A Self-Immolative Molecular Beacon for Amplified Nucleic Acid Detection

2021 ◽  
Author(s):  
Magdalena Roth ◽  
Oliver Seitz
Keyword(s):  
Nucleic Acid ◽  
Dna Sequences ◽  
Molecular Beacon ◽  
Homogeneous Solution ◽  
Nucleic Acid Detection ◽  
Loop Region ◽  
Hybridization Probes ◽  
The One ◽  
Reporter Group ◽  
Rna And Dna

Fluorogenic hybridization probes allow the detection of RNA and DNA sequences in homogeneous solution. Typically, one target molecule is activating the fluorescence of a single probe molecule. This limits the sensitivity of nucleic acid detection. Herein, we report a self-immolative Molecular Beacon (iMB), which escapes the one-target-one-probe dogma. The iMB probe includes a photoreductively cleavable N-alkylpicolinium (NAP) linkage within the loop region. A fluorophore at the 5'-end serves, on the one hand, as a reporter group and, on the other hand, as a photosensitizer of a NAP-linker cleavage reaction. In the absence of a target, the iMB adopts a hairpin shape. Quencher proups prevent photo-induced cleavage. The iMB opens upon hybridization with target, and both fluorescent emission as well as photo-inductive cleavage of the NAP-linker can occur. In contrast to previous chemical amplification probes, iMBs are unimolecular. Cleavage leads to products that have lower target affinity than the probes before reaction. Aided by catalysis, the method allowed the detection of 5 pM RNA target within 100 min. <br>

scholarly journals A Self-Immolative Molecular Beacon for Amplified Nucleic Acid Detection

2021 ◽  
Author(s):  
Magdalena Roth ◽  
Oliver Seitz
Keyword(s):  
Nucleic Acid ◽  
Dna Sequences ◽  
Molecular Beacon ◽  
Homogeneous Solution ◽  
Nucleic Acid Detection ◽  
Loop Region ◽  
Hybridization Probes ◽  
The One ◽  
Reporter Group ◽  
Rna And Dna

Fluorogenic hybridization probes allow the detection of RNA and DNA sequences in homogeneous solution. Typically, one target molecule is activating the fluorescence of a single probe molecule. This limits the sensitivity of nucleic acid detection. Herein, we report a self-immolative Molecular Beacon (iMB), which escapes the one-target-one-probe dogma. The iMB probe includes a photoreductively cleavable N-alkylpicolinium (NAP) linkage within the loop region. A fluorophore at the 5'-end serves, on the one hand, as a reporter group and, on the other hand, as a photosensitizer of a NAP-linker cleavage reaction. In the absence of a target, the iMB adopts a hairpin shape. Quencher proups prevent photo-induced cleavage. The iMB opens upon hybridization with target, and both fluorescent emission as well as photo-inductive cleavage of the NAP-linker can occur. In contrast to previous chemical amplification probes, iMBs are unimolecular. Cleavage leads to products that have lower target affinity than the probes before reaction. Aided by catalysis, the method allowed the detection of 5 pM RNA target within 100 min. <br>

scholarly journals Is Pool Testing Method of COVID-19 Employed in Germany and India Effective?

2020 ◽  
Author(s):  
Jia Liu ◽  
Yi Chen ◽  
Kefan Xie ◽  
Xiaohong Chen
Keyword(s):  
Nucleic Acid ◽  
Sample Size ◽  
Infection Rate ◽  
Large Population ◽  
Nucleic Acid Detection ◽  
Testing Method ◽  
Optimal Sample ◽  
The One ◽  
Novel Coronavirus ◽  
Test Result

Abstract At present, several countries, such as Germany and India, have employed a pool testing method on the nucleic acid testing of COVID-19 for the shortage of detection kits. In this method, the testing is performed on several samples of the cases together as a bunch. If the test result of the bunch is negative, then it is shown that none of the cases in the bunch has been infected with the novel coronavirus. On the contrary, if the test result of the bunch is positive, then the samples are tested one by one to confirm which cases are infected. We verified that the pool testing method of COVID-19 is effective in the situation of the shortage of nucleic acid detection kits based on probabilistic modeling. Moreover, the following interesting results are also obtained. (1) If the infection rate is extremely low, while the same number of detection kits are used, the expected number of cases that can be tested by the pool testing method is far more than that by the one-by-one testing method. (2) The pool testing method is effective only when the infection rate is less than 0.3078. While the infection rate decreases from 0.3078 to 0.0018, the optimal sample sizes in one bunch increases from 3 to 25. In general, the higher the infection rate, the smaller the optimal sample size in one bunch. (3) If N samples are tested by the pool testing method, while the sample size in one bunch is G, the number of detection kits required is in the interval (N/G, N). Additionally, the lower the infection rate, the fewer detection kits are needed. Therefore, the pool testing method is not only suitable for the situation of the shortage of detection kits, but also the situation of the overall or sampling detection for a large population.

