNA in a double-stranded state, yet several important biological processes transiently involve single-stranded regions. DNA, which consists of a polysugar-phosphate backbone possessing projections of purines (adenine and guanine) and pyrimidines (thymine and cytosine), forms a double helix that is held together by hydrogen bonds between these purines and pyrimidines (adenine to thymine and guanine to cytosine). DNA, Double-Stranded,Deoxyribonucleic Acid,ds-DNA,DNA, Double Stranded,Double-Stranded DNA,ds DNA
D005470 Fluorometry An analytical method for detecting and measuring FLUORESCENCE in compounds or targets such as cells, proteins, or nucleotides, or targets previously labeled with FLUORESCENCE AGENTS. Fluorimetry,Fluorometric Analysis,Analysis, Fluorometric
D006432 Hemochromatosis A disorder of iron metabolism characterized by a triad of HEMOSIDEROSIS; LIVER CIRRHOSIS; and DIABETES MELLITUS. It is caused by massive iron deposits in parenchymal cells that may develop after a prolonged increase of iron absorption. (Jablonski's Dictionary of Syndromes & Eponymic Diseases, 2d ed) Diabetes, Bronze,Bronze Diabetes,Bronzed Cirrhosis,Familial Hemochromatosis,Genetic Hemochromatosis,Haemochromatosis,Hemochromatoses,Iron Storage Disorder,Pigmentary Cirrhosis,Primary Hemochromatosis,Troisier-Hanot-Chauffard Syndrome,Von Recklenhausen-Applebaum Disease,Bronzed Cirrhoses,Cirrhoses, Bronzed,Cirrhoses, Pigmentary,Cirrhosis, Bronzed,Cirrhosis, Pigmentary,Disease, Von Recklenhausen-Applebaum,Diseases, Von Recklenhausen-Applebaum,Disorder, Iron Storage,Disorders, Iron Storage,Familial Hemochromatoses,Genetic Hemochromatoses,Haemochromatoses,Hemochromatose,Hemochromatoses, Familial,Hemochromatoses, Genetic,Hemochromatosis, Familial,Hemochromatosis, Genetic,Iron Storage Disorders,Pigmentary Cirrhoses,Recklenhausen-Applebaum Disease, Von,Recklenhausen-Applebaum Diseases, Von,Storage Disorder, Iron,Storage Disorders, Iron,Syndrome, Troisier-Hanot-Chauffard,Syndromes, Troisier-Hanot-Chauffard,Troisier Hanot Chauffard Syndrome,Troisier-Hanot-Chauffard Syndromes,Von Recklenhausen Applebaum Disease,Von Recklenhausen-Applebaum Diseases
D006801 Humans Members of the species Homo sapiens. Homo sapiens,Man (Taxonomy),Human,Man, Modern,Modern Man
D015345 Oligonucleotide Probes Synthetic or natural oligonucleotides used in hybridization studies in order to identify and study specific nucleic acid fragments, e.g., DNA segments near or within a specific gene locus or gene. The probe hybridizes with a specific mRNA, if present. Conventional techniques used for testing for the hybridization product include dot blot assays, Southern blot assays, and DNA:RNA hybrid-specific antibody tests. Conventional labels for the probe include the radioisotope labels 32P and 125I and the chemical label biotin. Oligodeoxyribonucleotide Probes,Oligonucleotide Probe,Oligoribonucleotide Probes,Probe, Oligonucleotide,Probes, Oligodeoxyribonucleotide,Probes, Oligonucleotide,Probes, Oligoribonucleotide
D016914 Ribonuclease H A ribonuclease that specifically cleaves the RNA moiety of RNA:DNA hybrids. It has been isolated from a wide variety of prokaryotic and eukaryotic organisms as well as RETROVIRUSES. Endoribonuclease H,RNase H,Ribonuclease H, Calf Thymus,RNAase H
D057230 Limit of Detection Concentration or quantity that is derived from the smallest measure that can be detected with reasonable certainty for a given analytical procedure. Limits of Detection,Detection Limit,Detection Limits

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