Histochemical aspects of nucleic acid detection

1995 ◽  
Vol 53 ◽  
pp. 746-747
Author(s):  
B. A. Hamkalo ◽  
Elizabeth R. Unger
Keyword(s):  
In Situ Hybridization ◽  
Nucleic Acid ◽  
High Resolution ◽  
Dna Sequences ◽  
Single Copy ◽  
Nucleic Acid Detection ◽  
Metaphase Chromosomes ◽  
Potential Applications ◽  
Nucleic Acid Sequences

This symposium brings together several approaches for the detection of specific nucleic acid sequences that have potential applications at the histochemical level.Trask et al. report on the use of fluorescence in situ hybridization (FISH) techniques to study the arrangement of DNA sequences in normal and diseaserelated chromosomes. The sites of specific DNA sequences can be fluorescently tagged. Different sequences can be labeled with different fluorochromes so that their arrangement can be studied using fluorescence microscopy. The distances between points on the same or different chromosomes can be determined in a large number of interphase nuclei or metaphase chromosomes. A variety of probe types, ranging from single-copy sequences to highly repeated sequences can be employed.Hamkalo and co-workers have used non-radioactive methods at the EM level for the detection of nucleic acid sequences by in situ hybridization. Analysis of metaphase chromosomes by electron microscopy allows for high resolution mapping of chromosomes. A variety of labelling procedures have been employed to illustrate the utility of high resolution nucleic acid sequence mapping in these preparations.

scholarly journals Fluorescent hybridization probes for nucleic acid detection

2011 ◽  
Vol 402 (10) ◽  
pp. 3115-3125 ◽  
Author(s):  
Jia Guo ◽  
Jingyue Ju ◽  
Nicholas J. Turro
Keyword(s):  
Nucleic Acid ◽  
Nucleic Acid Detection ◽  
Hybridization Probes

An autocatalytic DNA machine with autonomous target recycling and cascade circular exponential amplification for one-pot, isothermal and ultrasensitive nucleic acid detection

2016 ◽  
Vol 52 (74) ◽  
pp. 11108-11111 ◽  
Author(s):  
Xinya Sun ◽  
Li Wang ◽  
Mingsha Zhao ◽  
Changzhi Zhao ◽  
Shufeng Liu
Keyword(s):  
Nucleic Acid ◽  
Nucleic Acid Detection ◽  
Ultrasensitive Detection ◽  
One Pot ◽  
Target Recycling ◽  
Target Dna ◽  
Dna Machine ◽  
The One ◽  
Amplification Strategy

An autonomous target recycling and cascade circular exponential amplification strategy was proposed for the one-pot, isothermal and ultrasensitive detection of target DNA.

scholarly journals Enzymatic amplification of DNA/RNA hybrid molecular beacon signaling in nucleic acid detection

2013 ◽  
Vol 432 (2) ◽  
pp. 106-114 ◽  
Author(s):  
Thomas Jacroux ◽  
Daniel C. Rieck ◽  
Rong Cui ◽  
Yexin Ouyang ◽  
Wen-Ji Dong
Keyword(s):  
Nucleic Acid ◽  
Molecular Beacon ◽  
Nucleic Acid Detection ◽  
Enzymatic Amplification

scholarly journals Electrospray ionisation-cleavable tandem nucleic acid mass tag–peptide nucleic acid conjugates: synthesis and applications to quantitative genomic analysis using electrospray ionisation-MS/MS

2006 ◽  
Vol 35 (4) ◽  
pp. e28-e28 ◽  
Author(s):  
Andrew Thompson ◽  
Mark Prescott ◽  
Noorhan Chelebi ◽  
John Smith ◽  
Tom Brown ◽  
...  
Keyword(s):  
Nucleic Acid ◽  
Dna Sequences ◽  
Peptide Nucleic Acid ◽  
Ion Source ◽  
Esi Ms ◽  
Electrospray Ionisation ◽  
Hybridization Probes ◽  
Target Dna ◽  
Detection And Quantification ◽  
Mass Tag

Abstract The synthesis and characterization of isotopomer tandem nucleic acid mass tag–peptide nucleic acid (TNT–PNA) conjugates is described along with their use as electrospray ionisation-cleavable (ESI-Cleavable) hybridization probes for the detection and quantification of target DNA sequences by electrospray ionisation tandem mass spectrometry (ESI-MS/MS). ESI-cleavable peptide TNT isotopomers were introduced into PNA oligonucleotide sequences in a total synthesis approach. These conjugates were evaluated as hybridization probes for the detection and quantification of immobilized synthetic target DNAs using ESI-MS/MS. In these experiments, the PNA portion of the conjugate acts as a hybridization probe, whereas the peptide TNT is released in a collision-based process during the ionization of the probe conjugate in the electrospray ion source. The cleaved TNT acts as a uniquely resolvable marker to identify and quantify a unique target DNA sequence. The method should be applicable to a wide variety of assays requiring highly multiplexed, quantitative DNA/RNA analysis, including gene expression monitoring, genetic profiling and the detection of pathogens.

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